Bioorganic Chemistry 100 (2020) 103929

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Bioorganic Chemistry
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Design, synthesis and anticancer/antiestrogenic activities of novel indole- T

benzimidazoles
Fikriye Zengin Karadayia,1, Murat Yamanc,1, Mehmet Murat Kislaa,2, Ayse G. Keskusc,2,
Ozlen Konub,c,d, , Zeynep Ates-Alagoza,
⁎ ⁎

a
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Ankara, Turkey
b
Department of Molecular Biology and Genetics, Bilkent University, 06800 Ankara, Turkey
c
Interdisciplinary Program in Neuroscience, Bilkent University, 06800 Ankara, Turkey
d
UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey

ARTICLE INFO ABSTRACT

InChIKeys: Indole-benzimidazoles have recently gained attention due to their antiproliferative and antiestrogenic effects.
NKANXQFJJICGDU-QPLCGJKRSA-N However, their structural similarities and molecular mechanisms shared with selective estrogen receptor mod-
GZUITABIAKMVPG-UHFFFAOYSA-N ulators (SERMs) have not yet been investigated. In this study, we synthesized novel ethylsulfonyl indole-benzi-
UCJGJABZCDBEDK-UHFFFAOYSA-NKeywords: midazole derivatives by substituting the first (R1) and fifth (R2) positions of benzimidazole and indole groups,
Indole-benzimidazole
respectively. Subsequently, we performed 1H NMR, 13C NMR, and Mass spectral and in silico docking analyses, and
Molecular docking
anticancer activity screening studies of these novel indole-benzimidazoles. The antiproliferative effects of indole-
Comparative transcriptomics
Estrogen signaling benzimidazoles were found to be more similar between the estrogen (E2) responsive cell lines MCF-7 and HEPG2
in comparison to the Estrogen Receptor negative (ER-) cell line MDA-MB-231. R1:p-fluorobenzyl group members
were selected as lead compounds for their potent anticancer effects and moderate structural affinity to ER.
Microarray expression profiling and gene enrichment analyses (GSEA) of the selected compounds (R1:p-fluor-
obenzyl: 48, 49, 50, 51; R1:3,4-difluorobenzyl: 53) helped determine the similarly modulated cellular signaling
pathways among derivatives. Moreover, we identified known compounds that have significantly similar gene
signatures to that of 51 via queries performed in LINCS database; and further transcriptomics comparisons were
made using public GEO datasets (GSE35428, GSE7765, GSE62673). Our results strongly demonstrate that these
novel indole-benzimidazoles can modulate ER target gene expression as well as dioxin-mediated aryl hydrocarbon
receptor and amino acid deprivation-mediated integrated stress response signaling in a dose-dependent manner.

1. Introduction Estrogens (E2) play crucial roles in breast cancer development,

consequently a considerable amount of research has been done either to
Breast cancer, which is among the most prevalent cancer types af- block their synthesis or to modulate their activity [2]. Therefore, drugs
fecting women all over the world, can be conventionally subtyped ac- that function as antiestrogens in mammary tissue have been frequently
cording to the presence of estrogen receptor (ER), progesterone re- used for the treatment of hormone-dependent breast cancers. Nuclear
ceptor (PR), and/or human epidermal growth factor receptor 2 (HER2/ receptors ERα and ERβ, through E2 binding, take part in multiple cel-
ERBB2) activity. These subtypes possess differential characteristics re- lular activities such as proliferation and differentiation. In addition,
garding prognosis, incidence, therapeutic response and tumor aggres- they can be found at an equilibrium [2–4] and differentially regulate
siveness. The heterogeneous nature and adverse effects associated with their downstream elements upon exposure to selective estrogen re-
therapeutic targeting of such diverse and crucial pathways bring chal- ceptor modulators (SERMs) [5]. Moreover, their expression levels differ
lenges into the therapy and hence makes the discovery of novel, more among various tissues while the expression of ERα is tightly associated
effective, and subtype specific anticancer molecules invaluable [1]. with breast cancer physiology [6] as well as prognosis of breast tumors

⁎
Corresponding authors at: Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Ankara, Turkey (Z. Ates-Alagoz),
Department of Molecular Biology and Genetics, Bilkent University, 06800 Ankara, Turkey (O. Konu).
E-mail addresses: konu@[Link] (O. Konu), [Link]@[Link] (Z. Ates-Alagoz).
1
Equal contributors.
2
Equal contributors.

[Link]
Received 27 March 2020; Received in revised form 6 May 2020; Accepted 8 May 2020
Available online 17 May 2020
0045-2068/ © 2020 Elsevier Inc. All rights reserved.
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

HO S OH

OH

O N
N
N N O
O
O OH

Tamoxifen Raloxifene Bazedoxifene

Fig. 1. Chemical structure of tamoxifen, raloxifene and bazedoxifene.

Scheme 1. Scheme showing previous studies and starting point of the new syntheses.

[7]. ERβ on the other hand has been implicated in tumor suppression antiproliferative activity [31,32]. Aside from several crucial bioactive
and breast carcinogenesis [8]. compounds (tryptophan, serotonin and melatonin), some of the anti-
Multiple SERMs have been designed and assessed over the years for neoplastic compounds, such as vinblastine sulfate, vincristine sulfate, vi-
breast cancer treatment [9]. Moreover, ERα and ERβ binding affinities and norelbine ditartrate and lanreotide carry indole ring systems [33]. In ad-
downstream effects of these SERMs might differ leading to variable out- dition, phenyl-indole derivatives have been shown to inhibit breast cancer
comes [5,10,11]. Accordingly, tamoxifen (Fig. 1) belonging to the first development through different mechanisms [34–36]. Similarly, recent
generation of SERMs has been shown to significantly reduce the incidence studies on benzimidazoles reveal that different heterocycles at 2-position
of breast cancer. Raloxifene (Fig. 1) is a second-generation SERM ex- yield to potent anticancer agents for various carcinoma cell lines [37,38].
hibiting a role similar to tamoxifen yet it functions as a pure antagonist in Furthermore, indole-benzimidazole hybrids have been designed and syn-
the uterus and a partial agonist against tamoxifen-resistant breast cancers thesized by fusing the indole nucleus with benzimidazole to develop novel
[12]. ICI 182780 acts antagonistically in ER positive (ER+) MCF-7 cells selective ER modulators. These indole-benzimidazoles can represent novel
and can outperform raloxifene [13]. A third-generation SERM called ba- potent ERα antagonist properties and provide promising insight into the
zedoxifene (Fig. 1) that has been introduced for the treatment of breast discovery of novel SERMs for the management of breast cancer [39]. For
cancer and osteoporosis [14] is based on the pharmacophore of raloxifene. instance, in our previous studies, we have discovered a small molecule
Indole based derivatives (bazedoxifene, melatonin and KB9520), as well as with benzene sulfonyl structure exhibiting selectivity toward breast cancer
methyl and naphthyl-substituted benzimidazole derivatives also exhibit cells while sparing normal surrounding cells [40]. Also, benzene sulfonyl
different modes of actions on breast cancer cell lines some of which could structures have been shown to exhibit higher anticancer activity than
be through actions similar to SERMs [2,15–17]. Accordingly, a combina- doxorubicin in breast and prostate cancers [41,42]. However, the mole-
tion of affinity studies with toxicological approaches as well as molecular cular mechanism of action of novel indole-benzimidazoles carrying ben-
profiling could be highly beneficial to help identify more selective/effec- zene sulfonyl structures has not yet been assessed. Because of the above
tive breast cancer therapeutic agents [18–21]. and the need for new compounds with better anticancer and anti-
Indole and benzimidazole rings, which are bioavailable molecules, estrogenic properties, we designed, synthesized and tested a series of in-
constitute structures found in current drugs. These two ring structures are dole-benzimidazoles possessing ethylsulfonyl moiety (Scheme 1).
also isosteres of DNA bases that carry purine and pyrimidine cores, and
they can as well be purine antimetabolites. For this reason, indole and 2. Material and methods
benzimidazole rings are thought to interact easily with biopolymers in
biosystems [22]. Benzimidazole and its derivatives are effective agents 2.1. Chemistry
against cancer [23,24], inflammation [25] and oxidative stress [26,27]
while also having antiviral [28] and antibacterial [28–30] effects. Indole Melting points were determined with Buchi SMP-20
core has already been used to obtain novel derivatives with (BuchiLabortechnik, Flawil, Switzerland) and Electrotermal 9100

2
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

capillary melting point apparatus (Electrothermal, Essex, U.K.) and are eluent to give a white solid, m.p. 273 °C (0.095 g, 28% yield). 1H NMR
uncorrected. The 1H NMR spectra in DMSO‑d6 using Varian Mercury- (400 MHz, DMSO‑d6): δ ppm 1.11 (t, 3H), 3.31 (q, 2H), 4.06 (s, 3H),
400 FT-NMR spectrometer (Varian Inc., Palo Alto, CA, USA), and the 7.19–7.28 (m, 2H), 7.54 (d, J = 7.6 Hz, 1H), 7.72 (dd, J = 8.4 Hz,
Mass spectra based on ESI(+) method using Waters ZQ micromass LC- J = 2 Hz, 1H), 7.84 (d, J = 8.4 Hz, 1H), 8.13 (d, J = 1.6 Hz, 1H), 8.20
MS spectrometer (Waters Corporation, Milford, MA, USA) were re- (d, J = 2.8 Hz, 1H), 8.44 (d, J = 7.6 Hz, 1H), 11.93 (brd s, 1H, NH). 13C
corded. For elemental analysis we used LECO 932 CHNS (Leco-932, St. NMR (DMSO‑d6): 7.43, 32.01, 49.77, 104.33, 110.39, 111.81, 118.21,
Joseph, MI, USA) instrument. Silica gel 60 (40–63 mm particle size) was 120.52, 120.61, 121.53, 122.54, 126.29, 127.76, 131.26, 136.08, 139.35,
used for column chromatography. 142.54, 152.90. MS (ESI+) m/z: 340. Anal. calcd. For C18H17N3O2S-0.3
H2O: C, 62.69; H, 5.14; N, 12.18; S, 9.29 and found C, 62.57; H, 5.06; N,
2.1.1. General procedure for synthesis of 3–12 12.21; S, 9.08.
To a solution of 4-(Ethylsulfonyl)-1-chloro-2-nitrobenzene (2)
(5 mmol) in ethanol (5 mL), amine derivative (15 mmol) was added and [Link]. 5-(ethylsulfonyl)-2-(5-methoxy-1H-indol-3-yl)-1-methyl-1H-
heated under reflux, until the starting material was consumed (de- benzo[d]imidazole (26). Compound 26 was prepared according to
termined by TLC, 8–48 h). Upon cooling the mixture, water was added. general methods starting from N1-methyl-4-ethylsulfonyl-benzene-1,2-
The resultant yellow residue was crystallized from ethanol or purified diamine (0.92 mmol, 0.2197 g) and 5-methoxy-indole-3-carboxaldehyde
by column chromatography (cc) by using a mixture of hexane and ethyl (0.92 mmol, 0.161 g). The residue was purified by cc using the ethyl
acetate in varying concentrations as eluent (Table 1) [43]. acetate/hexane (1:1) as eluent to give a light yellow solid, m.p. 198 °C
(0.125 g, 37% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 1.11 (t, 3H),
2.1.2. General procedure for synthesis of 13–22 3.30 (q, 2H), 3.82 (s, 3H), 4.05 (s, 3H), 6.90 (dd, J = 8.8 Hz, J = 2 Hz,
Compounds 3–12 (3.5 mmol) in EtOH (75 mL) reduced by hydro- 1H), 7.43 (d, J = 8.8 Hz, 1H), 7.71 (dd, J = 8.4 Hz, J = 2 Hz, 1H), 7.82 (d,
genation using 40 psi of H2 and 10% Pd/C (40 mg) until cessation of H2 J = 8.4 Hz 1H), 7.97 (d, J = 2.4 Hz 1H), 8.14 (d, J = 2 Hz, 1H), 8.15 (s,
uptake to obtain the catalyst before filtering off on a bed of celite and 1H), 11.80 (brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.44, 32.03, 49.77,
washing with EtOH; and concentrating the filtrate in vacuo [44]. The 55.38, 103.24, 104.10, 110.30, 112.55, 112.69, 118.21, 120.55, 126.93,
crude amine was used without purification (Table 1). 128.08, 131.13, 131.19, 139.33, 142.53, 153.07, 154.53. MS (ESI+) m/z:
370. Anal. calcd. For C19H19N3O3S: C, 61.77; H, 5.18; N, 11.37; S, 8.67
2.1.3. General procedure for synthesis of 23–59 and found C, 61.21; H, 5.43; N, 11.52; S, 8.63.
A mixture of the appropriate o-phenylenediamine (1 mmol), related
indole derivative (1 mmol) and Na2S2O5 (40%) (2 mL) in EtOH (4 mL), [Link]. 2-(5-chloro-1H-indol-3-yl)-5-(ethylsulfonyl)-1-methyl-1H-benzo
was refluxed until starting materials were consumed (determined by [d]imidazole (27). Compound 27 was prepared according to general
TLC, 4–12 h). The precipitate was obtained upon pouring the reaction methods starting from N1-methyl-4-ethylsulfonyl-benzene-1,2-diamine
mixture and then filtering and washing. The residue was purified by (1.15 mmol, 0.247 g) and 5-chloro-indole-3-carboxaldehyde
column chromatography to give final product [45]. (1.15 mmol, 0.206 g). The residue was purified by cc using the ethyl
acetate /hexane (1:2) as eluent to give a light yellow solid, m.p. 264 °C
[Link]. 5-(ethylsulfonyl)-2-(1H-indole-3-yl)-1H-benzo[d]imidazole (0.098 g, 23% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 1.11 (t,
(23). Compound 23 was prepared according to general methods 3H), 3.32 (q, 2H), 4.07 (s, 3H), 7.26 (dd, J = 8.8 Hz, J = 2.4 Hz, 1H),
starting from 4-ethylsulfonyl-benzene-1,2-diamine (1.35 mmol, 0.27 g) 7.56 (d, J = 8.4 Hz, 1H), 7.72 (dd, J = 8.4 Hz, J = 2 Hz, 1H), 7.85 (d,
and indole-3-carboxaldehyde (1.35 mmol, 0.195 g). The residue was J = 8.8 Hz, 1H), 8.17 (d, J = 1.6 Hz, 1H), 8.30 (s, 1H), 8.50 (d,
purified by cc using the mixture of ethyl acetate-hexane (1:1) as eluent J = 2 Hz, 1H). 13C NMR (DMSO‑d6): 7.44, 32.02, 49.70, 104.08,
to give a light yellow solid, m.p. 157 °C (0.058 g, 13% yield).1H NMR 110.42, 113.58, 118.33, 120.69, 120.71, 122.53, 125.20, 127.47,
(400 MHz, DMSO‑d6): δ ppm 1.10 (t, 3H), 3.27 (q, 2H), 7.23 (dd, 129.35, 131.37, 134.74, 139.27, 142.41, 152.34. MS (ESI+) m/z:
J = 8.8 Hz, J = 2 Hz, 1H), 7.53 (d, J = 8.8 Hz, 1H), 7.64 (m, 2H), 374. Anal. calcd. For C18H16ClN3O2S.0,4 H2O: C, 56.73; H, 4.44; N,
7.83–8.26 (m, 3H), 8.51 (d, J = 1.6 Hz, 1H), 11.91 (brd s, 1H, NH), 11.02; S, 8.41; Found: C, 56.48; H, 4.38; N, 11.02; S, 8.26.
12.99 (brd d, 1H, NH).13C NMR (CD3OD): 8.02, 52.02, 106.93, 113.20,
114.42, 121.25, 123.03, 124.36, 125.67, 127.47, 128.20, 129.74, [Link]. 2-(5-bromo-1H-indol-3-yl)-5-(ethylsulfonyl)-1-methyl-1H-benzo
132.78, 132.90, 136.59, 136.96, 154.36. MS (ESI+) m/z: [d]imidazole (28). Compound 28 was prepared according to general
326.C17H15N3O2S·0.9H2O: C, 59.77; H, 4.95; N, 12.30; S, 9.38 and methods starting from N1-methyl-4-ethylsulfonyl-benzene-1,2-diamine
found C, 59.42; H, 5.23; N, 11.91; S, 9.10. (1.65 mmol, 0.228 g) and 5-bromo-indole-3-carboxaldehyde
(1.65 mmol, 0.238 g). The residue was purified by cc using the ethyl
[Link]. 2-(5-bromo-1H-indol-3-yl)-5-(ethylsulfonyl)-1H-benzo[d] acetate /hexane (1:1) as eluent to give a light yellow solid, m.p. 259 °C
imidazole (24). Compound 24 was prepared according to general (0.052 g, 8% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 1.11 (t, 3H),
methods starting from 4-ethylsulfonyl-benzene-1,2-diamine 3.31 (q, 2H), 4.06 (s, 3H), 7.35 (d, J = 8.4 Hz, 1H), 7.54 (d, J = 8 Hz,
(0.87 mmol, 0.175 g) and 5-bromo-indole-3-carboxaldehyde 1H), 7.71 (d, J = 8.8 Hz, 1H), 7.83 (d, J = 8.4 Hz, 1H), 8.17 (s, 1H),
(0.87 mmol, 0.195 g). The residue was purified by cc using the 8.26 (s, 1H), 8.64 (s, 1H). 13C NMR (DMSO‑d6): 7.54, 31.96, 49.72,
chloroform/ethyl acetate (1:1) as eluent to give a white solid, m.p. 103.76, 110.30, 113.05, 114.14, 118.22, 120.59, 123.60, 124.81,
192 °C (0.128 g, 36% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 128.16, 129.38, 131.35, 135.22, 139.24, 142.43, 152.42. MS (ESI+)
1.11 (t, 3H), 3.29 (q, 2H), 7.37 (d, J = 8.4 Hz, 1H), 7.51 (d, J = 8.8 Hz m/z: 418. Anal. calcd. For C18H16BrN3O2S.0,35 H2O: C, 50.91; H,
1H), 7.63–7.71 (m, 2H), 7.88 (m, 1H), 8.27 (s, 1H), 8.68(s, 1H), 11.97 3.96; N, 9.89; S, 7.55; Found: C, 50.85; H, 3.94; N, 10.27; S, 7.45.
(brd d, 1H, NH), 13.04 (brd d, 1H, NH). MS (ESI+) m/z: [Link].
calcd. For C17H14BrN3O2S·H2O: C, 48.35; H, 3.82; N, 9.95; S, 7.59 and [Link]. 1-ethyl-5-(ethylsulfonyl)-2-(1H-indol-3-yl)-1H-benzo[d]imidazole
found C, 48.16; H, 3.86; N, 9.68; S, 7.45. (29). Compound 29 was prepared according to general methods
starting from N1-ethyl-4-ethylsulfonyl-benzene-1,2-diamine (1 mmol,
[Link]. 5-(ethylsulfonyl)-2-(1H-indol-3-yl)-1-methyl-1H-benzo[d] 0.240 g) and indole-3-carboxaldehyde (1 mmol, 0.152 g). The residue
imidazole (25). Compound 25 was prepared according to general was purified by cc using the ethyl acetate/metanol (4:0.5) as eluent to
methods starting from N1-methyl-4-ethylsulfonyl-benzene-1,2-diamine give a white solid, m.p. 254 °C(0.130 g, 37% yield). 1H NMR (400 MHz,
(0.99 mmol, 0.211 g) and indole-3-carboxaldehyde (0.99 mmol, 0.143 g). DMSO‑d6): δ ppm 1.13 (t, 3H), 1.42 (t, 3H), 3.32 (q, 2H), 4.56 (q, 2H),
The residue was purified by cc using the ethyl acetate /hexane (1:1) as 7.19–7.28 (m, 2H), 7.54 (d, J = 8 Hz, 1H), 7.73 (dd, J = 8.4 Hz,

3
 F.Z. Karadayi, et al.

Table 1
Physicochemical data for compounds 3–22.

1
Comp. R1 H NMR M.p. (°C) Yield % Comp. Mass

3 -H 1.29 (t, 3H), 3.11 (q, 2H), 6.96 (d, J = 9.2 Hz, 1H), 7.77 (dd, J = 9.2 Hz, J = 2 Hz, 1H), 8.68 (d, J = 2 Hz, 143 88 13 201
1H).
4 -CH3 1.12 (t, 3H), 3.03 (d, 3H), 3.28 (q, 2H), 7.18 (d, J = 8.8 Hz, 1H), 7.89 (dd, J = 9 Hz, J = 2.4 Hz, 1H), 8.45 (d, 138 83 14 215
J = 2 Hz, 1H), 8.68 (d, 1H, NH).
5 -C2H5 1.09 (t, 3H), 1.2 (t, Hz, 3H), 3.25 (q, 2H), 3.46 (m, 2H), 7.22 (d, J = 8.8 Hz, 1H), 7.83 (dd, J = 9.2 Hz, 125 84 15 229

4
J = 2.4 Hz, 1H), 8.42 (d, J = 1.6 Hz, 1H), 8.59 (t, 1H, NH).
6 -C3H7 0.94 (t,3H), 1.12 (t, 3H), 1.64 (m, 2H), 3.28 (q, 2H), 3.40 (q, 2H), 7.25 (d, J = 9.2 Hz, 1H), 7.84 (dd, 90 81 16 243
J = 9.2 Hz, J = 2.4 Hz, 1H), 8.44 (d, J = 2.4 Hz, 1H), 8.61 (t,1H, NH).
7 -C4H9 0.92 (t,3H), 1.11 (t, 3H), 1.38 (m, 2H), 1.61 (m, 2H), 3.26 (q, 2H), 3.44 (q, 2H), 7.25 (d, J = 8.8 Hz, 1H), 7.85 76 82 17 257
(dd, J = 8.8 Hz, J = 2 Hz, 1H), 8.44 (d, J = 2 Hz, 1H), 8.60 (t,1H, NH).
8 -cyclohexyl 1.11 (t, 3H), 1.26 (m, 1H), 1.43 (m, 4H), 1.61 (d, 1H), 1.71 (m, 2H), 1.95 (m, 2H), 3.27 (q, 2H), 3.75 (m, 1H), 154 80 18 283
7.34 (d, J = 9.6 Hz, 1H), 7.85 (dd, J = 9.2 Hz, J = 2.4 Hz, 1H), 8.32 (d, J = 8 Hz, 1H), 8.55 (d, J = 2.4 Hz,
1H).
9 -benzyl 1.09 (t, 3H), 3.25 (q, 2H), 4.72 (d, 2H), 7.10 (d, J = 9.2 Hz, 1H), 7.30 (m, 5H), 7.79 (dd, J = 9.4 Hz, 120 75 19 291
J = 2.4 Hz, 1H), 8.47 (d, J = 2 Hz, 1H), 9.18 (t,1H, NH).
10 -p-fluorobenzyl 1.08 (t, 3H), 3.26 (q, 2H), 4.70 (d, 2H), 7.09 (d, J = 9.2 Hz, 1H), 7.17 (m, 2H), 7.43 (m, 2H), 7.79 (dd, 114 73 20 309
J = 9.2 Hz, J = 1.6 Hz, 1H), 8.46 (d, J = 2.4 Hz, 1H), 9.19 (t,1H, NH).
11 -3,4-difluorobenzyl 1.08 (t, 3H), 3.26 (q,2H), 4.70 (d, 2H), 7.07 (d, J = 9.2 Hz, 1H), 7.25 (m, 1H), 7.37–7.52 (m, 2H), 7.79 (dd, 121 71 21 357
J = 9.2 Hz, J = 2 Hz, 1H), 8.46 (d, J = 2.4 Hz, 1H), 9.20 (t,1H, NH).
12 -3,4-dichlorobenzyl 1.28 (t, 3H), 3.09 (q, 2H), 4.58 (d, 2H), 6.85 (d, J = 8.8 Hz, 1H), 7.18 (dd, J = 8 Hz, J = 1.2 Hz, 1H), 7.43 (m, 145 76 22 390
2H), 7.80 (dd, J = 9 Hz, J = 2 Hz, 1H), 8.73 (d, J = 2 Hz, 1H), 8.79 (t,1H, NH)
Bioorganic Chemistry 100 (2020) 103929
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

J = 1.6 Hz, 1H), 7.86 (d, J = 8.8 Hz, 1H), 8.09 (d, J = 1.6 Hz, 1H), 8.15 J = 8.4 Hz, J = 1.6 Hz, 1H), 7.78 (d, J = 8.8 Hz, 1H), 8.07 (s, 1H), 8.14
(d, J = 1.6 Hz, 1H), 8.40 (d, J = 8 Hz, 1H), 11.90 (brd s, 1H, NH). 13C (d, J = 1.6 Hz, 1H), 8.39 (m, 1H), 11.85 (brd s, 1H). 13C NMR
NMR (DMSO‑d6): 7.36, 14.61, 49.69, 104.04, 110.39, 111.79, 118.30, (DMSO‑d6): 7.40, 10.92, 22.36, 45.57, 49.74, 104.24, 110.73,
120.43, 120.70, 121.44, 122.46, 126.35, 126.73, 131.40, 136.04, 111.85, 118.37, 120.48, 120.71, 121.46, 122.49, 126.45, 126.75,
138.33, 142.65, 151.89. MS (ESI+) m/z: 354. Anal. calcd. For 131.43, 136.05, 138.91, 142.55, 152.20. MS (ESI+) m/z: 368. Anal.
C19H19N3O2S: C, 64.57; H, 5.41; N, 11.88; S, 9.07; Found: C, 64.67; calcd. For C20H21N3O2S: C, 65.22; H, 6.03; N, 11.54; S, 8.68; Found: C,
H, 5.14; N, 11.57; S, 8.84. 65.37; H, 5.76; N, 11.44; S, 8.72.

[Link]. 1-ethyl-5-(ethylsulfonyl)-2-(5-methoxy-1H-indol-3-yl)-1H-benzo [Link]. 5-(ethylsulfonyl)-2-(5-methoxy-1H-indol-3-yl)-1-propyl-1H-

[d]imidazole (30). Compound 30 was prepared according to general benzo[d]imidazole (34). Compound 34 was prepared according to
methods starting from N1-ethyl-4-ethylsulfonyl-benzene-1,2-diamine general methods starting from N1-(propyl)-4-ethylsulfonyl-benzene-
(1.22 mmol, 0.280 g) and 5-methoxy-indole-3-carboxaldehyde 1,2-diamine (1.06 mmol, 0.258 g) and 5-methoxy-indole-3-
(1.22 mmol, 0.214 g). The residue was purified by cc using the ethyl carboxaldehyde (1.06 mmol, 0.187 g). The residue was purified by cc
acetate as eluent to give a light yellow solid, m.p. 249 °C (0.165 g, 36% using the chloroform/ethyl acetate/hexane ([Link]) as eluent to give a
yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 1.12 (t, 3H), 1.41 (t, 3H), white solid, m.p. 159 °C (0.175 g, 41% yield). 1H NMR (400 MHz,
3.30 (q, 2H), 3.82 (s, 3H), 4.55 (q, 2H), 6.90 (dd, J = 8.8 Hz, DMSO‑d6): δ ppm 0.90 (t, 3H), 1.13 (t, 3H), 1.79–1.84 (m, 2H), 3.32 (q,
J = 2.4 Hz, 1H), 7.43 (d, J = 8.8 Hz, 1H), 7.71 (dd, J = 8.8 Hz, 2H), 3.82 (s, 3H), 4.48 (t, 2H), 6.90 (dd, J = 8.4 Hz, J = 2.4 Hz, 1H),
J = 1.6 Hz, 1H), 7.85 (d, J = 8.8 Hz, 1H), 7.95 (d, J = 2.4 Hz, 1H), 7.44 (d, J = 8.4 Hz, 1H), 7.71 (dd, J = 8,8 Hz, J = 1.6 Hz, 1H), 7.87 (d,
8.04 (d, J = 3.2 Hz, 1H), 8.15 (d, J = 1.6 Hz,1H), 11.76 (brd d, 1H, J = 8.8 Hz, 1H), 7.95 (d, J = 2.4 Hz, 1H), 8.02 (d, J = 2.8 Hz, 1H), 8.15
NH). 13C NMR (DMSO‑d6): 7.43, 14.66, 49.76, 55.35, 103.19, 103.87, (d, J = 2 Hz, 1H) 11.8 (brd s, 1H) 13C NMR (DMSO‑d6): 7.40, 10.93,
110.37, 112.57, 112.72, 118.36, 120.71, 127.05, 127.13, 131.14, 22.34, 45.57, 49.73, 55.35,103.20, 103.99, 110.62, 112.55, 112.67,
131.41, 138.39, 142.69, 152.13, 154.52. MS (ESI+) m/z: 384. Anal. 118.35, 120.66, 127.08, 131.08, 131.36, 138.91, 142.51, 152.36,
calcd. For C20H21N3O3S.0,9H2O: C, 60.10; H, 5.74; N, 10.51; S, 8.02; 154.51. MS(ESI+) m/z: 398. Anal. calcd. For C21H23N3O3S: C,
Found: C, 60.05; H, 5.75; N, 10.12; S, 7.85; 63.46; H, 5.83; N, 10.57; S, 8.07; Found: C, 63.18; H, 5.99; N, 10.50;
S, 7.93.
[Link]. 2-(5-chloro-1H-indol-3-yl)-1-ethyl-5-(ethylsulfonyl)-1H-benzo[d]
imidazole (31). Compound 31 was prepared according to general [Link]. 5-(ethylsulfonyl)-2-(5-chloro-1H-indol-3-yl)-1-propyl-1H-benzo
methods starting from N1-ethyl-4-ethylsulfonyl-benzene-1,2-diamine [d]imidazole (35). Compound 35 was prepared according to general
(1.5 mmol, 0.342 g) and 5-chloro-indole-3-carboxaldehyde (1.5 mmol, methods starting from N1-(propyl)-4-ethylsulfonyl-benzene-1,2-
0.269 g). The residue was purified by cc using the ethyl acetate as diamine (0.82 mmol, 0.199 g) and 5-chloro-indole-3-carboxaldehyde
eluent to give a light yellow solid, m.p. 280 °C (0.273 g, 47% yield). 1H (0.82 mmol, 0.147 g). The residue was purified by cc using the
NMR (400 MHz, DMSO‑d6): δ ppm 1.10 (t, 3H), 1.40 (t, 3H), 3.29 (q, chloroform/ethyl acetate/hexane ([Link]) as eluent to give a white
2H), 4.55 (q, 2H), 7.25 (dd, J = 8.8 Hz, J = 2 Hz, 1H), 7.54 (d, solid, m.p. 232 °C (0.050 g, 15% yield). 1H NMR (400 MHz,
J = 7.6 Hz, 1H), 7.71 (dd, J = 8.4 Hz, J = 1.6 Hz, 1H), 7.84 (d, DMSO‑d6): δ ppm 0.88 (t, 3H), 1.10 (t, 3H), 1.76–1.82 (m, 2H), 3.30
J = 8 Hz, 1H), 8.17 (t, 2H), 8.47 (d, J = 2 Hz, 1H), 12.07 (brd s, 1H, (q, 2H), 4.48 (t, 2H), 7.24 (dd, J = 8.8 Hz, J = 2 Hz, 1H), 7.54 (d,
NH). 13C NMR (DMSO‑d6): 7.41, 14.63, 49.69, 103.92, 110.46, 113.50, J = 8.8 Hz, 1H), 7.70 (dd, J = 8.8 Hz, J = 1.6 Hz, 1H), 7.86 (d,
118.51, 120.79, 120.88, 122.62, 125.28, 127.57, 128.29, 131.62, J = 8.4 Hz, 1H), 8.15–8.17 (m, 2H), 8.46 (d, J = 2 Hz, 1H), 12.03
134.63, 138.34, 142.57, 151.31. MS (ESI+) m/z: [Link]. calcd. (brd s, 1H). 13C NMR (DMSO‑d6): 7.34, 10.87, 22.30, 45.48, 49.60,
For C19H18ClN3O2S: C, 58.83; H, 4.67; N, 10.83; S, 8.26; Found: C, 103.97, 110.69, 113.45, 118.46, 120.71, 120.78, 122.54, 125.20,
58.56; H, 4.67; N, 10.64; S, 8.13. 127.56, 128.19, 131.50, 134.51, 138.82, 142.34, 151.49. MS (ESI+)
m/z: 402. Anal. calcd. For C20H20ClN3O2S: C, 59.77; H, 5.02; N,
[Link]. 2-(5-bromo-1H-indol-3-yl)-1-ethyl-5-(ethylsulfonyl)-1H-benzo 10.46; S, 7.98; Found: C, 59.85; H, 5.20; N, 10.54; S, 7.77.
[d]imidazole (32). Compound 32 was prepared according to general
methods starting from N1-ethyl-4-ethylsulfonyl)benzene-1,2-diamine [Link]. 5-(ethylsulfonyl)-2-(5-bromo-1H-indol-3-yl)-1-propyl-1H-benzo
(1.8 mmol, 0.406 g) and 5-bromo-indole-3-carboxaldehyde (1.8 mmol, [d]imidazole (36). Compound 36 was prepared according to general
0.401 g). The residue was purified by cc using the ethyl acetate as methods starting from N1-(propyl)-4-ethylsulfonyl-benzene-1,2-
eluent to give a light yellow solid, m.p. 288 °C (0.370 g, 48% yield). 1H diamine (1.11 mmol, 0.269 g) and 5-bromo-indole-3-carboxaldehyde
NMR (400 MHz, DMSO‑d6): δ ppm 1.10 (t, 3H), 1.40 (t, 3H), 3.29 (q, (1.11 mmol, 0.249 g). The residue was purified by cc using the
2H), 4.55 (q, 2H), 7.36 (dd, J = 8.8 Hz, J = 2 Hz, 1H), 7.50 (d, chloroform/ethyl acetate/hexane ([Link]) as eluent to give a white
J = 9.2 Hz, 1H), 7.71 (dd, J = 8.4 Hz, J = 1.6 Hz, 1H), 7.84 (d, solid, m.p. 234 °C (0.079 g, 16% yield). 1H NMR (400 MHz,
J = 8.4 Hz, 1H), 8.17 (t, 2H), 8.62 (d, J = 2 Hz, 1H), 12.08 (brd s, DMSO‑d6): δ ppm 0.87 (t, 3H), 1.11 (t, 3H), 1.76–1.82 (m, 2H), 3.29
1H, NH). 13C NMR (DMSO‑d6): 7.36, 14.57, 49.63, 103.74, 110.40, (q, 3H), 4.47 (t, 2H) 7.35 (d, J = 8 Hz, 1H), 7.49 (d, J = 8.8 Hz, 1H),
113.23, 113.89, 118.47, 120.84, 123.74, 125.10, 128.06, 128.14, 7.7 (d, J = 8.4 Hz, 1H), 7.84 (d, J = 8.4 Hz, 1H), 8.11 (s, 1H), 8.16 (s,
131.57, 134.81, 138.28, 142.50, 151.22. MS (ESI+) m/z: 434. Anal. 1H), 8.6 (s, 1H), 11.98 (brd s, 1H). 13C NMR (DMSO‑d6): 7.39, 10.92,
calcd. For C19H18BrN3O2S: C, 52.78; H, 4.19; N, 9.71; S, 7.41; Found: 22.35, 45.54, 49.66, 103.93, 110.76, 113.28, 113.95, 118.52, 120.85,
C, 52.48; H, 3.98; N, 9.58; S, 7.39. 123.77, 125.14, 128.09, 128.24, 131.59, 134.81, 138.87, 142.40,
151.52. MS (ESI+) m/z: 446. Anal. calcd. For C20H20BrN3O2S: C,
[Link]. 5-(ethylsulfonyl)-2-(1H-indol-3-yl)-1-propyl-1H-benzo[d] 53.81; H, 4.51; N, 9.41; S, 7.18; Found: C, 53.26; H, 4.51; N, 9.56; S,
imidazole (33). Compound 33 was prepared according to general 6.98.
methods starting from N1-(propyl)-4-ethylsulfonyl-benzene-1,2-
diamine (1.04 mmol, 0.253 g) and indole-3-carboxaldehyde [Link]. 5-(ethylsulfonyl)-2-(1H-indol-3-yl)-1-butyl-1H-benzo[d]
(1.04 mmol, 0.152 g). The residue was purified by cc using the imidazole (37). Compound 37 was prepared according to general
chloroform/ethyl acetate/hexane ([Link]) as eluent to give a white methods starting from N1-(butyl)-4-ethylsulfonyl-benzene-1,2-diamine
solid, m.p. 182 °C (0.199 g,52% yield). 1H NMR (400 MHz, (0.89 mmol, 0.228 g) and indole-3-carboxaldehyde (0.89 mmol,
DMSO‑d6): δ ppm 0.89 (t, 3H), 1.13 (t, 3H), 1.78–1.84 (m, 2H), 3,32 0.129 g). The residue was purified by cc using the chloroform/ethyl
(q, 2H), 4.49 (t, 2H), 7.18–7.27 (m, 2H), 7.53–7.55 (m, 1H), 7.72 (dd, acetate/hexane ([Link]) as eluent to give a white solid, m.p. 177 °C

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

(0.044 g, 13% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 0.82 (t, benzo[d]imidazole (41). Compound 41 was prepared according to
3H), 1.10 (t, 3H), 1.29 (m, 2H), 1.71–1.75 (m, 2H), 3.30 (q, 2H), 4.50 general methods starting from N1-cyclohexyl-4-ethylsulfonyl-benzene-
(t, 2H), 7.15–7.24 (m, 2H), 7.51 (d, J = 7.6 Hz, 1H), 7.70 (dd, 1,2-diamine (1.05 mmol, 0.297 g) and 5-methoxy-indole-3-
J = 8.8 Hz, J = 1.6 Hz, 1H), 7.85 (d, J = 8.4 Hz, 1H), 8.06 (d, carboxaldehyde (1.05 mmol, 0.184 g). The residue was purified by cc
J = 2.4 Hz, 1H), 8.12 (d, J = 1.6 Hz, 1H), 8.34 (d, J = 8 Hz, 1H), using the chloroform/ethyl acetate (1:1) as eluent to give a light yellow
11.84 (brd s, 1H). 13C NMR (DMSO‑d6): 7.33, 13.42, 19.31, 31.02, solid, m.p. 163 °C (0.061 g, 13% yield). 1H NMR (400 MHz, DMSO‑d6):
43.90, 49.65, 104.16, 110.62, 111.79, 118.31, 120.41, 120.67, 121.36, δ ppm 1.13 (t, 3H), 1.32–1.44 (m, 3H), 1.66 (d, 1H), 1.85–1.98 (m, 4H),
122.43, 126.36, 126.71, 131.35, 135.96, 138.77, 142.50, 152.10. MS 2.30–2.36 (m, 2H), 3.31 (q, 2H), 3.77 (s, 3H), 4.60–4.66 (m, 1H), 6.89
(ESI+) m/z: 382. Anal. calcd. For C21H23N3O2S-0,2 H2O: C, 65.49; (dd, J = 8.8 Hz, J = 2.4 Hz, 1H), 7.45 (m, 2H), 7.67 (dd, J = 8.8 Hz,
H, 6.12; N, 10.91; S, 8.30; Found: C, 65.20; H, 6.11; N, 11.10; S, 8.30. J = 1.6 Hz, 1H), 7.79 (d, J = 2.8 Hz, 1H), 8.09 (d, J = 8.8 Hz, 1H), 8.14
(d, J = 1.6 Hz, 1H), 11.68 (brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.37,
[Link]. 5-(ethylsulfonyl)-2-(5-chloro-1H-indol-3-yl)-1-butyl-1H-benzo 14.04, 24.38, 25.56, 30.55, 49.72, 55.24, 56.63, 59.71, 101.51, 104.01,
[d]imidazole (38). Compound 38 was prepared according to general 112.74, 112.82, 113.17, 118.88, 120.31, 126.95, 127.66, 131.10,
methods starting from N1-(butyl)-4-ethylsulfonyl-benzene-1,2-diamine 131.25, 136.92, 143.49, 152.45, 154.43. MS (ESI+) m/z: 438. Anal.
(1.08 mmol, 0.277 g) and 5-chloro-indole-3-carboxaldehyde calcd. For C24H27N3O3S. 0,9H2O: C, 63.52; H, 6.40; N, 9.26; S, 7.05;
(1.08 mmol, 0.194 g). The residue was purified by cc using the Found: C, 63.60; H, 6.40; N, 8.86; S, 6.81.
chloroform/ethyl acetate/hexane ([Link]) as eluent to give a white
solid, m.p. 221 °C (0.065 g, 14% yield). 1H NMR (400 MHz, [Link]. 2-(5-chloro-1H-indol-3-yl)-1-cyclohexyl-5-(ethylsulfonyl)-1H-
DMSO‑d6): δ ppm 0.87 (t, 3H), 1.13 (t, 3H), 1.32–1.37 (m, 2H), benzo[d]imidazole (42). Compound 42 was prepared according to
1.75–1.79 (m, 2H), 3.30 (q, 2H), 4.51 (t, 2H), 7.28 (dd, J = 8.4 Hz, general methods starting from N1-cyclohexyl-4-ethylsulfonyl-benzene-
J = 2.4 Hz, 1H), 7.58 (d, J = 8.4 Hz, 1H), 7.74 (dd, J = 8.4 Hz, 1,2-diamine (1.12 mmol, 0.315 g) and 5-chloro-indole-3-
J = 2 Hz, 1H), 7.88 (d, J = 8.8 Hz, 1H), 8.2 (s, 2H), 8.48 (d, carboxaldehyde (1.12 mmol, 0.200 g). The residue was purified by cc
J = 2.4 Hz, 1H), 12.08 (brd s, 1H). 13C NMR (DMSO‑d6): 7.45, using the chloroform/ethyl acetate (2:1) as eluent to give a white solid,
13.58, 19.44, 31.14, 44.01, 49.69, 104.05, 110.76, 113.57, 118.57, m.p. 182 °C (0.201 g, 41% yield). 1H NMR (400 MHz, DMSO‑d6): δ
120.78, 120.90, 122.65, 125.31, 127.63, 128.33, 131.59, 134.60, ppm 1.14 (t, 3H), 1.38–1.43 (m, 3H), 1.67–2.00 (m, 5H), 2.30–2.35 (m,
138.84, 142.45, 151.55. MS (ESI+) m/z: 416. Anal. calcd. For 2H), 3.33 (q, 2H), 4.63–4.69 (m, 1H), 7.26 (dd, J = 8.8 Hz, J = 2 Hz,
C21H22ClN3O2S: C, 60.64; H, 5.33; N, 10.10; S, 7.71; Found: C, 1H), 7.59 (d, J = 9.2 Hz, 1H), 7.71–7.73 (m, 1H), 7.98 (d, J = 2 Hz,
60.23; H, 5.37; N, 10.38; S, 7.62. 1H), 8.05 (d, J = 1.6 Hz, 1H), 8.14–8.19 (m, 2H), 12.06 (brd s, 1H,
NH). 13C NMR (DMSO‑d6): 7.35, 24.33, 25.43, 30.42, 49.65, 56.94,
[Link]. 5-(ethylsulfonyl)-2-(5-bromo-1H-indol-3-yl)-1-butyl-1H-benzo 103.06, 113.64, 113.78, 118.48, 119.64, 120.88, 122.60, 125.31,
[d]imidazole (39). Compound 39 was prepared according to general 127.56, 129.22, 131.93, 134.68, 136.47, 141.93, 151.22. MS (ESI+)
methods starting from N1-(butyl)-4-ethylsulfonyl-benzene-1,2-diamine m/z: 442. Anal. calcd. For C23H24ClN3O2S: C, 62.50; H, 5.47; N, 9.51;
(0.86 mmol, 0.220 g) and 5-bromo-indole-3-carboxaldehyde S, 7.25; Found: C, 62.23; H, 5.71; N, 8.94; S, 7.12.
(0.86 mmol, 0.194 g). The residue was purified by cc using the
chloroform/ethyl acetate/hexane ([Link]) as eluent to give a white [Link]. 2-(5-bromo-1H-indol-3-yl)-1-cyclohexyl-5-(ethylsulfonyl)-1H-
solid, m.p. 235 °C (0.040 g, 10% yield). 1H NMR (400 MHz, benzo[d]imidazole (43). Compound 43 was prepared according to
DMSO‑d6): δ ppm 0.86 (t, 3H), 1.13 (t, 3H), 1.30–1.39 (m, 2H), general methods starting from N1-cyclohexyl-4-ethylsulfonyl-benzene-
1.73–1.80 (m, 2H), 3.33 (q, 2H), 4.54 (t, 2H), 7.38 (dd, J = 8.8 Hz, 1,2-diamine (1.10 mmol, 0.311 g) and 5-bromo-indole-3-
J = 1.6 Hz, 1H), 7.53 (d, J = 8.4 Hz, 1H), 7.78 (dd, J = 8.4 Hz, carboxaldehyde (1.10 mmol, 0.246 g). The residue was purified by cc
J = 1.6 Hz, 1H), 7.88 (d, J = 8.8 Hz, 1H), 8.17 (s, 1H), 8.2 (d, using the chloroform/ethyl acetate (1:1) as eluent to give a white solid,
J = 1.6 Hz, 1H), 8.62 (d, J = 2 Hz, 1H), 12.06 (brd s, 1H). 13C NMR m.p. 184 °C (0.335 g, 79% yield). 1H NMR (400 MHz, DMSO‑d6): δ
(DMSO‑d6): 7.40, 13.52, 19.39, 31.09, 43.98, 49.66, 103.92, 110.72, ppm 1.13 (t, 3H), 1.40 (m, 3H), 1.67 (s, 1H), 1.86–1.98 (m, 4H),
113.28, 113.96, 118.54, 120.86, 123.73, 125.14, 128.11, 128.23, 2.29–2.35 (m, 2H), 3.31 (q, 2H), 4.63–4.69 (m, 1H), 7.36 (dd,
131.59, 134.81, 138.79, 142.42, 151.48. MS (ESI+) m/z: 460. Anal. J = 8.4 Hz, J = 1.6 Hz, 1H), 7.53 (d, J = 8.4 Hz, 1H), 7.68 (dd,
calcd. For C21H22BrN3O2S: C, 54.78; H, 4.81; N, 9.12; S, 6.96; Found: J = 8.4 Hz, J = 2 Hz, 1H), 7.93 (d, J = 2.8 Hz, 1H), 8.10 (d,
C, 54.28; H, 4.67; N, 9.51; S, 6.96. J = 8.8 Hz, 1H), 8.20 (dd, J = 11.2 Hz, J = 1.6 Hz, 2H), 11.99 (brd s,
1H, NH). 13C NMR (DMSO‑d6): 7.27, 24.32, 25.41, 30.45, 49.65,
[Link]. 1-cyclohexyl-5-(ethylsulfonyl)-2-(1H-indol-3-yl)-1H-benzo[d] 56.65, 103.78, 113.05, 113.21, 114.00, 118.91, 120.40, 122.70,
imidazole (40). Compound 40 was prepared according to general 124.92, 128.30, 128.40, 131.47, 134.83, 136.76, 143.23, 151.43. MS
methods starting from N1-cyclohexyl-4-ethylsulfonyl-benzene-1,2- (ESI+) m/z: 488. Anal. calcd. For C23H24BrN3O2S.0.45 H2O: C,
diamine (0.94 mmol, 0.265 g) and indole-3-carboxaldehyde 55.86; H, 5.07; N, 8.49; S, 6.48; Found: C, 55.85; H, 4.85; N, 8.15; S,
(0.94 mmol, 0.136 g). The residue was purified by cc using the 6.43.
chloroform/ethyl acetate (1:1) as eluent to give a light yellow solid,
m.p. 250 °C (0.263 g, 69% yield). 1H NMR (400 MHz, DMSO‑d6): δ [Link]. 1-benzyl-5-(ethylsulfonyl)-2-(1H-indol-3-yl)-1H-benzo[d]
ppm 1.14 (t, 3H), 1.32–1.43 (m, 3H), 1.66 (d, 1H), 1.85–1.98 (m, 4H), imidazole (44). Compound 44 was prepared according to general
2.29–2.37 (m, 2H), 3.30 (q, 2H), 4.62–4.68 (m, 1H), 7.15–7.26 (m, 2H), methods starting from N1-benzyl-4-ethylsulfonyl-benzene-1,2-diamine
7.55 (d, J = 8.4 Hz, 1H), 7.68 (dd, J = 8.8 Hz, J = 1.6 Hz, 1H), 7.84 (d, (0.80 mmol, 0.230 g) and indole-3-carboxaldehyde (0.80 mmol,
J = 2.8 Hz, 1H), 7.97 (d, J = 8 Hz, 1H), 8.10 (d, J = 8.8 Hz, 1H), 8.14 0.115 g). The residue was purified by cc using the chloroform/ethyl
(d, J = 1.6 Hz, 1H), 11.79 (brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.28, acetate (1:1) as eluent to give a white solid, m.p. 252 °C (0.066 g, 20%
24.32, 25.47, 30.49, 49.70, 56.58, 104.18, 111.96, 113.11, 118.84, yield).1H NMR (400 MHz, DMSO‑d6): δ ppm 1.14 (t, 3H), 3.31 (q, 2H),
120.12, 120.29, 122.27, 126.46, 127.13, 131.29, 136.05, 136.85, 5.85 (s, 2H), 7.09 (d, J = 7.2 Hz, 2H), 7.19–7.34 (m, 5H), 7.49 (d,
143.42, 152.21. MS (ESI+) m/z: 408. Anal. calcd. For J = 7.2 Hz, 1H), 7.68–7.78 (m, 3H), 8.19 (s, 1H), 8.44 (d, J = 7.2 Hz,
C23H25N3O2S.0,3H2O: C, 66.89; H, 6.25; N, 10.18; S, 7.74; Found: C, 1H), 11.77 (brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.38, 47.38, 49.68,
66.57; H, 5.95; N, 9.94; S, 7.97. 103.92, 110.74, 111.87, 118.48, 120.63, 121.09, 121.50, 122.63,
125.96, 126.33, 126.84, 127.48, 128.93, 131.90, 135.98, 136.57,
[Link]. 1-cyclohexyl-5-(ethylsulfonyl)-2-(5-methoxy-1H-indol-3-yl)-1H- 139.12, 142.69, 152.61. MS (ESI+) m/z: [Link]. calcd. For

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

C24H21N3O2S.0,5C4H8O2-0,5H2O: C, 66.65; H, 5.59; N, 8.97; S, 6.84; 152.47, 161.32 (d, J = 242.3 Hz), 170.23. MS (ESI+) m/z: 434. Anal.
Found: C, 66.68; H, 5.40; N, 8.98; S, 6.90. calcd. For C24H20FN3O2S.0,5C4H8O2: C, 65.39; H, 5.06; N, 8.79; S,
6.71; Found: C, 65.18; H, 5.02; N, 8.71; S, 6.68.
[Link]. 1-benzyl-5-(ethylsulfonyl)-2-(5-methoxy-1H-indol-3-yl)-1H-
benzo[d]imidazole (45). Compound 45 was prepared according to [Link]. 5-(ethylsulfonyl)-1-(4-fluorobenzyl)-2-(5-methoxy-1H-indol-
general methods starting from N1-benzyl-4-ethylsulfonyl-benzene-1,2- 3yl)-1H-benzo[d]imidazole (49). Compound 49 was prepared according
diamine (0.70 mmol, 0.203 g) and 5-methoxy-indole-3-carboxaldehyde to general methods starting from N1-(4-fluorobenzyl)-4-ethylsulfonyl-
(0.70 mmol, 0.123 g). The residue was purified by cc using the benzene-1,2-diamine (0.54 mmol, 0.168 g) and 5-methoxy-indole-3-
chloroform/ethyl acetate (1:1) as eluent to give a white solid, m.p. carboxaldehyde (0.54 mmol, 0.095 g). The residue was purified by cc
296 °C (0.036 g, 12% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm using the chloroform/ethyl acetate (2:1) as eluent to give a light yellow
1.13 (t, 3H), 3.32 (q, 2H), 3.80 (s, 3H), 5.83 (s, 2H), 6.88 (dd, solid, m.p. 260 °C (0.044 g, 18% yield). 1H NMR (400 MHz, DMSO‑d6):
J = 8.8 Hz, J = 2.4 Hz, 1H), 7.09 (d, J = 7.2 Hz, 2H), 7.23–7.39 (m, δ ppm 1.13 (t, 3H), 3.32 (q, 2H), 3.80 (s, 3H), 5.82 (s, 2H), 6.89 (dd,
4H), 7.67–7.74 (m, 3H), 7.96 (d, J = 2.4 Hz, 1H), 8.19 (d, J = 1.2 Hz, J = 8.8 Hz, J = 2.4 Hz, 1H), 7.10–7.18 (m, 4H), 7.39 (d, J = 8.8 Hz,
1H), 11.64 (brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.89, 47.89, 60.18, 1H), 7.67–7.77 (m, 3H), 7.96 (d, J = 2.4 Hz, 1H), 8.19 (d, J = 1.6 Hz,
55.81, 103.62, 104.17, 111.15, 113.09, 113.29, 118.98, 121.52, 1H), 11.66 (brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.31, 46.68, 49.60,
126.47, 127.44, 127.72, 127.96, 129.43, 131.47, 132.32, 137.08, 55.24, 103.08, 103.55, 110.55, 112.53, 112.72, 115.68 (d,
139.62, 143.19, 153.31, 155.07. MS (ESI+) m/z: 446. Anal. calcd. J = 21.7 Hz), 118.43, 120.98, 126.87, 127.16, 128.03 (d, J = 8.4 Hz),
For C25H23N3O3S: C, 67.39; H, 5.20; N, 9.43; S, 7.19; Found: C, 67.29; 130.92, 131.84, 132.64 (d, J = 3.5 Hz), 138.93, 142.64, 152.64,
H, 5.45; N, 9.30; S, 7.16. 154.51, 161.30 (d, J = 242.3 Hz). MS (ESI+) m/z: 464. Anal. calcd.
For C25H22FN3O3S.0,2H2O: C, 64.27; H, 4.83; N, 9.00; S, 6.85; Found:
[Link]. 1-benzyl-2-(5-chloro-1H-indol-3-yl)-5-(ethylsulfonyl)-1H-benzo C, 64.02; H, 4.98; N, 8.69; S, 6.62.
[d]imidazole (46). Compound 46 was prepared according to general
methods starting from N1-benzyl-4-ethylsulfonyl)benzene-1,2-diamine [Link]. 2-(5-chloro-1H-indol-3-yl)-5-(ethylsulfonyl)-1-(4-fluorobenzyl)-
(0.85 mmol, 0.246 g) and 5-chloro-indole-3-carboxaldehyde 1H-benzo[d]imidazole (50). Compound 50 was prepared according to
(0.85 mmol, 0.152 g). The residue was purified by cc using the general methods starting from N1-(4-fluorobenzyl)-4-ethylsulfonyl-
chloroform/ethyl acetate (1:1) as eluent to give a white solid, m.p. benzene-1,2-diamine (0.52 mmol, 0.162 g) and 5-chloro-indole-3-
265 °C (0.139 g, 36% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm carboxaldehyde (0.52 mmol, 0.094 g). The residue was purified by cc
1.15 (t, 3H), 3.32 (q, 2H), 5.86 (s, 2H), 7.09 (d, J = 7.6 Hz, 2H), using the chloroform/ethyl acetate (2:1) as eluent to give a white solid,
7.25–7.34 (m, 4H), 7.52 (d, J = 8.8 Hz, 1H), 7.70–7.78 (m, 2H), 7.8 (s, m.p. 230 °C (0.097 g, 40% yield). 1H NMR (400 MHz, DMSO‑d6): δ
1H), 8.25 (s, 1H), 8.51 (d, J = 2 Hz, 1H), 11.95 (brd s, 1H, NH). 13C ppm 1.12 (t, 3H), 3.32 (q, 2H), 5.83 (s, 2H), 7.08–7.15 (m, 4H), 7.24
NMR (DMSO‑d6): 7.31, 47.33, 49.62, 103.71, 110.71, 113.48, 118.61, (dd, J = 8.8 Hz, J = 2 Hz, 1H), 7.50 (d, J = 8.4 Hz, 1H), 7.69 (dd,
120.70, 121.16, 122.66, 125.34, 125.90, 127.45, 128.24, 128.89, J = 8.4 Hz, J = 2 Hz, 1H), 7.76 (d, J = 8.4 Hz, 1H), 7.9 (s, 1H), 8.22 (d,
132.05, 134.46, 136.38, 139.05, 142.53, 151.95. MS (ESI+) m/z: J = 1.6 Hz, 1H), 8.48 (d, J = 2.4 Hz, 1H), 11.96 (brd s, 1H, NH). 13C
450. Anal. calcd. For C24H20ClN3O2S: C, 64.06; H, 4.48; N, 9.33; S, NMR (DMSO‑d6): 7.31, 46.44, 49.55, 103.61, 110.68, 113.49, 115.72
7.12; Found: C, 63.47; H, 4.46; N, 9.19; S, 7.05. (d, J = 21.1 Hz), 118.62, 120.69, 121.20, 122.66, 125.33, 127.41,
128.03 (d, J = 7.7 Hz), 128.28, 132.04, 132.52 (d, J = 2.6 Hz),
[Link]. 1-benzyl-2-(5-bromo-1H-indol-3-yl)-5-(ethylsulfonyl)-1H-benzo 134.43, 138.92, 142.51, 151.82, 161.32 (d, J = 240 Hz). MS (ESI+)
[d]imidazole (47). Compound 47 was prepared according to general m/z: [Link]. calcd. For C24H19ClFN3O2S: C, 61.60; H, 4.09; N, 8.98;
methods starting from N1-benzyl-4-ethylsulfonyl-benzene-1,2-diamine S, 6.85; Found: C, 61.51; H, 4.10; N, 9.00; S, 6.86.
(0.83 mmol, 0.240 g) and 5-bromo-indole-3-carboxaldehyde
(0.83 mmol, 0.185 g). The residue was purified by cc using the [Link]. 2-(5-bromo-1H-indol-3-yl)-5-(ethylsulfonyl)-1-(4-fluorobenzyl)-
chloroform/ethyl acetate (1:1) as eluent to give a white solid, m.p. 1H-benzo[d]imidazole (51). Compound 51 was prepared according to
267 °C (0.226 g, 55% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm general methods starting from N1-(4-fluorobenzyl)-4-ethylsulfonyl-
1.13 (t, 3H), 3.33 (q, 2H), 5.87 (s, 2H), 7.08 (d, J = 7.2 Hz, 2H), benzene-1,2-diamine (0.66 mmol, 0.202 g) and 5-bromo-indole-3-
7.25–7.38 (m, 4H), 7.48 (d, J = 8.8 Hz, 1H),7.69–7.78 (m, 2H), 7.87 (s, carboxaldehyde (0.66 mmol, 0.146 g). The residue was purified by cc
1H), 8.25 (s, 1H), 8.66 (d, J = 1.6 Hz, 1H), 11.97 (brd s, 1H, NH). 13C using the chloroform/ethyl acetate/hexane ([Link]) as eluent to give a
NMR (DMSO‑d6): 7.38, 47.34, 49.63, 103.61, 110.75, 113.41, 113.97, white solid, m.p. 240 °C (0.099 g, 29% yield). 1H NMR (400 MHz,
118.68, 121.23, 123.77, 125.25, 125.94, 127.50, 128.10, 128.13, DMSO‑d6): δ ppm 1.13 (t, 3H), 3.32 (q, 2H), 5.86 (s, 2H), 7.10–7.18 (m,
128.95, 132.05, 134.73, 136.43, 139.10, 142.55, 151.95. MS (ESI+) 4H), 7.38 (dd, J = 8.8 Hz, J = 2 Hz, 1H), 7.48 (d, J = 8.4 Hz, 1H), 7.71
m/z: 496. Anal. calcd. For C24H20BrN3O2S.0,3H2O: C, 57.67; H, 4.15; (dd, J = 8.4 Hz, J = 1.6 Hz, 1H), 7.78 (d, J = 8.4 Hz, 1H), 7.91 (d,
N, 8.40; S, 6.41; Found: C, 57.66; H, 4.12; N, 8.17; S, 6.13. J = 2.8 Hz, 1H), 8.25 (d, J = 1.6 Hz, 1H), 8.66 (d, J = 2 Hz, 1H), 11.99
(brd s, 1H, NH). 13C NMR (DMSO‑d6): 7.31, 46.64, 49.64, 103.49,
[Link]. 5-(ethylsulfonyl)-1-(4-fluorobenzyl)-2-(1H-indol-3-yl)-1H-benzo 110.68, 113.34, 113.92, 115.72 (d, J = 21.2 Hz), 118.63, 121.20,
[d]imidazole (48). Compound 48 was prepared according to general 123.70, 125.20, 127.97, 128.02 (d, J = 8.3 Hz), 128.113, 132.05,
methods starting from N1-(4-fluorobenzyl)-4-ethylsulfonyl-benzene- 132.51 (d, J = 3.2 Hz), 134.67, 138.91, 142.50, 151.79, 161.32 (d,
1,2-diamine (0.68 mmol, 0.210 g) and indole-3-carboxaldehyde J = 241.5 Hz). MS (ESI+) m/z: 514. Anal. calcd. For
(0.68 mmol, 0.099 g). The residue was purified by cc using the C24H19BrFN3O2S: C, 56.26; H, 3.74; N, 8.20; S, 6.25; Found: C,
chloroform/ethyl acetate (2:1) as eluent to give a white solid, m.p. 56.51; H, 4.02; N, 7.72; S, 5.84.
234 °C (0.080 g, 27% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm
1.13 (t, 3H), 3.31 (q, 2H), 5.82 (s, 2H), 7.08–7.24 (m, 6H), 7.48 (d, [Link]. 5-(ethylsulfonyl)-1-(3,4-difluorobenzyl)-2-(1H-indol-3-yl)-1H-
J = 7.2 Hz, 1H), 7.69 (dd, J = 8.4 Hz, J = 1.6 Hz, 1H), 7.71 (d, benzo[d]imidazole (52). Compound 52 was prepared according to
J = 8.8 Hz, 1H), 7.80 (d, J = 2.4 Hz, 1H), 8.17 (d, J = 1.2 Hz, 1H), general methods starting from N1-(3,4-difluorobenzyl)-4-
8.41 (d, J = 8.4 Hz, 1H), 11.73 (brd s, 1H, NH). 13C NMR (DMSO‑d6): ethylsulfonyl-benzene-1,2-diamine (0.64 mmol, 0.209 g) and indole-3-
7.31, 46.68, 49.62, 103.80, 110.66, 111.82, 115.69 (d, J = 21.3 Hz), carboxaldehyde (0.64 mmol, 0.093 g). The residue was purified by cc
118.46, 120.57, 121.07, 121.45, 122.57,126.26, 126.81, 128.04 (d, using the chloroform/ethyl acetate/hexane (2:1.5:1) as eluent to give a
J = 8.4 Hz), 131.90, 132.65 (d, J = 3.1 Hz), 135.94, 138.95, 142.66, white solid, m.p. 262 °C (0.175 g, 61% yield). 1H NMR (400 MHz,

7
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

DMSO‑d6): δ ppm 1.11 (t, 3H), 3.31 (q, 2H), 5.82 (s, 2H), 6.77 (d, 152.43, 161.22. MS (ESI+) m/z: 484. Anal. calcd. For
J = 8.4 Hz, 1H), 7.16–7.36 (m, 4H), 7.48 (d, J = 7.6 Hz, 1H), 7.69 (dd, C24H19Cl2N3O2S-0.5 H2O: C, 58.42; H, 4.08; N, 8.51; S, 6.49; Found:
J = 8.8 Hz, J = 1.6 Hz, 1H), 7.75 (d, J = 8.4 Hz, 1H), 7.80 (d, C, 58.30; H, 4.31; N, 8.78; S, 6.04.
J = 2.8 Hz, 1H), 8.18 (d, J = 1.6 Hz, 1H), 8.41 (d, J = 8.4 Hz, 1H),
11.77 (brd s, 1H). MS (ESI+) m/z: 452. Anal. calcd. For [Link]. 5-(ethylsulfonyl)-1-(3,4-diclorobenzyl)-2-(5-methoxy-1H-indol-
C24H19F2N3O2S: C, 63.85; H, 4.24; N, 8.42; S, 7.10; Found: C, 63.61; 3-yl)-1H-benzo[d]imidazole (57). Compound 57 was prepared
H, 4.41; N, 8.97; S, 6.91 according to general methods starting from N1-(3,4-dichlorobenzyl)-4-
ethylsulfonyl-benzene-1,2-diamine (1.01 mmol, 0.363 g) and 5-
[Link]. 5-(ethylsulfonyl)-1-(3,4-difluorobenzyl)-2-(5-methoxy-1H-indol- methoxy-indole-3-carboxaldehyde (1.01 mmol, 0.177 g). The residue
3-yl)-1H-benzo[d]imidazole (53). Compound 53 was prepared was purified by cc using the chloroform/ethyl acetate (2:1) as eluent to
according to general methods starting from N1-(3,4-difluorobenzyl)-4- give a white solid, m.p. 242 °C (0.065 g, 12% yield). 1H NMR
ethylsulfonyl-benzene-1,2-diamine (0.71 mmol, 0.233 g) and 5- (400 MHz, DMSO‑d6): δ ppm 1.11 (t, 3H), 3.31 (q, 2H), 3.79 (s, 3H),
methoxy-indole-3-carboxaldehyde (0.71 mmol, 0.125 g). The residue 5.83 (s, 2H), 6.89 (m, 2H), 7.37 (d, J = 8.8 Hz, 1H), 7.46 (d, J = 2 Hz,
was purified by cc using the chloroform/ethyl acetate/hexane ([Link]) as 1H), 7.53 (d, J = 8.4 Hz, 1H), 7.67–7.76 (m, 3H), 7.95 (d, J = 2.4 Hz,
eluent to give a white solid, m.p. 271 °C (0.151 g, 44% yield). 1H NMR 1H), 8.19 (d, J = 1.6 Hz, 1H), 11.65 (brd s, 1H).13C NMR (DMSO‑d6):
(400 MHz, DMSO‑d6): δ ppm 1.11 (t, 3H), 3.30 (q, 2H), 3.79 (s, 3H), 7.31, 46.30, 49.61, 55.25, 103.08, 103.39, 110.50, 112.57, 112.79,
5.80 (s, 2H), 6.78 (d, 1H), 6.87 (dd, J = 9 Hz, J = 2.4 Hz, 1H), 118.52, 121.15, 126.06, 126.87, 127.20, 128.37, 130.05, 130.94,
7.24–7.39 (m, 3H), 7.67–7.76 (m, 3H), 7.94 (d, 1H), 8.19 (d, 131.09, 131.40, 132.08, 137.74, 138.87, 142.64, 152.61, 154.57. MS
J = 1.2 Hz, 1H), 11.65 (brd s, 1H).MS (ESI+) m/z: 482. Anal. calcd. (ESI+) m/z: 514. Anal. calcd. For C25H21Cl2N3O3S C, 58.37; H, 4.11;
For C25H21F2N3O3S: C, 62.36; H, 4.40; N, 8.73; S, 6.66; Found: C, N, 8.17; S, 6.23; Found: C, 58.04; H, 4.06; N, 7.83; S, 5.98.
61.94; H, 4.60; N, 8.61; S, 6.68.
[Link]. 5-(ethylsulfonyl)-1-(3,4-dichlorobenzyl)-2-(5-chloro-1H-indol-
[Link]. 5-(ethylsulfonyl)-1-(3,4-difluorobenzyl)-2-(5-chloro-1H-indol-3- 3-yl)-1H-benzo[d]imidazole (58). Compound 58 was prepared
yl)-1H-benzo[d]imidazole (54). Compound 54 was prepared according according to general methods starting from N1-(3,4-dichlorobenzyl)-4-
to general methods starting from N1-(3,4-difluorobenzyl)-4- ethylsulfonyl-benzene-1,2-diamine (0.56 mmol, 0.202 g) and 5-chloro-
ethylsulfonyl-benzene-1,2-diamine (0.89 mmol, 0.293 g) and 5-chloro- indole-3-carboxaldehyde (0.56 mmol, 0.101 g). The residue was
indole-3-carboxaldehyde (0.89 mmol, 0.160 g). The residue was purified by cc using the chloroform/ethyl acetate (2:1) as eluent to
purified by cc using the chloroform/ethyl acetate/hexane ([Link]) as give a white solid, m.p. 278 °C (0.045 g, 15% yield). 1H NMR
eluent to give a white solid, m.p. 258 °C (0.209 g, 48% yield). 1H NMR (400 MHz, DMSO‑d6): δ ppm 1.12 (t, 3H), 3.32 (q, 2H), 5.86 (s, 2H),
(400 MHz, DMSO‑d6): δ ppm 1.11 (t, 3H), 3.30 (q, 2H), 5.83 (s, 2H), 6.86 (dd, J = 8.4 Hz, J = 2 Hz, 1H), 7.24 (dd, J = 8.8 Hz, J = 2 Hz,
6.76 (d, 1H), 7.22–7.36 (m, 3H), 7.50 (d, J = 8.4 Hz, 1H), 7.70 (dd, 1H),7.47–7.53 (m, 3H), 7.71 (dd, J = 8.2 Hz, J = 1.6 Hz, 1H),7.77 (d,
J = 8.6 Hz, J = 1.6 Hz, 1H), 7.76 (d, J = 8.4 Hz, 1H), 7.9 (d, J = 8.4 Hz, 1H), 7.90 (d, J = 3.2 Hz, 1H),8.24 (d, J = 1.6 Hz, 1H), 8.49
J = 1.6 Hz, 1H), 8.23 (d, J = 1.6 Hz, 1H), 8.47 (d, J = 2.4 Hz, 1H), (d, J = 2 Hz, 1H), 11.96 (brd s, 1H).13C NMR (DMSO‑d6): 7.31, 46.26,
11.96 (brd s, 1H). MS (ESI+) m/z: 486. Anal. calcd. For 49.55, 103.44, 110.61, 113.52, 118.69, 120.69, 121.35, 122.72,
C24H18ClF2N3O2S: C, 59.32; H, 3.73; N, 8.65; S, 6.60; Found: C, 125.39, 125.99, 127.39, 128.32, 128.39, 130.09, 131.11, 131.42,
59.01; H, 3.74; N, 8.45; S, 6.45 132.21, 134.45, 137.60, 138.85, 142.51, 151.80. MS (ESI+) m/z:
518. Anal. calcd. For C24H18Cl3N3O2S:C, 55.56; H, 3.50; N, 8.10; S,
[Link]. 5-(ethylsulfonyl)-1-(3,4-diflorobenzyl)-2-(5-bromo-1H-indol-3- 6.18; Found: C, 55.19; H, 3.35; N, 7.92; S, 5.98.
yl)-1H-benzo[d]imidazole (55). Compound 55 was prepared according
to general methods starting from N1-(3,4-difluorobenzyl)-4- [Link]. 5-(ethylsulfonyl)-1-(3,4-dichlorobenzyl)-2-(5-bromo-1H-indol-
ethylsulfonyl-benzene-1,2-diamine (0.72 mmol, 0.234 g) and 5-bromo- 3-yl)-1H-benzo[d]imidazole (59). Compound 59 was prepared
indole-3-carboxaldehyde (0.72 mmol, 0.160 g). The residue was according to general methods starting from N1-(3,4-dichlorobenzyl)-4-
purified by cc using the chloroform/ethyl acetate/hexane ([Link]) as ethylsulfonyl-benzene-1,2-diamine (0.78 mmol, 0.280 g) and 5-bromo-
eluent to give a white solid, m.p. 248 °C (0.141 g, 37% yield). 1H NMR indole-3-carboxaldehyde (0.78 mmol, 0.174 g). The residue was
(400 MHz, DMSO‑d6): δ ppm 1.14 (t, 3H), 3.33 (q, 2H), 5.86 (s, 2H), purified by cc using the chloroform/ethyl acetate (2:1) as eluent to
6.80 (d, 1H), 7.29–7.39 (m, 3H), 7.49 (d, J = 8.8 Hz, 1H), 7.75 (dd, give a white solid, m.p. 156 °C (0.055 g, 12% yield). 1H NMR
J = 8.4 Hz, J = 1.6 Hz, 1H), 7.79 (d, J = 8.8 Hz, 1H), 7.91 (d, (400 MHz, DMSO‑d6): δ ppm 1.13 (t, 3H), 3.33 (q, 2H), 5.89 (s, 2H),
J = 2.8 Hz, 1H), 8.26 (d, J = 1.2 Hz, 1H), 8.65 (d, J = 2 Hz, 1H), 6.88 (dd, J = 8.4 Hz, J = 1.6 Hz, 1H), 7.38 (dd, J = 8.8 Hz, J = 2 Hz,
12.00 (brd s, 1H). MS (ESI+) m/z: 532. Anal. calcd. For 1H),7.48–7.56 (m, 3H), 7.73 (dd, J = 8.2 Hz, J = 1.6 Hz, 1H),7.80 (d,
C24H18BrF2N3O2S: C, 54.35; H, 3.42; N, 7.92; S, 6.04; Found: C, J = 8.8 Hz, 1H), 7.91 (d, J = 3.2 Hz, 1H),8.27 (d, J = 0.8 Hz, 1H), 8.66
54.43; H, 3.20; N, 7.84; S, 6.01. (d, J = 1.6 Hz, 1H), 12.00 (brd s, 1H). 13C NMR (DMSO- d6): 12.45,
47.26, 56.68, 103.65, 110.68, 113.47, 118.45, 120.69, 121.03, 122.65,
[Link]. 5-(ethylsulfonyl)-1-(3,4-diclorobenzyl)-2-(1H-indol-3-yl)-1H- 125.31, 125.87, 127.40, 127.42, 128.23, 128.88, 132.60, 134.41,
benzo[d]imidazole (56). Compound 56 was prepared according to 136.37, 139.00, 142.47, 151.90. MS (ESI+) m/z: 564. Anal. calcd.
general methods starting from N1-(3,4-dichlorobenzyl)-4- For C24H18BrCl2N3O2S-0,5H2O:C, 50.52; H, 3.35; N, 7.37; S, 5.60;
ethylsulfonyl-benzene-1,2-diamine (0.44 mmol, 0.158 g) and indole-3- Found: C, 50.14; H, 3.05; N, 7.12; S, 5.35.
carboxaldehyde (0.44 mmol, 0.064 g). The residue was purified by cc
using the chloroform/ethyl acetate (2:1) as eluent to give a white solid, 2.2. Biological activity assays
m.p. 247 °C (0.070 g, 33% yield). 1H NMR (400 MHz, DMSO‑d6): δ
ppm 1.15 (t, 3H), 3.34 (q, 2H), 5.88 (s, 2H), 6.90 (dd, J = 8.2 Hz, 2.2.1. Cytotoxic assays on human cancer lines
J = 2.4 Hz, 1H), 7.20–7.27 (m, 2H), 7.49–7.60 (m, 3H), 7.71 (dd, 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium Bromide
J = 8.2 Hz, J = 2 Hz, 1H), 7.78 (d, J = 8.8 Hz, 1H), 7.82 (d, J = 2.8 Hz, (MTT) (Molecular Probes) was used to measure cell viability. Cell lines
1H), 8.21 (d, J = 1.6 Hz, 1H), 8.45 (d, J = 7.2 Hz, 1H), 11.81 (brd s, (MCF-7, MDA-MB-231 and HEPG2) were seeded onto 96-well plates
1H).13C NMR (DMSO‑d6): 7.30, 46.30, 49.61, 103.62, 110.58, 111.84, with 10,000 cells/well in phenol-free media (DMEM-low-glucose,
118.52, 120.62, 121.45, 122.63, 126.04, 126.85, 128.37, 130.07, GIBCO). After 24 h, the cells were exposed to compounds listed in
130.80, 131.09, 131.41, 132.07, 135.95, 137.73, 138.88, 142.65, Table 2 with different concentrations for another day. All compounds

8
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

were tested first at 0.25 µM, 2 µM, 16 µM and 40 µM doses using MCF-7 2.4. Microarray analyses of novel-indole benzimidazole derivatives and
cells. At each dose, percent cell viability was calculated in relationship comparative transcriptomics
to the DMSO control for each concentration. Selected compounds were
further studied using three different cell lines (MCF-7, MDA-MB-231, MCF-7 cells were exposed to compounds 48, 49, 50, 51, and 53 for
and HEPG2) at eight different concentrations to calculate IC50 values. 24 h at a dose of 20 µM. Total RNA was extracted from each sample
Camptothecin was used as a positive control (0.25 and 2 µM) as there where DMSO control and 51, each, had two biological replicates
was a DMSO group for calibration for each drug concentration. Cells (RNeasy Mini Kit (QIAGEN)) before performing microarray experi-
were then fixed according to the manufacturer’s instructions and in- ments using HuGene 2.0 ST platform (Affymetrix). Data were normal-
tensities were measured spectrophotometrically (BIO-TEK/µQuant ized via Transcriptome Analysis Console Software (V3.0.0.466) using
Universal Microplate Spectrophotometer and BIO-TEK/KC junior soft- default Affymetrix analysis parameters and rma using affy package
ware (v.1.418)). Percent viability was calculated at each dose, sepa- [54]. For differential expression analysis of 51 (n = 2) in comparison
rately, by dividing the blank subtracted average OD values of each with DMSO (n = 2), the limma toolbox of R was used [55]). Volcano
treated sample with the blank subtracted average ODs of corresponding plot of statistical significance against fold change between control and
DMSO treated counterparts; and the resulting values were multiplied by 51 treated MCF-7 cells was generated in MATLAB. For multiple probes
100 to obtain percentile viabilities. One-way ANOVA followed by hitting the same gene, the probe with the lowest adjusted p-value was
multiple comparisons (MATLAB R2016a) were used to test differences used.
in group means between the drug and DMSO control groups at each GSEA was performed for each compound separately with default
concentration. For clustering the MTT data, percentiles were divided by parameters to calculate the KEGG pathway enrichment using MSigDB
100 and logarithmically transformed at base two before performing [56]. Significantly enriched pathways were chosen (false discovery rate
hierarchical clustering. For testing the significance of mean differences (FDR) q value < 0.25); and commonly enriched KEGG pathways were
between groups from the MCF-7 four-concentration screening, raw data reported. LINCS database was used to identify compounds with the
from each plate of compounds were statistically compared with respect most and least similar expression profiles to significantly up- and down-
to their corresponding DMSO control values at each concentration, regulated gene lists obtained from 51 (top 150 and bottom 150 ranked
separately. For wider dose screens, IC50 values for each cell line were genes according to their logFC values) [57].
calculated using GraphPad Prism (v. 6.05). Further statistical analyses Limma analyses were performed between expression profiles of
were performed by using the viability values obtained from MCF-7 and 48–49 and those of 50–51-53 compound series to identify the sig-
other cell lines, to determine any relationship between the viability and nificantly differentially expressed genes at the adjusted p-value <
R1 or R2 status of the derivatives. n-way ANOVA analyses with log2 0.05. Pathway enrichment was done on the significantly up- and down-
transformed viability values (in R environment), and one-sided Wil- regulated genes between groups via STRING database with Reactome
coxon-rank sum test and logIC50 (GRcalculator [46]) were performed Pathways option while Venn Diagrams of unique and variably affected
by taking into account the triplicate values of viability scores and pathways were also shown [58,59].
corresponding treatment concentrations. In GRcalculator analyses, For comparative transcriptomics, GSE35428, GSE7765 and
sigmoidal fit and capping GR values below 1 were used. Additionally, GSE62673 were retrieved and normalized with rma [60]. Differential
two-way ANOVA with Tukey’s multiple comparisons was performed to expression analyses of normalized dataset were done using limma be-
test the significance of difference between specific groups of com- tween groups as follows: for GSE35428: E2, tamoxifen (4OHT), ICI
pounds in GraphPad Prism (v. 6.05), by using cell viability values in 182780, Lasofoxifene, Bazedoxifene or Raloxifene and EtOH (control)
triplicates. Principal component analysis (PCA) was used for further treatments; for GSE7765: Dioxin and DMSO (control) treatments; and
investigating the effect of cell line and concentration; and log2 trans- for GSE62673: AA depletion (AA (–)) and control samples. For
formed cell viability was used for the analysis. GSE7765, the results from hgu133A and hgu133B were merged. For
multiple probes hitting the same gene, the probe with the lowest ad-
2.3. Molecular docking analyses with multiple targets justed p-value was used. For GSE35428 and for GSE62673 best jetset
probesets were selected for further analysis [61].
ERα ligand-binding domain (PDB ID:1a52, resolution: 2.8 Å) file Venn diagrams were generated to represent the expression pattern
was obtained from the RCSB Protein database website [47]. Additional (i.e., log2 fold changes) of the significantly altered genes (N = 2177, p-
proteins were tested to analyze the selectivity of compounds against value < 0.05 between 51 & E2; N = 111, p-value < 0.05 between 51
ERα. These compounds were protein kinase C beta II (PDB ID:1pfq, & Dioxin; N = 1480, p-value < 0.05 between 51 & AA (–)). KEGG
resolution: 1.9 Å), glycogen synthase kinase 3 (PDB ID:1io9, resolution: pathway enrichment analysis was performed using the STRING data-
2.7 Å), platelet-derived growth factor receptor beta (PDB ID:3mjg, re- base; and Venn diagrams were generated based on the lists of sig-
solution: 2.3 Å), tubulin (PDB ID:1sa0, resolution: 3.58 Å) and vEGFR2 nificantly enriched pathways. Obtained diagrams were further utilized
kinase domain (PDB ID:2xir, resolution:1.5 Å), respectively. Proteins to form contingency tables where counts of shared and unique upre-
were prepared with Maestro’s Protein Preparation Wizard [48] and the gulated or downregulated genes were used in performing Fisher’s exact
gridbox was prepared via the Receptor Grid Generation module of test in R.
Maestro [49]. Binding sites of co-ligands were used for gridbox gen- Genes altered more than one-fold (FDR adj p-value < 0.05), in
eration. 2D builder was used to draw the ligands and same ligands were response to treatment with 51, were selected for the correlation ana-
minimized and prepared with the LigPrep module [50]. Tautomers and lysis. The Pearson’s correlation coefficient between each pair of treat-
conformers were generated to maximize the number of conformers. For ments was used for the hierarchical clustering and heatmap was per-
all the complexes, bound ligands were used. Structures of these com- formed using ComplexHeatmap toolbox in R [62].
pounds were procured from DrugBank [51], and were subjected to the
identical LigPrep procedure. After this, Ligand Docking process of the 2.5. RT-QPCR assays for validation of treatment effects in MCF-7
Glide program was initiated [52]. Precision was set to SP (Standard
precision) and Ligand Sampling was set to Flexible. 10 poses were Differential effects of candidate compounds on selected genes,
generated for each ligand and poses having the least binding energies known to be modulated by E2, dioxin, AA depletion, and/or to have
amongst them were evaluated. 2D-interaction diagrams were visualized roles in cell cycle, DNA damage/repair, drug metabolism were eval-
via Ligand Interactions. Additionally, molecular descriptors of these uated via RT-QPCR (LightCycler 480 II–Roche) in MCF-7 breast cancer
compounds were calculated via the QikProp module and assessed ac- cells exposed to 40 µM of each compound for 24 h. Following exposure,
cordingly [53]. total mRNA was isolated and collected using the RNeasy Mini Kit

9
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

(QIAGEN) according to the manufacturer’s instructions. Total RNA was consumed (determined by TLC, 4–12 h). The precipitate was obtained
then converted into cDNA using RevertAid First Strand cDNA Synthesis upon pouring the reaction mixture and then filtering and washing. The
Kit (Thermo Scientific). Logarithmically transformed relative expres- residue was purified by cc to obtain the final product (23–59) [45]. The
sion (-ΔΔCt) levels were calculated based on TPT1 as the reference gene synthesis details of the compounds were provided in the Experimental
and DMSO treatment as the control group. The results were analyzed Section.
via either One-way ANOVA followed by Tukey’s multiple comparisons
to evaluate the compound-based effects or a Two-way ANOVA to assess 3.2. Biological evaluation of indole-benzimidazole derivatives
dose-dependent effects (GraphPad Prism (v. 6.05)). ComplexHeatmap
toolbox in R was utilized; and GSE35428 (E2), GSE7765 (dioxin), and 3.2.1. Anti-cancer activity of novel indole-benzimidazole compounds in
GSE62673 (AA (–)) logFC data for the tested genes were annotated on MCF-7 cell line
top of the RT-QPCR data, for comparative representation. A list of All ethylsulfonyl derivatives were analyzed for their cytotoxicity
primers was given in Table A. 1. using MTT assays. A four-dose (0.25 µM, 2 µM, 16 µM and 40 µM)
screening panel in MCF-7, an ER+ and TP53 (p53) wild-type breast
3. Results cancer cell line, was used to identify highly effective compounds. This
allowed us to screen large numbers of derivatives before pursuing se-
3.1. Design and synthesis of indole-benzimidazole derivatives lected compounds in more detail. As a result, the primary anticancer
activity screening in MCF-7 showed that most of the compounds ex-
The synthesis of compounds (Scheme 2) was initiated from 4- hibited significance at one or more of the concentrations (Table 2).
chloro-benzenesulfonyl chloride. 4-(ethylsulfonyl)-1-chlorobenzene (1) Hierarchical clustering of the compound relative cell viabilities (at log2
and 4-(ethylsulfonyl)-1-chloro-2-nitrobenzene (2) were synthesized scale) helped summarize similarities between activities across doses
according our previous publication [42]. To a solution of 4-(ethylsul- (Fig. 2). Accordingly, molecules numbered 23, 35, 53, 36, 27, 29, 45,
fonyl)-1-chloro-2-nitrobenzene (2) (5 mmol) in ethanol (5 mL), amine 37, 50 and 51 clustered together, since they were highly effective at the
derivative (15 mmol) was added and heated under reflux until the highest dose, and one or more of the other three concentrations. The
starting material was consumed (determined by TLC, 8–48 h). Upon remaining compounds were less effective than the above-mentioned
cooling the mixture, water was added. The resultant yellow residue was compounds with respect to their level of activity. In addition, com-
crystallized from ethanol or purified by column chromatography (cc) by pound 49 was highly effective at the highest dose, i.e., 40 µM, yet was
using a mixture of hexane and ethyl acetate in varying concentrations not effective at lower doses (Fig. 2). None of the molecules exhibited
as eluent (Table 1) [43]. 5-methoxy-indole-3-carboxaldehyde was activity at the lowest dose (0.25 µM).
synthesized from 5-methoxy-indole, N,N-dimethylformamide, and Synthesized compounds had either -H, -OCH3, -Cl, or -Br at their R2
phosphorus oxychloride [63]. position for each of the R1 (Table 2). Therefore, the most active mole-
Compounds 3–12 (3.5 mmol) in EtOH (75 mL) were reduced by cule could be determined for each of the R1. According to the n-way
hydrogenation using 40 psi of H2 and 10% Pd/C (40 mg) until cessation ANOVA, molecular substitutions by R1 and R2 resulted in alterations on
of H2 uptake to obtain the catalyst before filtering off on a bed of celite cytotoxic activities of the sulfonylethyl structures (p-value < 2e−16)
and washing with EtOH, and concentrating the filtrate in vacuo [44]. where the R1 group was the major predictor (p-value < 2e−16) of
The crude amine was used without purification (13–22) (see for details anticancer activity rather than the R2 group (p-value: 0.0885). How-
Experimental Section). A mixture of the appropriate o-phenylenedia- ever, there was a significant interaction between R1 and R2 groups
mine (1 mmol), related indole derivative (1 mmol) and Na2S2O5 (40%) based on the cell viability scores (R1x2 interaction p-value < 2e−16)
(2 mL) in EtOH (4 mL), was refluxed until starting materials were suggesting that substitution on indoles could modify the activity of

Scheme 2. Synthesis of new indole-benzimidazoles (23–59).

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

Table 2
Relative cell viability from four-dose screening with the ethylsulfonyl derivatives in MCF-7 cells. p-values were calculated using One-Way ANOVA followed by
multiple comparisons.

No R1 R2 % Relative viabilities p-values

40 µM 16 µM 2 µM 0.25 µM 40 µM 16 µM 2 µM 0.25 µM

23 -H -H 24.36 67.57 100 110.16 0.0000 0.0005 1.0000 0.2498

24 -H -Br 67.53 85.44 90.04 105.73 0.0055 0.0391 0.2914 0.9979
25 -CH3 -H 64.68 72.12 94.01 95.39 0.0000 0.0293 0.9361 0.9238
26 -CH3 -OCH3 63.70 65.96 87.64 111.74 0.0028 0.0002 0.1572 0.9931
27 -CH3 -Cl 40.38 48.75 60.56 86.70 0.0001 0.0000 0.0000 0.1723
28 -CH3 -Br 69.58 79.32 94.45 92.97 0.0000 0.0089 0.0426 0.5252
29 -C2H5 -H 44.16 45.09 77.02 87.82 0.0000 0.0000 0.0150 0.2749
30 -C2H5 -OCH3 72.80 74.36 93.02 97.33 0.0112 0.0000 0.3659 0.9644
31 -C2H5 -Cl 66.03 79.80 85.35 86.52 0.0000 0.0102 0.0001 0.1001
32 -C2H5 -Br 58.80 58.13 85.41 111.86 0.0012 0.0000 0.0862 0.9742
33 -C3H7 -H 69.52 98.64 101.48 112.94 0.0000 0.9871 0.9979 0.1720
34 -C3H7 -OCH3 69.76 99.09 91.76 91.25 0.0000 0.9961 0.7629 0.4445
35 -C3H7 -Cl 26.90 68.60 92 97.79 0.0000 0.0003 0.7776 0.9773
36 -C3H7 -Br 32.85 48.06 77.12 89.86 0.0000 0.0000 0.0089 0.3313
37 -C4H9 -H 43.76 55.21 91.36 101.55 0.0000 0.0000 0.3874 0.9919
38 -C4H9 -Cl 89.88 81.38 94.29 110.80 0.0760 0.0021 0.6895 0.2854
39 -C4H9 -Br 62.15 88.91 100.98 101.15 0.0009 0.4355 0.9990 0.9993
40 -cyclohexyl -H 42.19 83.28 103.84 108.25 0.0005 0.8736 0.1878 0.9742
41 -cyclohexyl -OCH3 64.12 85.42 91.05 102.61 0.0000 0.0008 0.3503 0.9805
42 -cyclohexyl -Cl 63.80 82.62 97.92 105.45 0.0025 0.0498 0.9865 0.9742
43 -cyclohexyl -Br 68.96 80.98 88.39 93.54 0.0000 0.0001 0.1768 0.7885
44 -benzyl -H 89.26 95.42 104.85 99.40 0.0957 0.5882 0.3247 0.9979
45 -benzyl -OCH3 39.58 54.85 84.41 95.28 0.0000 0.0000 0.0585 0.9010
46 -benzyl -Cl 80.60 109.71 93.24 92.42 0.0700 0.3435 0.7116 0.9931
47 -benzyl -Br 79.31 85.37 91.90 91.11 0.0456 0.0000 0.2589 0.4536
48 -p-fluoro benzyl -H 59.55 92.02 92.69 93.24 0.0012 0.4955 0.6626 0.9979
49 -p-fluoro benzyl -OCH3 52.00 92.06 105.67 105.33 0.0000 0.0124 0.1202 0.7249
50 -p-fluoro benzyl -Cl 40.52 46.74 96.32 109.39 0.0000 0.0000 0.3942 0.3171
51 -p-fluoro benzyl -Br 45.69 46.37 97.05 106.44 0.0000 0.0000 0.5654 0.6023
52 -3,4-difluorobenzyl -H 73.53 92.77 85.60 101.92 0.0190 0.8907 0.3750 0.9918
53 -3,4-difluorobenzyl -OCH3 33.53 43.94 86.09 95.01 0.0000 0.0000 0.0748 0.8098
54 -3,4-difluorobenzyl -Cl 65.13 70.69 91.71 90.78 0.0000 0.0003 0.3661 0.4076
55 -3,4-difluorobenzyl -Br 66.23 75.12 93.55 95.20 0.0000 0.0009 0.5591 0.8262
56 -3,4-dichlorobenzyl -H 84.14 91.57 104.71 99.27 0.1014 0.6394 0.9074 0.9998
57 -3,4-dichlorobenzyl -OCH3 86.39 90.78 90.94 106.51 0.0110 0.2980 0.3872 0.8039
58 -3,4-dichlorobenzyl -Cl 73.06 72.70 100.18 115.78 0.0001 0.0022 1.0000 0.2061
59 -3,4-dichlorobenzyl -Br 81.31 71.81 94.90 100.67 0.0016 0.0018 0.7792 0.9997

benzimidazoles differentially. Analysis by GRcalculator tool indicated significant effects on viability while the effect of the R2 side chain was
that p-fluorobenzyl R1 group was one of the most effective R1 moiety also significant (p-value < 2e−16) and varied depending on the type
outstanding from the rest of the substitutions (p-value: 0.023) and other of R1 (R1x2 interaction p-value < 2e−16). Moreover, there was also a
cyclic aromatic side chain groups (p-value: 0.012) (Fig. 3; Fig. A.1). In significant cell line effect (p-value: 2.62e−08) as well as a treatment
addition to the p-fluorobenzyl, the substitutions of methyl (as in com- effect (p-value < 2e−16). Additional analyses with two-way ANOVA
pound 27) and propyl on R1 exhibited anti-proliferative trends. and multiple comparison tests have implied possible trends by cell line
and R2 (Table 3; Fig. 4; Fig. A.3; Fig. A.4). Cell line specific effects in
3.2.2. Anti-cancer activity of selected compounds on different cell lines response to treatments were observable via Principal Component Ana-
Upon analysis of Table 2, we selected, for further screening, several lysis (PCA) where both MCF-7 and HEPG2 lines interestingly yielded
compounds that were highly effective in reducing viability at the parallel profiles in comparison to MDA-MB-231 (Fig. 4). PCA showed
highest dose 40 µM (compounds: 23 (24.36%); 27 (40.38%); 29 that E2 responsive cell lines MCF-7 and HEPG2 were more similar to
(44.16%); 35 (26.90%); 36 (32.85%); and 37 (43.76%)); 40 (42.19%); each other than they were to the ER- MDA-MB-231 cells at lower
45 (39.58%); 48 (59.55%); 49 (52.00%); 50 (40.52%); 51(45.69%); 53 concentrations (up to 16 μM) while at the highest dose tested (40 μM)
(33.53%) and a control molecule with relatively less cytotoxic activity each cell line assumed a relatively distinct response profile. In parti-
(compound 46 (80.60%)). Among these, 48–51 spanning the full -p- cular, the compound 53 exhibited low IC50 values for the TP53 wild-
fluorobenzyl series exhibited similar activity at 40 µM whereas 50 and type MCF-7 and HEPG2 cells (19.23 µM and 24.10 µM, respectively)
51 were also significantly antiproliferative at a relatively lower con- while it was not as effective in MDA-MB-231, a cell line with a mutant
centration of 16 µM along with another related compound 53 con- TP53 allele. In accord with two-way ANOVA comparisons, most of the
taining 3,4-difluorobenzyl group. In the wider dose panel, IC50 values of candidate compounds exhibited a cell-line dependency, but not com-
these 13 molecules across multiple cell lines (Table 3) were studied pound 37 with butyl (R1) and -H (R2) substitutions (Table 3; Fig. A.4).
along with n-way ANOVA. Overall, R1 chain (p-value < 2e−16) had Nonetheless, GRcalculator assessments showed that MCF-7 was the cell

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

analyses in order to get an understanding on the mechanisms of action.

3.3. Molecular docking studies

Structurally related R1 groups with relatively high potencies were

taken into docking analyses. On the basis of the literature on indoles
and benzimidazoles as well as PCA clusters in this study, we primarily
focused on ERα, and assessed dockings of R1:p-fluorobenzyl derivatives
and 53. Compound based statistical comparisons between the cell lines
were also in accord with these observations (Fig. A.2). Our indole-
benzimidazole derivatives tended to exhibit increased affinity to ERα,
vEGFR2, and tubulin rather than the other ones which were discussed
in Section 2.3, such as Protein kinase C beta II, glycogen synthase ki-
nase 3, Platelet-derived growth factor receptor beta.
Based on the structural analysis (Fig. 5) ERα ligand binding domain
mainly consists of hydrophobic residues. Therefore, utilization of hy-
drophobic moieties such as indole and benzimidazole may play a key
role in inhibiting or activating this receptor. The binding mode of 4-
hydroxytamoxifen with ERα suggested that a hydrogen donator group
could be important for H-bond interaction with polar residue Gly521 in
this cavity. This interaction’s distance was 2.28 Å. In the literature,
these residues including Glu353, Arg394, Phe404 and Lys529 take part
in the modulation of this receptor. Hydrophobic interactions with
Phe404 and Trp383, H-bond interactions with Glu353 and Arg394, also
a salt bridge interaction with Asp351 are important according to both
bazedoxifene and 4-hydroxytamoxifen’s patterns [64]. List of molecular
Fig. 2. Hierarchical clustering of anti-cancer activity of the novel indole-ben- properties and ERα docking energies for all compounds were given in
zimidazoles. Darker tones of blue indicate stronger inhibition of cell growth. Table A. 10.
Euclidean distance and complete linkage were used for clustering (MATLAB®). One of the prominent compounds that stood out in transcriptomic
analyses, compound 51, created halogen bond interactions with both
line that seemed to be affected the most by the compounds, whereas -Br Glu353 and Arg394. In the case of the another potent ligand 53, Phe404
carrying R2 moieties on the Table 2 compounds were also observed to joins a Pi-Pi interaction with an indole ring while the sulfonyl group
have more effect on viability (Fig. A.2; Fig. A.3). After obtaining the acts as the hydrogen bond donor (Fig. 6). Both ligands have provided
toxicity data, we continued with docking studies and transcriptomic necessary interactions in the reference study. Their energy values were
relatively close to that of standard compound bazedoxifene.

Fig. 3. Log10(IC50) based representation and comparison of R1 carrying derivatives (GRcalculator tool was used for this purpose and comparisons between all
derivatives versus p-fluorobenzyl substituted compounds were made with a built-in one-sided Wilcoxon rank-sum test).

12
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

Table 3
IC50 (μM) values and two-way ANOVA cell line specific p-value for each selected candidate tested on MCF-7, MDA-MB-231 and HEPG2 cells (NA: Unmeasurable IC50
values, ns: not significant).
Comp. IC50 Cell line effect Comp. IC50 Cell line effect

MCF-7 MDA-MB-231 HEPG2 p-value MCF-7 MDA-MB-231 HEPG2 p-value

23 42.9536 51.4043 47.9733 < 0.0001 45 32.2849 22.3872 9.9540 < 0.0001
27 5.71 NA NA < 0.0001 46 43.4510 10.9396 89.54 < 0.0001
29 89.3305 NA 73.7904 < 0.0001 48 27.2270 20.8450 78.70 < 0.0001
35 54.4503 126.7652 32.7341 < 0.0001 49 39.5367 44.2588 41.11 < 0.0001
36 15.7398 49.8884 7.8163 < 0.0001 50 18.0717 36.1410 58.6138 < 0.0001
37 30.4089 66.6807 31.5500 0.3538 (ns) 51 35.1560 38.2825 17.2584 < 0.0001
40 40.2717 76.9130 NA < 0.0001 53 19.2309 NA 24.0991 < 0.0001

According to the glide docking score results in Table 4, compounds the compounds 48 and 49 at 20 μM. Candidate pathways as well as
48, 49 and 51 have exhibited favorable affinity value against ER when dose-dependent effects were further taken into account in under-
compared with those against tubulin and vEGFR2. standing the mechanisms of action of these derivatives. We compared
the expression profiles of compounds 48–49 with those of 50–51–53
showing that 553 genes were differentially expressed between these
3.4. Gene level alterations upon exposure to indole-benzimidazoles two groups (adjusted p-value < 0.05). Pathway enrichment by
STRING – Reactome Pathways demonstrated that compounds
3.4.1. Transcriptomics analysis of compounds 48–51 and 53 50–51–53 led to significantly more reduction in expression of genes
Based on Fig. 3, derivatives with p-fluorobenzyl and the structurally related with cell cycle and ESR1 signaling while increasing the stress
related compound 53 represented strong candidates for understanding response in MCF-7 cells (Fig. A.5; Table A. 5).
the molecular mechanisms of action of the effective novel indole-ben-
zimidazoles. For that purpose, we initiated gene level analyses in a
3.4.2. LINCS analysis
parallel line with molecular docking studies. Limma analysis of ex-
Query of the top 150 up- and 150 down-regulated genes by 51
pression data obtained upon exposure to compound 51 demonstrated
against a large collection of compounds, gene knockdown and gene
that MCF-7 transcriptome was significantly modulated leading to up-
overexpression datasets obtained from MCF-7 cells was performed
regulation and downregulation of a considerable number of genes
using LINCS database and the most positively and negatively correlated
(Fig. 7; Table 5).
compounds were provided (Table 6; Table A. 6). Among the compounds
Additionally, the STRING protein-protein interaction network and
most similar to 51 were the inhibitors of various classes such as ER
KEGG pathway analyses for the compound 51 were implemented to
antagonists, calcium channel inhibitors (niguldipine, an amino acid
reveal various molecular pathways that might be involved in the anti-
(AA) response/integrated stress response activator [65]), tubulin and
cancer effects of the derivatives (Table A. 2). Accordingly, stress me-
microtubule inhibitors. Besides, three out of the top ten compounds also
chanisms, apoptosis and ferroptosis, as well as p53 and cellular sig-
were carrying indole or benzimidazole backbones. Interestingly, the top
naling via MAPK pathway, were observed in addition to the metabolic
compound oxindole-I and an ER antagonist, i.e., ZK-164015, were
process of aminoacyl-tRNA biosynthesis. List of these pathways were
among them. Many of the tubulin and microtubule inhibitors from this
also common when the gene signatures of the compounds 50, 51 and
analysis were also found to carry either an indole or benzimidazole
53 are compared, confirming similarity of the derivative exposures on
scaffold (Table A. 6).
molecular level (Table A. 3). In addition to that, overall comparisons
with all the microarrayed compounds together resulted in a relatively
limited set of mutual pathways such as cell cycle and DNA replication 3.4.3. Comparative transcriptomics
(Table A. 4) which might be due to milder effects on the expression by Comparative transcriptomics analysis of the selected indole-

Fig. 4. PCA representation on cell viabilities of the cell lines upon exposure to varying concentrations of novel derivatives.

13
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

Fig. 5. 2D diagram of aminoacid interactions of bazedoxifene with ERα ligand-binding domain. Hydrophobic interactions are shown as green, whereas the red line
represents Pi-cation interactions. H-bond interactions are depicted as purple. Red-blue represents salt bridge interaction.

Fig. 6. 2D interaction diagrams of the two most potent compounds against MCF-7 and in microarray analyses. Brown arrow indicates halogen bond interaction and
purple one indicate hydrogen bond interaction, whilst green line represents Pi-Pi steric interaction.

Table 4 benzimidazoles was performed using public microarray datasets for AA

Data showing the glide scores of microarrayed compounds against different (–) and exposure to E2/SERMs or dioxin, an aryl hydrocarbon activator
proteins. known to be activated by plant-based estrogens [66–68]. This approach
Compounds ERα Tubulin vEGFR2 kinase has further demonstrated a pattern of inverse correlation with E2 and
domain positive correlations with SERMs, AhR/dioxin, and AA (–) signatures
(Fig. 8). AA deprivation was the most closely associated treatment
48 −7.776 −5.851 −6.348
followed by dioxin and SERMs while indole-benzimidazoles formed the
49 −7.726 −5.575 −6.786
50 Unsuccessful Unsuccessful −6.435 tightest cluster. Our results showed that novel indole-benzimidazoles
binding binding exhibited transcript-level effects that were more pronounced than the
51 −7.802 −5.458 −6.131 generic SERMs on reverting E2 driven expression modulation. Fur-
53 −6.610 −5.662 −6.813 thermore, compounds 50, 51 and 53 were found in the same cluster
Vincristine – −8.1 –
Tivozanib – – −10.265
while compounds 48 and 49 formed another cluster which was placed
Bazedoxifene −9.852 – – closer to the generic SERMs. In accord with this expression profile
based clustering, compounds 48 (R2: -H) and 49 (R2: -OCH3) had higher
IC50 values, thus lower drug effectivity than 50 (R2:-Cl), 51 (R2:-Br) and
53 (R1:3,4-difluorobenzyl; R2:-OCH3) (Fig. A.4).

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

Table 6
Top 10 ranking compounds that possess transcriptomic similarity with 51 in
MCF-7 line. Compounds with either indole or benzimidazole moieties are given
with bold characters.
Rank Score Name Description

1 99.98 oxindole-I VEGFR inhibitor

2 99.98 niguldipine Calcium channel blocker
3 99.97 AG-592 Tyrosine kinase inhibitor
4 99.96 AG-879 Angiogenesis inhibitor
5 99.96 FCCP Mitochondrial oxidative phosphorylation uncoupler
6 99.96 ZK-164015 ER antagonist
7 99.96 reserpine Vesicular monoamine transporter inhibitor
8 99.96 PD-198306 MAP kinase inhibitor
9 99.96 CGK-733 ATR kinase inhibitor
10 99.96 suloctidil Adrenergic receptor antagonist

Fig. 7. Volcano plot of statistical significance against fold change between

control and compound 51 treated MCF-7 cells. 546 genes were statistically
altered more than two folds (adjusted p-value with FDR < 0.05).

To further investigate how expression profiles of novel indole-ben-

zimidazole compounds relate with those obtained from E2 exposure,
AA depletion and dioxin treatments, we performed KEGG pathway [69]
enrichment analyses using GSEA [70,71]. The numbers of significantly
affected genes between exposures to E2 and compound 51 were re-
presented using a Venn diagram and enriched pathways were indicated
(Fig. 9; p-value < 0.05 (compound 51 & E2)). According to the com-
parisons with E2 exposure in MCF-7 cells, the inversely associated
signaling pathways included upregulation of TGF-β pathway and
downregulation of DNA replication, cell-cycle, mismatch repair, pyr-
imidine metabolism, cysteine and methionine metabolism and spli-
ceosome pathways by the novel indole-benzimidazole compounds.
Mutually upregulated and downregulated pathways were provided in
Table A. 7. Interestingly, the downregulation of similar pathways, but Fig. 8. Clustergram analysis of the pairwise-correlation between generic SERMs
this time in the same direction, were observed in the comparisons and compounds 48, 49, 50, 51 and 53. The genes were selected with the p-
performed with 51 versus AA (-), whereas dioxin versus 51 revealed value (< 0.05) and log fold difference (> 1) cut-offs for compound 51. Ward
involvement of steroid and amino acid related metabolisms, including linkage and Euclidian distance were used for the clustering. Red indicates po-
sitive correlation while blue indicates negative correlation in between samples
downregulation of E2 signaling pathway. Furthermore, the term “fer-
on the heatmap.
roptosis” was enriched in mutually upregulated pathways for both di-
oxin and AA (–) and 51 profile. Fisher’s exact tests showed significance
(Table A. 7). identified multiple genes that were modulated by E2, dioxin or AA
deprivation and/or involved in cell cycle, integrated stress response,
and drug metabolism (Fig. 10).
3.4.4. Validation of molecular pathways by RT-QPCR in MCF-7 cells Our findings first showed that minor structural differences could
High throughput comparative transcriptomic analysis led to the contribute to detectable changes on the expression of the genes we
identification of several pathways and genes whose expressions were analyzed (Fig. 10; Table A. 8; Table A. 9). For example, the compounds
altered upon exposure to the novel derivatives as well as E2, one or 49, 50 and 51 have influenced CDKN1A expression remarkably, while
more SERMs, dioxin or AA depletion. For validation by RT-QPCR, we

Table 5
The top 10 significantly altered genes in compound 51 treated samples. Adjusted (Adj.) p reflects the FDR corrected p-value, calculated with limma.
Downregulated Upregulated

Gene Symbol LogFC p-value Adj.p value Gene Symbol LogFC p-value Adj.p value

FAM111B −3.46 1.38E−07 0.001 SLC7A11 4.5 5.09E−07 0.002

IGFBP5 −2.87 1.21E−06 0.002 FAM129A 3.78 2.84E−08 0.001
GRPR −2.8 4.62E−06 0.004 ERRFI1 3.4 6.66E−08 0.001
TARP −2.79 7.62E−07 0.002 MT1F 3.35 5.07E−07 0.002
GINS2 −2.62 7.15E−07 0.002 CLGN 3.35 4.34E−07 0.002
CCNE2 −2.52 4.74E−07 0.002 GDF15 3.33 6.56E−08 0.001
DTL −2.51 5.47E−07 0.002 CYP1A1 3.31 5.57E−08 0.001
MCM10 −2.37 6.26E−07 0.002 SLFN5 2.97 1.83E−07 0.001
UCA1 −2.3 1.71E−06 0.002 DDIT3 2.97 1.11E−06 0.002
IL20 −2.23 8.91E−07 0.002 ANXA3 2.96 1.39E−07 0.001

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

Fig. 9. KEGG pathway enrichment analysis

results for Compound 51 and (A) E2, (B)
Dioxin and (C) AA (–). Significantly en-
riched (p-value < 0.05) genes and related
pathways that are mutually affected are
depicted, especially for E2 comparisons.
Fisher’s exact p-values are (A) < 2.2e−16,
(B) 4.415e-05 and (C) < 2.2e−16.
Detailed list of enriched pathways (for A, B
and C) and the contingency table for the
comparisons are provided in Table A. 7.

the compound 48 (R1: -H) was less effective. Moreover, compounds 51 SLC7A11 and HMOX1 were similarly affected by indole-benzimidazoles
and 53 caused significant decreases in ANLN expression and 48 and 50 and AA depletion which further suggested the involvement of multiple
were additionally more effective in altering the levels of WDHD1. In- mechanisms in compound responses. Later analyses, where we com-
terestingly, GADD45A expression was modulated by compounds 48, 50 pared gene expression levels of the primary E2 target genes, CCND1,
and 51 while compound 49 did not lead to overexpression of TFF1 and PGR, using different exposure concentrations (20 µM vs
GADD45A. Compound 53 containing 3,4-difluorobenzyl at R1 position 40 µM), also presented additional confirmation on the dose-dependent
also induced CDKN1A and GADD45A expression while having reduced relationship between the derivatives and E2 signaling (Fig. A.6). Here,
expression of cell cycle related genes (at both ANLN and WDHD1). only TFF1 gene represented a dose-dependent difference (p-value:
Further taking GSE35428 and GSE7765 data into account, the ex- 0.0207) whereas CCND1 and PGR did not (p-values: 0.6284 and
posures to E2 and indole-benzimidazole were found to be inversely 0.4252, respectively). Moreover, the microarray and RT-QPCR experi-
associated implicating the derivatives investigated herein as E2 an- ments performed with doses of 20 µM and 40 µM respectively, had
tagonists. In addition to the E2 signaling, CYP1B1 and HMOX1 were shown that compounds 50, 51 and 53 yielded stronger effects on the
also upregulated by AhR agonist dioxin while changes in DDIT3, expression of these genes. However, a 40 µM exposure to 48 or 49

Fig. 10. Validation of selected AhR/dioxin, in-

tegrated stress response/AA (–), and E2/SERM
modulated genes by RT-QPCR in MCF-7 cells ex-
posed to the compounds 48, 49, 50, 51 and 53 for
24 h at 40 µM. Relative quantity (RQ) values are
depicted in log2 and color scale (blue-to-red (ne-
gative-to-positive)). TPT1 is used as the house-
keeping gene; along the x-axes, the compound
names were given. Top annotation values are
gathered from three different public datasets and
our own microarray data; and log fold change va-
lues are represented for the corresponding genes in
a color scale (blue-to-red (negative-to-positive)
where gray points represent missing values due to
microarray platform used in aminoacid depletion
study. Exact log2 relative quantity values and sig-
nificance signs can be accessed in Table A. 8 and
Table A. 9. (For interpretation of the references to
colour in this figure legend, the reader is referred to
the web version of this article.)

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F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

exhibited similar responses when compared with the other three mo- silico. In addition, glide scores overall yielded positive results, even
lecules investigated, suggesting a dose-dependent increase in tran- though observed affinity levels were lesser in the derivatives than the
scriptional response. standard compounds, meaning that the derivatives had the tendency to
form stable ligand-protein complexes with ERα. Moreover, it was clear
4. Discussion that ERα might not be the only binding target of the derivatives, but
also some other proteins in inducing cell death. Nevertheless, in this
In the present study, we have synthesized and characterized a set of current study, in silico findings and literature investigations [72,73]
novel indole-benzimidazoles carrying benzene sulphonyl structures, to nominate ERα as the most favorable indole-benzimidazole target in
assess their cytotoxicity, structural affinity to potential targets (mainly comparison to ERβ, tubulin and vEGFR.
ER), molecular expression profiles and association with the regulators Aside from docking studies, the expression profiling of compounds
of anticancer pathways. Accordingly, we found most of our compounds 48–51 (R1:p-fluorobenzyl; R2:-H, -OCH3, -Br, -Cl) and 53 (R1:3,4-di-
significantly reduced the cell viability of ER+ MCF-7 cells, especially at fluorobenzyl; R2:-OCH3) and comparative transcriptomics with public
a concentration equaling to 40 µM. In addition, we have utilized dif- datasets have significantly increased our understanding of the mole-
ferent statistical tools to understand the structure-activity relationships cular mechanisms mediating the effects of indole-benzimidazoles in ER
(SARs) better. For that purpose, we have analyzed our data using + breast cancer cells. The use of comparative transcriptomics and RT-
ANOVA and multivariate techniques such as PCA and hierarchical QPCR analyses further validated and supported our findings.
clustering which proved valuable to make distinctions among the Previously, altered expression of cell cycle, DNA replication, en-
compounds with respect to dose, molecular group, and cell line dif- doplasmic reticulum stress and DNA damage response-related processes
ferences. Regarding the substitutions (Table 1 & Table 2), both R1 and have been reported in MCF-7 cells when exposed to CTet, an indole-3-
R2 groups were found to be important in altering the anticancer effect carbinol derivative [74,75]. However, herein we, for the first time,
of the indole-benzimidazole scaffold. However, there was a significant show significant and positive associations between the expression
interaction between these two groups of which future studies should profiles of indole-benzimidazoles and those of the selected ER antago-
take into consideration. nists, AhR agonist dioxin, and AA deprivation. Furthermore, these
Structurally related R1 group members (48, 49, 50 and 51) ex- comparative transcriptomics approaches implicate indole-benzimida-
hibited single position changes yet showed differential anti-pro- zoles in simultaneous modulation of multiple cancer-relevant pathways
liferative activity on MCF-7 cells. In addition, this group had the lowest leading to a strong anticancer behavior in a dose-dependent manner,
average IC50 values when compared with the other molecule series where the effects were more profound for 50, 51 and 53 at 20 μM, than
warranting further analyses. Our strategy also involved differential the compounds 48 and 49.
expression profiling of MCF-7 cells exposed to compound 51 exhibiting STRING analyses have shown that stress mechanisms, aminoacyl-
the lowest growth inhibition at 16 μM, along with compound 50, fol- tRNA metabolism and ferroptosis might be involved in these anti-cancer
lowed by stringent transcriptomics comparisons across full series and effects. For instance, aminoacyl-tRNA metabolism can be driven by
with an additional related compound 53 from R1:3,4-difluorobenzyl steroids and sex hormones in breast cancer where the ER status of the
group, exhibiting even stronger anti-proliferative effects towards E2 cancer matters in cell proliferation rate, in return [76–78]. In addition,
responsive cell lines. Future studies should consider extending the AA deprivation can affect the charging status of specific tRNA iso-
above mentioned approach to other compound series and cell lines with acceptor, underlying interaction between abundant amino acids in the
differing characteristics to better understand the molecular mechanisms environment which further influences the efficiency of the translation
by which novel indole-benzimidazoles exert their effects. processes [79,80]. The transcriptomic similarity between our deriva-
The differences observed in cell viability profiles can be due to tives and AA deprivation profiles further supports the involvement of
multiple factors, such as the dose and/or tissue specificity (breast vs. aminoacyl-tRNA biosynthesis pathway where ER modulation can in-
liver) as well as the cell line’s batch, molecular receptor status (e.g., ER fluence this pathway. Interestingly, aminoacyl-tRNA metabolism and
and AhR) and pathway activity (e.g., TP53 and AA (–) stress). For ex- AA signaling have regulatory roles also in ferroptosis which can further
ample, compound 53, whose microarray-based molecular effects explain the selected derivatives’ anti-cancer responses [81–83].
(20 μM) closely resembling those of compounds 50 and 51 in MCF-7 GSEA results also helped identify the conserved and associated al-
cells, might lead to a different expression profile in the ER-/TP53 mu- terations in the molecular/cellular pathways driven by 51 and E2, di-
tant MDA-MB-231 cell line, exhibiting lower sensitivity to 53. On the oxin or AA (–) exposures. Results pointed to some shared mechanisms
other hand, a compound which is similarly active in the breast cancer among the treatments that have been previously indicated with cancers.
cells based on IC50 values can be more active in another batch or type of Among the associated pathways, TGF-β and cell cycle pathways have
cancer cell line, as in the case of compound 51. In conclusion, although been widely studied while pyrimidine metabolism is one of the path-
our structural models have suggested potential affinity to ER for com- ways more recently gained attention in breast cancer therapy [84,85].
pounds 51 and 53, a comparative transcriptomics approach further Inversely correlated signatures between E2 and AA(–) further under-
demonstrated that downstream molecular effects of these novel indole- lined the close relationship between amino acid metabolism and ER
benzimidazoles are likely to be driven via multiple routes/pathways signaling [86]. Besides that, downregulation of ER signaling was a
(e.g., AhR), and not just ER. This notion can further explain the ob- mutual mechanism between 51 and dioxin exposures further under-
served cell- and dose-dependent differences in anti-cancer activity. lying ER modulatory roles for the indole-benzimidazoles and AhR sig-
Taking the docking results into account, one possible reason of the naling [66,68]. Moreover, aminoacyl and AA-related pathways, as well
higher activity shown by compounds 51 and 53′s could be the increased as ferroptosis, were among the enriched terms across multiple dataset
amount of halogen bond (a type of H-bond) interactions. Also, the comparisons strongly pinpointing crucial roles in the downstream ef-
presence of bromine group may enhance lipophilic characteristic of fects of indole-benzimidazole derivatives.
indole moiety creating a more successful binding pattern. Therefore Additionally, transcriptomic signature of the compound 51 had re-
compound 51 was elected as a possible candidate for future assessment markable similarities with certain LINCS database compounds that
and pharmacokinetic development studies. Unsuccessful ER binding were screened in MCF-7 cells. At the top of the most similar compounds
profile obtained for the compound 50 was an unexpected case, con- was a multitargeting compound oxindole-I, which also carries an indole
sidering its similarity to the compounds 51 and 53 based on the gene moiety and constitutes the pharmacophore of the drug sunitinib [87].
expression and cytotoxicity results obtained. Although the situation Derivatives of this compound have been found to be involved in gen-
here is suggestive for alternative binding profiles towards ER or other eration of oxidative stress leading to cell death [88]. In support of that,
protein targets, such cases demand further re-evaluations, primarily in double-stranded RNA-dependent protein kinase (PKR) that mediates

17
F.Z. Karadayi, et al. Bioorganic Chemistry 100 (2020) 103929

stress responses can be targeted by an imidazole-oxindole type deri- fluorobenzyl or small alkyl groups at their R1 position in addition to
vative (C16 compound) also mediating ferroptosis in the end [89]. electron-withdrawing groups in R2 might have relatively more effective
Additionally, its derivative compound sunitinib shares similar features anticancer activities. The compound 51 containing p-fluorobenzyl at R1
on cell death with sorafenib, another known ferroptotic agent [90,91]. position and –Br at R2 position was one of the prominent compounds
The presence of oxindole structure can also affect the aryl hydrocarbon against MCF-7 cells as validated by microarray analyses as well as
receptor which is in a strong relationship with stress pathways, fer- docking studies. Although the limited range of sample size and inter-
roptosis, amino acid metabolism and ER signaling [92–96]. Tran- action between side-chain moieties obscure more definitive conclu-
scriptomic similarity with dioxin further supports the involvement of sions, applied statistical approaches underline the nature of R1 and R2
this pathway and others in downstream effects of indole-benzimidazole groups and their effects on multiple cell lines. Therefore, not only p-
exposure. The second top hit compound, niguldipine, is a calcium fluorobenzyl, but also difluorobenzyl (53), methyl (27) and propyl
channel blocker that can lead to unfolded amino acid stress response substitutions (36) on R1 might warrant future studies where genotypes
and ferroptosis [65,97]. One of the other top hit compounds were FCCP, of the samples and applicable doses should be taken into account.
a mitochondrial oxidative phosphorylation uncoupler and again a fer- Binding profiles of the derivatives also supported the notion that
roptosis inhibitor [98], and ZK-164015, an ER antagonist containing an there can be multiple targets involved in their cytotoxic action. As we
indole moiety. Moreover, the transcriptional profile of reserpine, an- have seen here, the derivatives can play roles as SERMs, tubuline in-
other indole carrying structure, which also strongly influences the Nrf2- hibitors, as well as modulators of amino acid metabolism, AhR sig-
mediated anti-oxidative stress pathway [99] also has exhibited sig- naling, and ferroptosis. The relevance of these derivatives as significant
nificant similarity with compound 51. The presence of indole or ben- antiestrogen molecules demands functional investigations which will
zimidazole backbones in multiple ER modulators and tubulin inhibitors clearly provide useful information in the therapy of breast cancer.
strongly supported the notion for the involvement of tubulin related
mechanisms in response to indole-benzimidazole derivatives Declaration of Competing Interest
[100–102]. Even though in silico docking results revealed low potency
of the derivatives in tubulin binding, actual binding and affinity profiles The authors declare that they have no known competing financial
should be further tested via in situ experiments. interests or personal relationships that could have appeared to influ-
In this study we have identified several effective novel indole-ben- ence the work reported in this paper.
zimidazole compound series and found out that some bearing p-fluor-
obenzyl and alkyl groups on R1 were active at concentrations lower Acknowledgements
than 40 μM. In addition, molecular profiling of five related compounds
with varying anti-proliferative efficacies enabled us to address the as- The work was supported by TUBITAK (grant number: 1001 -
sociation between levels of anti-proliferation and gene expression 213S037).
modulation. Molecular pathways contributing to drug efficacy included
unfolded protein/stress response, cytosolic tRNA aminoacylation, ESR1 Appendix A. Supplementary material
signaling and cell cycle. Accordingly the chemical structure of the re-
latively more active compounds 50, 51 and 53 could be used as tem- Supplementary data to this article can be found online at https://
plates for future designs. [Link]/10.1016/[Link].2020.103929. These data include MOL files
Among the screened compounds, substitutions on R2 were restricted and InChiKeys of the most important compounds described in this ar-
to four bases only, and the alterations on R2 moieties were able to affect ticle.
the potency of R1 bearing scaffolds differentially, suggesting that a
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