Streptochlorin analogues as potential antifungal agents: Design, synthesis, antifungal activity and molecular docking study

Article abstract of DOI:10.1016/j.bmc.2021.116073

Streptochlorin is a small molecule of indole alkaloid isolated from marine Streptomyces sp., it is a promising lead compound due to its potent bioactivity in preventing many phytopathogens in our previous study, but further structural modifications are re

Full text of DOI:10.1016/j.bmc.2021.116073

Bioorg. Med. Chem. 35 (2021) 116073
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry
journal homepage: www.elsevier.com/locate/bmc
Streptochlorin analogues as potential antifungal agents: Design, synthesis,
antifungal activity and molecular docking study
Ya Gaoa, Dai-Chuan Huanga, Chang Liua, Zi-Long Songa, Jing-Rui Liua, Shu-Ke Guoa,
Jun-Yang Tana, Run-Ling Qiua, Bing Jina, Haifeng Zhangb, Nick Mulhollandc, Xinya Hand,
,
,*
Qinfei Xiad, Abdallah S. Alie, Dale Guof, Yun Dengf, Yu-Cheng Guc *, Ming-Zhi Zhanga
a Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
b Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests,
Ministry of Education, Nanjing, China
c Syngenta Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, United Kingdom
d School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan 243002, China
e Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
f State Key Laboratory Breeding Base of Systematic Research Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of
Traditional Chinese Medicine, Chengdu 611137, China
A R T I C L E I N F O
A B S T R A C T
Streptochlorin is a small molecule of indole alkaloid isolated from marine Streptomyces sp., it is a promising lead
compound due to its potent bioactivity in preventing many phytopathogens in our previous study, but further
structural modifications are required to improve its antifungal activity. Our work in this paper focused on the
replacement of oxazole ring in streptochlorin with the imidazole ring, to discover novel analogues. Based on this
design strategy, three series of streptochlorin analogues were efficiently synthesized through sequential
Vilsmeier-Haack reaction, Van Leusen imidazole synthesis and halogenation reaction. Some of the analogues
displayed excellent activity in the primary assays, and this is highlighted by compounds 4g and 4i, the growth
This Paper is Dedicated to Professor Youyou
Tu, the 2015 Nobel Prize Laureate of Physi-
ology or Medicine, on the Occasion of Her 90th
Birthday, and Dedicated to Professor Weihua
Zhang and Professor Guangfu Yang for Their
50th Birthdays.
inhibition against Alternaria Leaf Spot and Rhizoctorzia solani under 50 μg/mL are 97.5% and 90.3%, respectively,
Keywords:
Natural products
Streptochlorin
Imidazole
even more active than those of streptochlorin, pimprinine and Osthole. Molecular docking models indicated that
streptochlorin binds with Thermus thermophiles Leucyl-tRNA Synthetase in a similar mode to AN2690, offering a
perspective on the mode of action study for antifungal activities of streptochlorin derivatives. Further study is
still ongoing with the aim of discovering synthetic analogues, with improved antifungal activity and clear mode
of action.
Antifungal activity
Molecular docking
1. Introduction
Pimprinine, 5-Hydroxy-2′-Isobutyl-Streptochlorin, Pimprinaphine, WS-
30581 A and B, Labradorins 1 and 2, Almazole C, Diazonamide A,
As is well known, natural product has served as a powerful source in
the drug and agrochemical discovery, there have been many important
drugs developed from plants and microorganisms.1,2 Streptochlorin is a
bioactive compound, firstly isolated from marine Streptomyces sp. by
Japanese scientist H. Watanabe in 1988.3 The chemical structure of
streptochlorin was revealed as 4-chloro-5-(3′-indolyl)oxazole based on
the data of X-ray diffraction. Members of this family, including
exhibit a wide range of potent biological activities (Figure 1), such as
anticancer,4 antiviral,5,6 anti-angiogenesis,7 antibiotic,8 anti-cell pro-
liferation.9 Bioassay conducted at Syngenta showed streptochlorin is
also a promising antifungal substance demonstrating good bioactivity
against many phytopathogens,10 for example displaying excellent anti-
fungal activity against Pythium dissimile, Botrytis cinerea, Zymoseptoria
tritici, Pyriculariaory zae, Fusarium culmorum and Rhizoctonia solani in
Abbreviations: aaRS, aminoacyl-tRNA Synthetase; AMP, Adenosine monophosphate; DME, 1,2-dimethoxyethane; DMF, N,N-dimethylformamide; DMSO, dime-
thylsulfoxide; HR-MS, high-resolution mass spectra; LeuRS, Leucyl-tRNA Synthetase; mp, melting point; NBS, N-Bromosuccinimide; NCS, N-Chlorosuccinimide; NMR,
nuclear magnetic resonance; THF, tetrahydrofuran; TLC, thin layer chromatography; tLeuRS, Thermus thermophiles Leucyl-tRNA Synthetase; TosMIC, Tosylmethyl
Isocyanide; v/v, ratio by volume; vdw, van der waals’ force.
* Corresponding authors.
E-mail addresses: yucheng.gu@syngenta.com (Y.-C. Gu), mzzhang@njau.edu.cn (M.-Z. Zhang).
https://doi.org/10.1016/j.bmc.2021.116073
Received 11 January 2021; Received in revised form 5 February 2021; Accepted 6 February 2021
Available online 14 February 2021
0968-0896/© 2021 Elsevier Ltd. All rights reserved.

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
Figure 1. Structures of streptochlorin and related natural products.
Figure 2. Design strategy of target molecules.
Figure 3. Structures of imidazole-containing drugs and agrochemicals.
artificial media.11 While, this compound lack potency at lower con-
centrations, rarely warranting further study. In our latest study on the
structural optimizations including different modifications at the indole
ring and oxazole ring, we found that the indole ring was an essential
moiety in streptochlorin derivative for the antifungal activity.12–16
Therefore, further structural modifications are required to improve
its antifungal activity, as streptochlorin is not potent enough to be an
agricultural fungicide, and the mode of action for the antifungal activity
of streptochlorin is still unclear. So our new study in this paper would be
focused on the replacement of oxazole ring of streptochlorin with the
imidazole ring to discover novel streptochlorin analogues (Figure 2),
and the molecular docking of streptochlorin with potential target was
also performed.
As the bioisostere of oxazole, imidazole is an important nitrogen-
containing aromatic heterocycle, it is widely incorporated into the
structures of commercial drugs and agrochemicals (Figure 3), for ex-
amples, Histidine is an essential amino acid containing an imidazole side
chain and a precursor for histamine produced in the body necessary for
inflammation. Ondansetron containing both an indole and an imidazole
ring, is one of the most prescribed medication for relieving nausea and
vomiting in US.17 Prochloraz is a typical imidazole fungicide, it could
effectively control many agricultural fungi by inhibiting the biosynthesis
of ergosterol.18 Miconazole is an antifungal medicine and considered as
one of the most effective and safe medicines by World Health
2

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
Figure 4. Structural optimization–introduction of the imidazole ring.
Organization.19 Ingavirin is an antiviral drug, which mainly targets the
nucleoprotein of influenza A and B and impairs viral replication.20
Fexinidazole is the first effective drug candidate for all-oral treatment of
sleeping sickness developed by Sanofi-Aventis and DNDi.21
2.1.3. General procedure for the synthesis of target compounds (4 and 5)
NCS or NBS (1.10 mmol) was added portionwsie to a solution of
compound 3 (1.00 mmol) in THF-CCl4 (20 mL, 1:1) at 50 ◦C. The re-
action was stirred for 0.5–1 h, the reaction was monitored by TLC and
when judged to be complete, the solvent was evaporated. and extracted
with CH2Cl2 (50 mL × 3). The residue was extracted with CH2Cl2, The
organic layer was washed with water and brine, then dried (Na2SO4) and
concentrated under reduced pressure. The residue was purified by col-
umn chromatography on silica using (ethyl acetate-petroleum ether
(1:2) as eluent to give compounds 4 and 5.
Introducing an imidazole ring into the molecules is an effective
protocol for structural optimization (Figure 4), for example, Nilotinib, a
drug targeting to treat Imatinib-resistant chronic myelogenous leuke-
mia, the replacement of the piperazine ring with the imidazole sub-
structure improved the binding affinity with Abltyrosine kinase.22 As a
result, Nilotinib could inhibit Abltyrosine kinase with 30-fold increased
potency compared with the parent compound Imatinib.23
2.2. Compound data
2. Materials and methods
2.2.1. 3-(1-propyl-1H-imidazol-5-yl)-1H-indole (3a)
2.1. Chemistry
A yellow solid, yield 94%, mp: 128.9–130.1 ◦C; 1H NMR (400 MHz,
CD3OD) δ 7.68 (s, 1H), 7.56–7.51 (m, 2H), 7.49 (s, 1H), 7.22–7.16 (m,
1H), 7.13–7.07 (m, 1H), 7.03 (d, J = 7.4 Hz, 1H), 4.01 (t, J = 7.2 Hz,
2H), 1.64 (dd, J = 14.6, 7.3 Hz, 2H), 0.78 (t, J = 7.4 Hz, 3H). 13C NMR
(100 MHz, DMSO‑d6) δ 137.8, 136.2, 127.3, 126.6, 126.0, 124.2, 121.8,
119.7, 118.9, 111.9, 104.0, 46.2, 23.6, 10.9; HRMS (ESI) calcd for
C14H15N3 ([M+H]+) 226.1339, found 226.1343.
All reagents and substrates commercially available were purchased
from Crystal Chemicals or Alfa Aesar Co. and used without further pu-
rification. All solvents and liquid reagents were dried by standard
methods in advance and distilled before use. Column chromatography
was performed using silica gel (200–300 mesh). Melting points were
determined using a Büchi Mꢀ 560 melting point apparatus (uncorrec-
ted). 1H NMR and 13C NMR spectra were recorded on a Bruker Avance
400 MHz spectrometer in DMSO‑d6, CD3OD-d4 or (CD3)2CO-d6 solution,
the chemical shifts (δ) and coupling constants (J) relative to tetrame-
thylsilane are given in parts per million (ppm) and Hertz (Hz), respec-
tively. HR-MS (ESI) spectra was obtained on an Agilent Technologies
6540 UHD Q-TOF LC-MS. Reaction yields were not optimized.
2.2.2. 3-(1-butyl-1H-imidazol-5-yl)-1H-indole (3b)
A white crystal, yield 84%, mp: 110.1–111.9 ◦C; 1H NMR (400 MHz,
CD3OD) δ 7.77 (s, 1H), 7.47–7.43 (m, 2H), 7.36 (s, 1H), 7.19 (t, J = 7.6
Hz, 1H), 7.09 (t, J = 7.5 Hz, 1H), 7.00 (s, 1H), 4.02 (td, J = 7.3, 4.2 Hz,
2H), 1.62–1.53 (m, 2H), 1.18 (dd, J = 14.7, 7.2 Hz, 2H), 0.78 (dd t, J =
8.4, 6.4 Hz, 3H); 13C NMR (100 MHz, DMSO‑d6) δ 138.1, 136.4, 127.6,
126.9, 126.3, 124.5, 122.1, 119.9, 119.2, 112.2, 104.3, 44.6, 32.6, 19.5,
13.7; HRMS (ESI) calcd for C15H17N3 ([M+H]+) 240.1495, found
240.1503.
2.1.1. Preparation of 1H-indole-3-carbaldehyde (2)
Phosphorus oxychloride (1.0 mL, 10.00 mmol) was added dropwise
to DMF (7.0 mL) maintaining the temperature at 0–5 ◦C with ice bath.
The reaction was stirred for 30 min, then a solution of indole 1 (1.17 g,
10.00 mmol)) in DMF (10 mL) was added and the reaction was heated at
35 ◦C for one hour. The solution was then cooled and treated with H2O
(6 mL) followed by NaOH (13 mL, 30% in water), and the reaction was
heated at reflux for 30 min, then allowed to cool gradually to room
temperature, during which the crude product precipitated from the so-
lution. The precipitate was filtered, washed with water, then petroleum
ether and vacuum dried gave compound 1H-indole-3-carbaldehyde (2),
yield 98%.
2.2.3. 3-(1-isobutyl-1H-imidazol-5-yl)-1H-indole (3c)
A white solid, yield 30%, mp: 118.1–119.2 ◦C; 1H NMR (400 MHz,
Acetone‑d6) δ change in style 10.66 (s, 1H), 7.64 (s, 1H), 7.56–7.46 (m,
3H), 7.18 (t, J = 7.6 Hz, 1H), 7.10 (t, J = 7.5 Hz, 1H), 7.03 (s, 1H), 3.88
(d, J = 7.4 Hz, 2H), 1.92–1.80 (m, 1H), 0.74 (d, J = 6.7 Hz, 6H). 13C
NMR (100 MHz, DMSO‑d6) δ 138.7, 136.4, 127.8, 127.0, 126.5, 124.5,
122.1, 120.0, 119.3, 112.2, 104.5, 52.3, 29.2, 19.9; HRMS (ESI) calcd
for C15H17N3 ([M+H]+) 240.1495, Found 240.1490.
2.2.4. 3-(1-(2-methoxyethyl)-1H-imidazol-5-yl)-1H-indole (3d)
2.1.2. General procedure for the synthesis of target compounds (3)
The primary amine RNH2 (6.00 mmol) was added in one portion to a
stirred solution of 1H-indole-3-carbaldehyde (2) (0.58 g, 4.00 mmol,) in
MeOH-DME (20 mL, 1:1), at 20 ◦C. The solution was stirred for 0.5–1 h,
then TosMIC (6.00 mmol, 1.17 g) and K2CO3 (6.00 mmol, 0.83 g) were
added portion wise, the reaction was monitored by TLC when judged
complete, the reaction solvent was evaporated under reduced pressure.
The residue was extracted with CH2Cl2 (50 mL × 3), The organic layer
was washed with water and brine, then dried (Na2SO4) and concentrated
under reduced pressure. The residue was purified by column chroma-
tography on silica using ethyl acetate-petroleum ether-methanol)
(40:20:1) as eluent to give the pure compound 3.
A light yellow solid, yield 71%, mp: 112.9–114.5 ◦C; 1H NMR (400
MHz, DMSO‑d6) δ 11.55 (s, 1H), 7.79 (s, 1H), 7.59–7.57 (m, 1H), 7.54
(d, J = 7.9 Hz, 1H), 7.50 (d, J = 8.0 Hz, 1H), 7.21–7.15 (m, 1H),
7.12–7.06 (m, 2H), 4.15 (t, J = 5.4 Hz, 2H), 3.50 (t, J = 5.4 Hz, 2H), 3.18
(s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 138.4, 136.6, 127.5, 127.0,
126.6, 125.0, 122.2, 120.1, 119.3, 112.3, 104.1, 71.4, 58.5, 44.7; HRMS
(ESI) calcd for C14H15N3O ([M+H]+) 242.1288, Found 242.1289.
2.2.5. 3-(1-cyclohexyl-1H-imidazol-5-yl)-1H-indole (3e)
A light yellow solid, yield 49%, mp: 159.4–160.5 ◦C; 1H NMR (400
MHz, CD3OD) δ 7.87 (s, 1H), 7.42 (dd, J = 23.7, 8.0 Hz, 2H), 7.32 (s,
1H), 7.22–7.16 (m, 1H), 7.08 (t, J = 7.4 Hz, 1H), 6.95 (s, 1H), 3.97 (dd,
J = 15.8, 7.3 Hz, 1H), 2.02 (d, J = 11.3 Hz, 2H), 1.86–1.57 (m, 5H), 1.23
(dd, J = 20.9, 11.3 Hz, 3H); 13C NMR (100 MHz, CD3OD) δ 137.7, 135.6,
3

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
128.6, 127.5, 127.5, 125.8, 123.0, 120.8, 119.4, 112.5, 104.8, 55.9,
35.4, 26.6, 26.0; HRMS (ESI) calcd for C17H19N3 ([M+H]+) 266.1652,
found 266.1666.
113.2, 112.5, 112.2, 104.1, 55.3, 48.1; HRMS (ESI) calcd for C19H17N3O
([M+H]+) 304.1444, Found 304.1448.
2.2.13. 3-(1-(2-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole (3m)
A white solid, yield 66%, mp: 170.5–172.0 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.36 (s, 1H), 7.76 (s, 1H), 7.57 (d, J = 7.9 Hz, 1H), 7.44 (d,
J = 8.0 Hz, 1H), 7.29–7.20 (m, 2H), 7.20–7.13 (m, 2H), 7.07 (t, J = 7.5
Hz, 1H), 6.98 (d, J = 8.2 Hz, 1H), 6.83 (t, J = 7.5 Hz, 1H), 6.54 (dd, J =
7.5, 1.7 Hz, 1H), 5.21 (s, 2H), 3.75 (s, 3H). 13C NMR (100 MHz,
DMSO‑d6) δ 156.4, 138.8, 136.4, 129.3, 127.6, 127.4, 127.0, 126.9,
126.2, 124.2, 122.2, 120.9, 120.1, 119.4, 112.2, 111.1, 104.1, 55.8,
43.8; HRMS (ESI) calcd for C19H17N3O ([M+H]+) 304.1444, Found
304.1459.
2.2.6. 3-(1-benzyl-1H-imidazol-5-yl)-1H-indole (3f)
A light yellow crystal, yield 44%, mp: 136.5–137.6 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.81 (s, 1H), 7.47 (d, J = 8.0 Hz, 1H), 7.42 (d, J = 8.1
Hz, 1H), 7.25–7.15 (m, 4H), 7.11–7.04 (m, 3H), 6.97 (d, J = 7.3 Hz, 2H),
5.22 (d, J = 2.5 Hz, 2H). 13C NMR (100 MHz, DMSO‑d6) δ 138.4, 138.2,
136.1, 128.7, 127.4, 126.6, 126.4, 126.4, 123.9, 121.9, 119.8, 119.0,
111.9, 103.7, 47.8; HRMS (ESI) calcd for C18H15N3 ([M+H]+) 274.1339,
found 274.1357.
2.2.7. 3-(1-(4-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (3g)
A light yellow crystal, yield 57%, mp: 169.2–170.3 ◦C; 1H NMR (400
MHz, CD3OD) δ 7.76 (s, 1H), 7.43 (dd, J = 19.1, 8.0 Hz, 2H), 7.16 (t, J =
7.4 Hz, 1H), 7.07 (dd, J = 13.6, 5.3 Hz, 4H), 6.85 (d, J = 7.9 Hz, 2H),
4.88 (s, 3H), 2.26 (s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 138.4, 136.6,
136.1, 135.2, 129.3, 127.3, 126.5, 126.5, 126.4, 123.9, 121.9, 119.8,
119.1, 111.9, 103.8, 47.7, 20.7; HRMS (ESI) calcd for C19H17N3
([M+H]+) 288.1495, found 288.1496.
2.2.14. 3-(1-(3-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (3n)
A light yellow solid, yield 34%, mp: 156.4–157.9 ◦C. 1H NMR (400
MHz, Acetone‑d6) δ 10.93 (s, 1H), 7.85 (s, 1H), 7.61 (d, J = 7.9 Hz, 1H),
7.50 (d, J = 8.1 Hz, 1H), 7.34–7.28 (m, 2H), 7.24–7.17 (m, 2H), 7.12 (t,
J = 7.5 Hz, 1H), 7.03–6.96 (m, 1H), 6.87 (d, J = 7.7 Hz, 1H), 6.79 (d, J =
10.0 Hz, 1H), 5.37 (s, 2H). 13C NMR (100 MHz, Acetone‑d6) δ 164.1,
161.7, 141.1 (d, J = 7.2 Hz), 138.3, 136.4, 130.6 (d, J = 8.4 Hz), 127.9,
127.0 (d, J = 14.8 Hz), 124.0, 122.4 (d, J = 2.9 Hz), 122.1, 119.9, 119.0,
114.1 (d, J = 21.2 Hz), 113.4 (d, J = 22.4 Hz), 111.8, 104.0, 47.6 (d, J =
2.0 Hz). 19F NMR (376 MHz, Acetone‑d6) δ ꢀ 114.2; HRMS (ESI) calcd
for C18H14FN3 ([M+H]+) 292.1245, Found 292.1258.
2.2.8. 3-(1-(4-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole (3h)
A light yellow solid, yield 50%, mp: 150.1–152.0 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.76 (s, 1H), 7.44 (dd, J = 11.9, 8.0 Hz, 2H), 7.20–7.15
(m, 1H), 7.13 (s, 1H), 7.10–7.05 (m, 2H), 6.90 (d, J = 8.7 Hz, 2H),
6.82–6.75 (m, 2H), 5.13 (s, 2H), 4.89 (s, 3H). 13C NMR (100 MHz,
DMSO‑d6) δ 158.8, 138.4, 136.4, 130.2, 128.3, 127.6, 126.7, 126.7,
124.3, 122.1, 120.0, 119.3, 114.3, 112.2, 104.1, 55.3, 47.6; HRMS (ESI)
calcd for C19H17N3O ([M+H]+) 304.1444, found 304.1442.
2.2.15. 3-(1-(2-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (3o)
A yellow solid, yield 45%, mp: 150.8–151.5 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.37 (s, 1H), 7.81 (s, 1H), 7.51 (d, J = 7.9 Hz, 1H), 7.42 (d,
J = 8.1 Hz, 1H), 7.34–7.25 (m, 2H), 7.19–7.12 (m, 3H), 7.10–7.02 (m,
2H), 6.74–6.68 (m, 1H), 5.34 (s, 2H). 13C NMR (100 MHz, DMSO‑d6) δ
161.0, 158.6, 138.8, 136.4, 130.1 (d, J = 8.1 Hz), 128.9 (d, J = 4.0 Hz),
127.9, 126.9 (d, J = 9.0 Hz), 125.3 (d, J = 14.4 Hz), 125.1 (d, J = 3.5
Hz), 124.5, 122.2, 120.1, 119.3, 115.7 (d, J = 20.7 Hz), 112.3, 103.9,
42.5 (d, J = 4.8 Hz). 19F NMR (376 MHz, DMSO‑d6) δ ꢀ 118.4 (d, J = 9.3
Hz); HRMS (ESI) calcd for C18H14FN3 ([M+H]+) 292.1245, Found
292.1239.
2.2.9. 3-(1-(4-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (3i)
A white solid, yield 43%, mp: 182.1–182.8 ◦C. 1H NMR (400 MHz,
CD3OD) δ 7.82 (s, 1H), 7.44–7.40 (m, 2H), 7.17 (t, J = 7.5 Hz, 1H), 7.12
(s, 1H), 7.09–7.04 (m, 2H), 6.94 (d, J = 7.0 Hz, 4H), 5.19 (s, 2H). 13
C
NMR (100 MHz, DMSO‑d6) δ 161.3 (d, JC-F = 244.2 Hz, 1C), 138.3,
136.0, 134.2, 134.2, 128.6, 128.5, 127.5, 126.4, 124.0, 121.8, 119.7,
118.9, 115.5, 115.3, 111.8, 103.6, 47.1; HRMS (ESI) calcd for
C
18H14FN3 ([M+H]+) 292.1245, found 292.1244.
2.2.16. 3-(1-(4-chlorobenzyl)-1H-imidazol-5-yl)-1H-indole (3p)
A gray solid, yield 30%, mp: 204.7–206.5 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.39 (s, 1H), 7.86 (s, 1H), 7.54 (d, J = 7.9 Hz, 1H), 7.44 (d,
J = 8.1 Hz, 1H), 7.32 (d, J = 8.3 Hz, 2H), 7.30 (d, J = 2.7 Hz, 1H), 7.16
(q, J = 7.6, 6.0 Hz, 2H), 7.06 (t, J = 7.5 Hz, 1H), 6.97 (d, J = 8.1 Hz, 2H),
5.30 (s, 2H). 13C NMR (100 MHz, DMSO‑d6) δ 138.8, 137.6, 136.4,
132.4, 129.0, 128.7, 127.9, 126.9, 126.8, 124.4, 122.2, 120.1, 119.3,
112.3, 103.9, 47.6; HRMS (ESI) calcd for C18H14ClN3 ([M+H]+)
308.0949, Found 308.0964.
2.2.10. 3-(1-(3-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (3j)
A yellow solid, yield 39%, mp:145.9–146.6 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.84 (s, 1H), 7.77 (s, 1H), 7.61 (d, J = 7.9 Hz, 1H), 7.50
(d, J = 8.1 Hz, 1H), 7.29–7.27 (m, 1H), 7.22–7.16 (m, 3H), 7.15–7.08
(m, 2H), 7.05 (d, J = 7.6 Hz, 1H), 6.89–6.82 (m, 2H), 5.27 (s, 2H), 2.22
(s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 138.7, 138.5, 138.2, 136.4,
129.0, 128.4, 127.7, 127.4, 126.9, 126.8, 124.3, 123.9, 122.2, 120.1,
119.4, 112.2, 104.1, 48.1, 21.4; HRMS (ESI) calcd for C19H17N3
([M+H]+) 288.1495, Found 288.1489.
2.2.17. 3-(1-(4-bromobenzyl)-1H-imidazol-5-yl)-1H-indole (3q)
A light yellow solid, yield 38%, mp: 211.5–213.0 ◦C. 1H NMR (400
MHz, DMSO‑d6) δ 11.34 (s, 1H), 7.84 (s, 1H), 7.52 (d, J = 8.1 Hz, 1H),
7.46 (d, J = 7.9 Hz, 2H), 7.42 (d, J = 8.6 Hz, 1H), 7.28 (s, 1H), 7.14 (d, J
= 5.2 Hz, 2H), 7.06 (d, J = 7.5 Hz, 1H), 6.90 (d, J = 8.0 Hz, 2H), 5.28 (s,
2H). 13C NMR (100 MHz, DMSO‑d6) δ 138.8, 138.0, 136.4, 132.0, 129.0,
128.0, 126.8, 124.4, 122.3, 120.9, 120.1, 119.4, 112.3, 103.9, 47.7;
HRMS (ESI) calcd for C18H14BrN3 ([M+H]+) 352.0444, Found
352.0440.
2.2.11. 3-(1-(2-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (3k)
A yellow solid, yield 87%, mp: 176.7–178.1 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.31 (s, 1H), 7.70 (s, 1H), 7.59 (d, J = 7.9 Hz, 1H), 7.41 (d,
J = 8.0 Hz, 1H), 7.19–7.16 (m, 4H), 7.15–7.11 (m, 2H), 7.11–7.06 (m,
2H), 5.26 (s, 2H), 2.17 (s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 138.6,
136.7, 136.4, 135.2, 130.5, 127.7, 127.6, 127.2, 126.7, 126.7, 126.1,
123.9, 122.2, 120.1, 119.4, 112.2, 104.1, 46.5, 18.9; HRMS (ESI) calcd
for C19H17N3 ([M+H]+) 288.1495, Found 288.1502.
2.2.18. 3-(1-(4-(trifluoromethyl)benzyl)-1H-imidazol-5-yl)-1H-indole
(3r)
2.2.12. 3-(1-(3-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole (3l)
A white solid, yield 80%, mp: 152.6–154.5 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.60 (s, 1H), 7.76 (s, 1H), 7.62 (dd, J = 7.9, 1.0 Hz, 1H),
7.51–7.46 (m, 1H), 7.28 (d, J = 2.6 Hz, 1H), 7.23–7.08 (m, 4H),
6.84–6.76 (m, 1H), 6.65–6.61 (m, 1H), 6.59 (t, J = 2.0 Hz, 1H), 5.30 (s,
2H), 3.67 (s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 159.8, 140.2, 138.8,
136.4, 130.2, 127.7, 126.8, 126.8, 124.3, 122.2, 120.1, 119.4, 118.9,
A light yellow solid, yield 25%, mp: 203.5–204.5 ◦C. 1H NMR (400
MHz, DMSO‑d6) δ 11.34 (s, 1H), 7.90 (s, 1H), 7.64 (d, J = 8.1 Hz, 2H),
7.52 (d, J = 7.9 Hz, 1H), 7.41 (d, J = 8.1 Hz, 1H), 7.27 (d, J = 7.2 Hz,
1H), 7.17–7.12 (m, 4H), 7.08–7.02 (m, 1H), 5.42 (s, 2H). 13C NMR (100
MHz, DMSO‑d6) δ 143.3, 138.9, 136.4, 127.9, 127.4, 126.9, 126.7,
126.0, 126.0, 125.9, 124.4, 122.3, 120.1, 119.3, 112.3, 103.8, 47.8. 19
F
4

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
NMR (376 MHz, DMSO‑d6) δ ꢀ 60.9 (s, 3F); HRMS (ESI) calcd for
7.41 (d, J = 7.9 Hz, 1H), 7.30 (d, J = 2.6 Hz, 1H), 7.27–7.16 (m, 4H),
7.09 (t, J = 7.2 Hz, 1H), 7.01–6.98 (m, 2H), 5.19 (s, 2H). 13C NMR (100
MHz, Acetone‑d6) δ 138.2, 137.1, 136.8, 129.3, 129.0, 128.3, 127.8,
127.6, 126.9, 122.7, 122.5, 120.6, 120.0, 112.6, 102.7, 49.9; HRMS
(ESI) calcd for C18H14ClN3 ([M+H]+) 308.0949, found 308.0982.
C
19H14F3N3 ([M+H]+) 342.1213, Found 342.1216.
2.2.19. 3-(1-(pyridin-3-ylmethyl)-1H-imidazol-5-yl)-1H-indole (3s)
A light yellow solid, yield 59%, mp: 118.8–120.5 ◦C; 1H NMR (400
MHz, DMSO‑d6) δ 11.43 (s, 1H), 8.39–8.37 (m, 1H), 8.19 (d, J = 7.6 Hz,
1H), 7.91 (s, 1H), 7.51 (d, J = 7.9 Hz, 1H), 7.44 (d, J = 8.1 Hz, 1H), 7.40
(d, J = 2.6 Hz, 1H), 7.33–7.29 (m, 1H), 7.27–7.23 (m, 1H), 7.19–7.12
(m, 2H), 7.08–7.03 (m, 1H), 5.36 (s, 2H). 13C NMR (100 MHz, DMSO‑d6)
δ 149.0, 148.4, 138.8, 136.4, 134.8, 133.9, 128.1, 126.8, 126.7, 124.6,
124.1, 122.2, 120.1, 119.3, 112.3, 103.8, 46.0; HRMS (ESI) calcd for
2.2.26. 3-(4-chloro-1-(4-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (4g)
A light yellow solid, yield 40%, mp: 190.8–192.8 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.76 (s, 1H), 7.44 (d, J = 8.2 Hz, 1H), 7.29 (d, J = 8.0
Hz, 1H), 7.18 (t, J = 7.6 Hz, 1H), 7.13 (s, 1H), 7.07 (d, J = 7.2 Hz, 1H),
7.02 (d, J = 7.9 Hz, 2H), 6.80 (d, J = 7.9 Hz, 2H), 5.04 (s, 2H), 2.25 (s,
3H). 13C NMR (100 MHz, DMSO‑d6) δ 136.8, 136.5, 136.0, 134.3, 129.2,
127.1, 126.7, 126.4, 121.7, 121.5, 119.7, 119.0, 112.1, 100.9, 99.6,
48.5, 20.7; HRMS (ESI) calcd for C19H16ClN3 ([M+H]+) 322.1106,
found 322.1135.
C
17H14N4 ([M+H]+) 275.1291, Found 275.1283.
2.2.20. 3-(4-chloro-1-propyl-1H-imidazol-5-yl)-1H-indole (4a)
A white crystal, yield 43%, mp: 144.9–146.1 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.75 (s, 1H), 7.67 (s, 1H), 7.56–7.49 (m, 2H), 7.40 (d, J
= 7.9 Hz, 1H), 7.20 (t, J = 7.5 Hz, 1H), 7.10 (t, J = 7.4 Hz, 1H), 3.92 (t, J
= 7.2 Hz, 2H), 1.56 (dd, J = 14.5, 7.3 Hz, 2H), 0.73 (t, J = 7.4 Hz, 3H).
13C NMR (100 MHz, Acetone‑d6) δ 137.2, 136.4, 128.8, 127.9, 126.8,
122.7, 122.0, 120.6, 119.9, 112.6, 103.0, 48.2, 24.4, 10.9; HRMS (ESI)
calcd for C14H14ClN3 ([M+H]+) 260.0949, found 260.0964.
2.2.27. 3-(4-chloro-1-(4-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole
(4h)
A light yellow solid, yield 50%, mp: 176.3–177.6 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.78 (s, 1H), 7.45 (d, J = 8.2 Hz, 1H), 7.27 (d, J = 8.0
Hz, 1H), 7.21–7.14 (m, 2H), 7.06 (t, J = 7.5 Hz, 1H), 6.82 (d, J = 8.6 Hz,
2H), 6.73 (d, J = 8.7 Hz, 2H), 5.01 (s, 2H), 3.71 (s, 3H). 13C NMR (100
MHz, DMSO‑d6) δ 158.7, 136.4, 136.0, 129.1, 128.3, 127.1, 126.5,
126.5, 121.8, 121.4, 119.7, 119.0, 114.0, 112.1, 101.0, 55.1, 48.3;
2.2.21. 3-(1-butyl-4-chloro-1H-imidazol-5-yl)-1H-indole (4b)
A white crystal, yield 94%, mp: 171.5–173.3 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.54 (s, 1H), 7.81 (s, 1H), 7.57–7.53 (m, 1H), 7.47 (d, J =
8.1 Hz, 1H), 7.29 (dd, J = 7.7, 4.7 Hz, 1H), 7.16 (t, J = 7.4 Hz, 1H), 7.06
(t, J = 7.4 Hz, 1H), 3.86 (t, J = 7.1 Hz, 2H), 1.42 (dq, J = 14.6, 7.2 Hz,
2H), 1.09–1.01 (m, 2H), 0.67 (td, J = 7.3, 3.5 Hz, 3H). 13C NMR (100
MHz, Acetone‑d6) δ 137.2, 136.4, 128.8, 127.9, 126.8, 122.8, 121.9,
120.6, 119.9, 112.6, 103.1, 46.3, 33.2, 20.0, 13.5; HRMS (ESI) calcd for
HRMS (ESI) calcd for
338.1084.
C
19H16ClN3O ([M+H]+) 338.1055, found
2.2.28. 3-(4-chloro-1-(4-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (4i)
A white solid, yield 43%, mp: 174.7–176.5 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.52 (s, 1H), 7.90 (s, 1H), 7.45 (s, 1H), 7.35 (s, 1H), 7.27 (s,
1H), 7.15 (t, J = 6.9 Hz, 1H), 7.03 (t, J = 8.0 Hz, 3H), 6.93 (s, 2H), 5.12
(s, 2H). 13C NMR (100 MHz, DMSO‑d6) δ 161.5 (d, JC-F = 243.7 Hz, 1C),
136.6, 136.0, 133.5, 128.9, 128.9, 127.4, 126.5, 126.4, 121.8, 121.5,
119.7, 118.9, 115.5, 115.3, 112.1, 100.8, 48.1; HRMS (ESI) calcd for
C
15H16ClN3 ([M+H]+) 274.1106, found 274.1101.
2.2.22. 3-(4-chloro-1-isobutyl-1H-imidazol-5-yl)-1H-indole (4c)
A light yellow solid, yield 56%, mp: 168.7–169.9 ◦C. 1H NMR (400
MHz, DMSO‑d6) δ 11.56 (s, 1H), 7.77 (s, 1H), 7.57–7.55 (m, 1H), 7.48
(d, J = 8.1 Hz, 1H), 7.30 (d, J = 7.9 Hz, 1H), 7.16 (t, J = 7.5 Hz, 1H),
7.06 (t, J = 7.5 Hz, 1H), 3.72 (d, J = 7.4 Hz, 2H), 1.72–1.59 (m, 1H),
0.62 (d, J = 6.7 Hz, 6H). 13C NMR (100 MHz, DMSO‑d6) δ 137.0, 136.4,
127.5, 126.9, 126.8, 122.1, 121.6, 120.1, 119.3, 112.5, 101.7, 53.1,
28.9, 19.8; HRMS (ESI) calcd for C15H16ClN3 ([M+H]+) 274.1106,
Found 274.1108.
C
18H13ClFN3 ([M+H]+) 326.0855, found 326.0850.
2.2.29. 3-(4-chloro-1-(3-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (4j)
A pink solid, yield 65%, mp: 146.3–147.4 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.78 (s, 1H), 7.76 (s, 1H), 7.53 (d, J = 8.1 Hz, 1H), 7.42
(d, J = 7.9 Hz, 1H), 7.36 (d, J = 2.7 Hz, 1H), 7.24–7.18 (m, 1H), 7.12 (q,
J = 7.3 Hz, 2H), 7.03 (d, J = 7.6 Hz, 1H), 6.84–6.77 (m, 2H), 5.15 (s,
2H), 2.19 (s, 3H). 13C NMR (100 MHz, Acetone‑d6) δ 138.2, 137.2,
136.4, 136.1, 128.5, 128.3, 128.1, 127.7, 127.1, 126.3, 124.0, 122.0,
121.8, 119.9, 119.3, 111.9, 101.9, 49.2, 20.4; HRMS (ESI) calcd for
2.2.23. 3-(4-chloro-1-(2-methoxyethyl)-1H-imidazol-5-yl)-1H-indole
(4d)
A light yellow solid, yield 30%, mp: 154.6–155.9 ◦C. 1H NMR (400
MHz, Acetone‑d6) δ 10.78 (s, 1H), 7.68 (s, 1H), 7.57–7.53 (m, 1H), 7.54
(d, J = 8.4 Hz, 1H), 7.43 (d, J = 8.0 Hz, 1H), 7.22 (t, J = 7.6 Hz, 1H),
7.12 (t, J = 7.5 Hz, 1H), 4.10 (t, J = 5.3 Hz, 2H), 3.49 (t, J = 5.3 Hz, 2H),
3.22 (s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 136.9, 136.5, 127.2,
127.2, 126.9, 122.2, 121.7, 120.2, 119.4, 112.5, 101.4, 70.8, 58.4, 45.6;
C
19H16ClN3 ([M+H]+) 322.1106, Found 322.1105.
2.2.30. 3-(4-chloro-1-(2-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (4k)
A pink solid, yield 54%, mp: 205.4–206.6 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.65 (s, 1H), 7.58 (s, 1H), 7.50 (d, J = 8.1 Hz, 1H), 7.46
(d, J = 8.0 Hz, 1H), 7.32–7.30 (m, 1H), 7.23–7.08 (m, 5H), 6.82 (d, J =
7.1 Hz, 1H), 5.18 (s, 2H), 2.09 (s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ
137.1, 136.3,135.8, 135.3, 130.5, 127.9, 127.4, 126.8, 126.6, 126.6,
126.5, 122.3, 122.1, 120.1, 119.5, 112.4, 101.3, 47.2, 18.8; HRMS (ESI)
calcd for C19H16ClN3 ([M+H]+) 322.1106, Found 322.1108.
HRMS (ESI) calcd for
276.0898.
C
14H14ClN3O ([M+H]+) 276.0898, Found
2.2.24. 3-(4-chloro-1-cyclohexyl-1H-imidazol-5-yl)-1H-indole (4e)
A yellow solid, yield 67%, mp: 190.3–192.2 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.76 (s, 1H), 7.77 (s, 1H), 7.56–7.50 (m, 2H), 7.38 (d, J
= 7.9 Hz, 1H), 7.23–7.17 (m, 1H), 7.14–7.07 (m, 1H), 3.94–3.84 (m,
1H), 2.03–1.96 (m, 2H), 1.74 (dd, J = 16.3, 7.4 Hz, 4H), 1.62–1.57 (m,
1H), 1.23–1.11 (m, 3H). 13C NMR (100 MHz, CD3OD) δ 136.4, 132.9,
127.0, 126.9, 126.0, 121.9, 121.4, 119.7, 118.3, 111.5, 101.2, 55.8,
33.8, 25.3, 24.7; HRMS (ESI) calcd for C17H18ClN3 ([M+H]+) 300.1262,
found 300.1274.
2.2.31. 3-(4-chloro-1-(3-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole
(4l)
A pink solid, yield 38%, mp: 175.5–176.8 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.70 (s, 1H), 7.77 (s, 1H), 7.52 (d, J = 8.1 Hz, 1H), 7.43
(d, J = 8.0 Hz, 1H), 7.37– 7.35 (m, 1H), 7.19 (dt, J = 12.5, 7.7 Hz, 2H),
7.11 (t, J = 7.5 Hz, 1H), 6.78 (dd, J = 8.2, 2.6 Hz, 1H), 6.61 (d, J = 7.6
Hz, 1H), 6.53 (d, J = 2.1 Hz, 1H), 5.18 (s, 2H), 3.63 (s, 3H). 13C NMR
(100 MHz, DMSO‑d6) δ 159.7, 139.3, 137.0, 136.4, 130.1, 127.6, 126.8,
122.2, 122.0, 120.1, 119.5, 119.3, 113.6, 112.7, 112.5, 101.4, 55.3,
49.1; HRMS (ESI) calcd for C19H16ClN3O ([M+H]+) 338.1055, Found
338.1053.
2.2.25. 3-(1-benzyl-4-chloro-1H-imidazol-5-yl)-1H-indole (4f)
A light yellow solid, yield 58%, mp: 179.2–180.4 ◦C. 1H NMR (400
MHz, Acetone‑d6) δ 10.68 (s, 1H), 7.74 (s, 1H), 7.50 (d, J = 8.2 Hz, 1H),
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2.2.32. 3-(4-chloro-1-(2-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole
(4m)
2.2.38. 3-(4-chloro-1-(pyridin-3-ylmethyl)-1H-imidazol-5-yl)-1H-indole
(4s)
A white solid, yield 63%, mp: 195.4–196.2 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.68 (s, 1H), 7.65 (s, 1H), 7.54–7.49 (m, 1H), 7.44 (dd, J
= 7.9, 1.0 Hz, 1H), 7.36 (d, J = 7.2 Hz, 1H), 7.28–7.17 (m, 2H),
7.13–7.08 (m, 1H), 6.94 (dd, J = 8.3, 1.0 Hz, 1H), 6.85–6.80 (m, 1H),
6.71 (dd, J = 7.6, 1.7 Hz, 1H), 5.12 (s, 2H), 3.74 (s, 3H). 13C NMR (100
MHz, DMSO‑d6) δ 156.5, 137.1, 136.3, 129.6, 127.8, 127.3, 126.9,
126.8, 125.3, 122.2, 122.1, 120.8, 120.1, 119.4, 112.4, 111.1, 101.3,
55.7, 44.7; HRMS (ESI) calcd for C19H16ClN3O ([M+H]+) 338.1055,
Found 338.1050.
A yellow solid, yield 50%, mp: 123.8–124.8 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.74 (s, 1H), 8.42–8.40 (m, 1H), 8.21 (d, J = 7.6 Hz, 1H),
7.84 (s, 1H), 7.53–7.50 (m, 1H), 7.42–7.37 (m, 2H), 7.37–7.33 (m, 1H),
7.26–7.16 (m, 2H), 7.13–7.07 (m, 1H), 5.29 (s, 2H). 13C NMR (100 MHz,
DMSO‑d6) δ 149.2, 148.6, 137.1, 136.4, 135.1, 133.2, 128.0, 127.0,
126.8, 124.0, 122.2, 121.9, 120.2, 119.3, 112.5, 101.2, 47.0; HRMS
(ESI) calcd for C17H13ClN4 ([M+H]+) 309.0902, Found 309.0908.
2.2.39. 3-(4-bromo-1-propyl-1H-imidazol-5-yl)-1H-indole (5a)
A light yellow crystal, yield 55%, mp: 145.3–146.4 ◦C. 1H NMR (400
MHz, Acetone‑d6) δ 10.75 (s, 1H), 7.71 (s, 1H), 7.54–7.52 (m, 2H), 7.39
(d, J = 7.9 Hz, 1H), 7.24–7.16 (m, 1H), 7.13–7.07 (m, 1H), 3.93 (t, J =
7.2 Hz, 2H), 1.61–1.50 (m, 2H), 0.72 (t, J = 7.4 Hz, 3H). 13C NMR (100
MHz, Acetone‑d6) δ 137.8, 137.2, 127.8, 127.0, 124.9, 122.7, 120.6,
119.9, 116.5, 112.6, 103.4, 48.2, 24.4, 10.9; HRMS (ESI) calcd for
C14H14BrN3 ([M+H]+) 304.0444, found 304.0443.
2.2.33. 3-(4-chloro-1-(3-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (4n)
A pink solid, yield 39%, mp: 183.6–184.1 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.55 (s, 1H), 7.94 (s, 1H), 7.45 (t, J = 7.0 Hz, 1H), 7.37–
7.35 (m, 1H), 7.30–7.22 (m, 2H), 7.15 (q, J = 6.8 Hz, 1H), 7.03 (q, J =
7.0 Hz, 2H), 6.71 (q, J = 7.9, 7.3 Hz, 2H), 5.16 (d, J = 5.5 Hz, 2H). 13C
NMR (100 MHz, DMSO‑d6) δ 163.7, 161.3, 140.5 (d, J = 7.2 Hz), 137.1,
136.4, 131.0 (d, J = 8.4 Hz), 127.8, 126.8 (d, J = 8.8 Hz), 123.1, 122.2,
122.0, 120.1, 119.3, 114.8 (d, J = 20.8 Hz), 114.0 (d, J = 22.1 Hz),
112.5, 101.1, 48.7. 19F NMR (376 MHz, DMSO‑d6) δ ꢀ 113.0; HRMS
(ESI) calcd for C18H13ClFN3 ([M+H]+) 326.0855, Found 326.0857.
2.2.40. 3-(4-bromo-1-butyl-1H-imidazol-5-yl)-1H-indole (5b)
A white crystal, yield 63%, mp: 176.1–178.0 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.53 (s, 1H), 7.82 (s, 1H), 7.55–7.53 (m, 1H), 7.47 (d, J =
8.1 Hz, 1H), 7.28 (d, J = 7.9 Hz, 1H), 7.16 (t, J = 7.5 Hz, 1H), 7.05 (t, J
= 7.5 Hz, 1H), 3.86 (t, J = 7.1 Hz, 2H), 1.45–1.37 (m, 2H), 1.05 (dd, J =
14.8, 7.4 Hz, 2H), 0.66 (t, J = 7.4 Hz, 3H). 13C NMR (100 MHz, Ace-
tone‑d6) δ 137.3, 136.8, 127.5, 126.6, 124.5, 122.4, 120.2, 119.6, 116.1,
112.3, 103.2, 46.0, 32.8, 19.6, 13.1; HRMS (ESI) calcd for C15H16BrN3
([M+H]+) 318.0600, found 318.0618.
2.2.34. 3-(4-chloro-1-(2-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (4o)
A pink solid, yield 61%, mp: 177.0–178.0 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.70 (s, 1H), 7.74 (s, 1H), 7.51 (d, J = 8.2 Hz, 1H),
7.43–7.36 (m, 2H), 7.33–7.26 (m, 1H), 7.22–7.16 (m, J = 8.2, 7.0, 1.2
Hz, 1H), 7.12–7.02 (m, 3H), 6.86–6.80 (m, 1H), 5.26 (s, 2H). 13C NMR
(100 MHz, DMSO‑d6) δ 161.0, 158.6, 137.1, 136.4, 130.3 (d, J = 8.2 Hz),
129.2 (d, J = 3.7 Hz), 127.7, 126.8 (d, J = 2.0 Hz), 125.0 (d, J = 3.4 Hz),
124.4 (d, J = 14.4 Hz), 122.1, 122.1, 120.1, 119.3, 115.7 (d, J = 20.8
Hz), 112.4, 101.1, 43.4 (d, J = 4.4 Hz); 19F NMR (376 MHz, DMSO‑d6) δ
ꢀ 118.5; HRMS (ESI) calcd for C18H13ClFN3 ([M+H]+) 326.0855, Found
326.0859.
2.2.41. 3-(4-bromo-1-isobutyl-1H-imidazol-5-yl)-1H-indole (5c)
A yellow solid, yield 64%, mp: 133.8–135.2 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.56 (s, 1H), 7.82 (s, 1H), 7.55–7.53 (m, 1H), 7.48 (d, J =
8.1 Hz, 1H), 7.29 (d, J = 7.9 Hz, 1H), 7.16 (t, J = 7.5 Hz, 1H), 7.05 (t, J
= 7.5 Hz, 1H), 3.71 (d, J = 7.5 Hz, 2H), 1.69–1.57 (m, 1H), 0.61 (d, J =
6.7 Hz, 6H). 13C NMR (100 MHz, DMSO‑d6) δ 138.4, 136.4, 126.9,
126.9, 124.5, 122.1, 120.1, 119.4, 115.6, 112.5, 102.1, 53.2, 29.0, 19.8;
2.2.35. 3-(4-chloro-1-(4-chlorobenzyl)-1H-imidazol-5-yl)-1H-indole (4p)
A yellow solid, yield 44%, mp: 198.4–199.6 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.69 (s, 1H), 7.79 (s, 1H), 7.51 (d, J = 8.2 Hz, 1H), 7.39
(d, J = 8.0 Hz, 1H), 7.35–7.33 (m, 1H), 7.27 (d, J = 8.4 Hz, 2H),
7.22–7.17 (m, 1H), 7.13–7.07 (m, 1H), 7.00 (d, J = 8.4 Hz, 2H), 5.22 (s,
2H). 13C NMR (100 MHz, DMSO‑d6) δ 137.1, 136.7, 136.3, 132.6, 128.9,
127.8, 126.9, 126.8, 122.2, 121.9, 120.1, 119.3, 112.5, 101.2, 48.5;
HRMS (ESI) calcd for
318.0607.
C
15H16BrN3 ([M+H]+) 318.0600, Found
2.2.42. 3-(4-bromo-1-(2-methoxyethyl)-1H-imidazol-5-yl)-1H-indole
(5d)
A white solid, yield 89%, mp:139.9–140.5 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.77 (s, 1H), 7.73 (s, 1H), 7.57–7.56 (m, 1H), 7.53 (s,
1H), 7.42 (d, J = 7.9 Hz, 1H), 7.22 (ddd, J = 8.1, 6.9, 1.2 Hz, 1H),
7.15–7.10 (m, 1H), 4.10 (t, J = 5.3 Hz, 2H), 3.47 (t, J = 5.3 Hz, 2H), 3.22
(s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ 138.3, 136.5, 127.3, 126.9,
124.5, 122.1, 120.1, 119.5, 115.4, 112.5, 101.8, 70.8, 58.4, 45.7; HRMS
(ESI) calcd for C14H14BrN3O ([M+H]+) 320.0393, Found 320.0399.
HRMS (ESI) calcd for
342.0574.
C
18H13Cl2N3 ([M+H]+) 342.0559, Found
2.2.36. 3-(1-(4-bromobenzyl)-4-chloro-1H-imidazol-5-yl)-1H-indole (4q)
A light yellow solid, yield 30%, mp: 233.8–235.1 ◦C. 1H NMR (400
MHz, Acetone‑d6) δ 10.68 (s, 1H), 7.79 (s, 1H), 7.51 (d, J = 8.2 Hz, 1H),
7.45–7.37 (m, 3H), 7.34–7.33 (m, 1H), 7.22–7.17 (m, 1H), 7.12–7.07
(m, 1H), 6.94 (d, J = 8.4 Hz, 2H), 5.20 (s, 2H). 13C NMR (100 MHz,
DMSO‑d6) δ 137.2, 137.1, 136.3, 131.9, 129.2, 127.8, 126.9, 126.8,
122.2, 121.9, 121.1, 120.1, 119.3, 112.5, 101.1, 48.6; HRMS (ESI) calcd
for C18H13BrClN3 ([M+H]+) 386.0054, Found 386.0056.
2.2.43. 3-(4-bromo-1-cyclohexyl-1H-imidazol-5-yl)-1H-indole (5e)
A yellow solid, yield 47%, mp: 197.6–199.1 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.75 (s, 1H), 7.82 (s, 1H), 7.53 (t, J = 5.4 Hz, 2H), 7.37
(d, J = 7.9 Hz, 1H), 7.20 (m, 1H), 7.11 (m, 1H), 3.89 (m, 1H), 1.99 (m,
2H), 1.76 (d, J = 10.2 Hz, 4H), 1.58 (d, J = 9.5 Hz, 1H), 1.18 (dt, J =
20.7, 9.1 Hz, 3H). 13C NMR (100 MHz, CD3OD) δ 136.4, 134.4, 127.0,
126.2, 124.4, 121.8, 119.7, 118.4, 114.3, 111.5, 101.7, 56.0, 33.9, 25.3,
24.7; HRMS (ESI) calcd for C17H18BrN3 ([M+H]+) 344.0757, found
344.0784.
2.2.37. 3-(4-chloro-1-(4-(trifluoromethyl)benzyl)-1H-imidazol-5-yl)-1H-
indole (4r)
A purple solid, yield 32%, mp: 219.4–220.3 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.68 (s, 1H), 7.84 (s, 1H), 7.58 (d, J = 8.1 Hz, 2H), 7.50
(d, J = 8.1 Hz, 1H), 7.37 (d, J = 8.0 Hz, 1H), 7.35–7.33 (m, 1H),
7.21–7.16 (m, J = 7.9, 4.7 Hz, 3H), 7.08 (t, J = 7.5 Hz, 1H), 5.34 (s, 2H).
13C NMR (100 MHz, DMSO‑d6) δ 142.4, 137.2, 136.3, 128.5 (q, J = 31.8
Hz), 127.7, 126.9, 126.8, 125.9 (d, J = 2.8 Hz), 125.8 (d, J = 3.8 Hz),
122.1, 122.0, 121.0 (q, J = 119 Hz), 120.1, 119.3, 112.4, 101.1, 48.7.
19F NMR (376 MHz, Acetone‑d6) δ ꢀ 63.0 (s, 3F); HRMS (ESI) calcd for
2.2.44. 3-(1-benzyl-4-bromo-1H-imidazol-5-yl)-1H-indole (5f)
A light yellow crystal, yield 58%, mp: 204.6–206.0 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.83 (s, 1H), 7.43 (d, J = 8.2 Hz, 1H), 7.28 (d, J = 8.0
Hz, 1H), 7.22–7.15 (m, 4H), 7.13 (s, 1H), 7.05 (t, J = 7.5 Hz, 1H), 6.90
(dd, J = 6.4, 2.6 Hz, 2H), 5.10 (s, 2H). 13C NMR (100 MHz, DMSO‑d6) δ
138.0, 137.3, 136.0, 128.7, 128.6, 127.6, 126.7, 126.6, 126.4, 126.1,
124.5, 121.7, 119.7, 119.1, 115.4, 112.1, 101.4, 48.8; HRMS (ESI) calcd
C
19H13ClF3N3 ([M+H]+) 376.0823, Found 376.0829.
6

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
for C18H14BrN3 ([M+H]+) 352.0444, found 352.0477.
2.2.51. 3-(4-bromo-1-(2-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole
(5m)
2.2.45. 3-(4-bromo-1-(4-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (5g)
A light yellow crystal, yield 64%, mp: 196.9–198.1 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.79 (s, 1H), 7.44 (d, J = 8.2 Hz, 1H), 7.28 (d, J = 8.0
Hz, 1H), 7.17 (s, 1H), 7.14 (s, 1H), 7.05 (s, 1H), 7.01 (d, J = 7.8 Hz, 2H),
6.79 (d, J = 7.9 Hz, 2H), 5.04 (s, 2H), 2.24 (s, 3H). 13C NMR (100 MHz,
DMSO‑d6) δ 138.2, 137.2, 136.4, 134.7, 129.5, 127.2, 127.0, 126.8,
124.8, 122.1, 120.1, 119.5, 115.7, 112.5, 101.8, 49.0, 21.1; HRMS (ESI)
calcd for C19H16BrN3 ([M+H]+) 366.0600, found 366.0630.
A light yellow solid, yield 70%, mp: 186.2–186.9 ◦C. 1H NMR (400
MHz, DMSO‑d6) δ 11.51 (s, 1H), 7.81 (s, 1H), 7.46 (d, J = 8.1 Hz, 1H),
7.38 (d, J = 7.6 Hz, 1H), 7.32 (d, J = 7.9 Hz, 1H), 7.18 (dt, J = 19.7, 7.7
Hz, 2H), 7.05 (t, J = 7.5 Hz, 1H), 6.90 (d, J = 8.2 Hz, 1H), 6.79 (t, J =
7.4 Hz, 1H), 6.57 (d, J = 7.5 Hz, 1H), 5.07 (s, 2H), 3.64 (s, 3H). 13C NMR
(100 MHz, DMSO‑d6) δ 156.5, 138.4, 136.4, 129.5, 127.9, 127.0, 126.9,
125.3, 125.0, 122.1, 120.8, 120.1, 119.5, 115.5, 112.4, 111.1, 101.8,
55.7, 44.7; HRMS (ESI) calcd for C19H16BrN3O ([M+H]+) 382.0550,
Found 382.0563.
2.2.46. 3-(4-bromo-1-(4-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole
(5h)
2.2.52. 3-(4-bromo-1-(3-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (5n)
A white solid, yield 65%, mp: 197.3–198.3 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.54 (s, 1H), 7.97 (d, J = 7.8 Hz, 1H), 7.46 (d, J = 8.1 Hz,
1H), 7.37 (t, J = 7.6 Hz, 1H), 7.29–7.21 (m, 2H), 7.15 (t, J = 7.5 Hz, 1H),
7.07–6.97 (m, 2H), 6.70 (t, J = 9.1 Hz, 2H), 5.17 (s, 2H). 13C NMR (100
MHz, DMSO‑d6) δ 163.7, 161.3, 140.5 (d, J = 7.4 Hz), 138.5, 136.3,
131.0 (d, J = 8.4 Hz), 126.9 (d, J = 30.1 Hz), 124.8, 123.1 (d, J = 2.7
Hz), 122.1, 120.1, 119.4, 115.9, 114.8 (d, J = 20.9 Hz), 114.0 (d, J =
22.1 Hz), 112.4, 101.6, 48.7. 19F NMR (376 MHz, DMSO‑d6) δ ꢀ 113.0;
A light yellow crystal, yield 56%, mp: 187.5–189.1 ◦C. 1H NMR (400
MHz, CD3OD) δ 7.74 (s, 1H), 7.45 (d, J = 8.2 Hz, 1H), 7.29 (d, J = 8.0
Hz, 1H), 7.21–7.15 (m, 2H), 7.06 (t, J = 7.5 Hz, 1H), 6.84 (d, J = 8.6 Hz,
2H), 6.74 (d, J = 8.7 Hz, 2H), 5.02 (s, 2H), 3.71 (s, 3H). 13C NMR (100
MHz, DMSO‑d6) δ 158.7, 137.7, 136.0, 129.1, 128.4, 126.7, 126.5,
124.3, 121.7, 119.7, 119.1, 115.3, 114.0, 112.1, 101.5, 55.1 (s), 48.4 (s);
HRMS (ESI) calcd for
382.0584.
C
19H16BrN3O([M+H]+) 382.0550, found
HRMS (ESI) calcd for
370.0346.
C
18H13BrFN3 ([M+H]+) 370.0350, Found
2.2.47. 3-(4-bromo-1-(4-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (5i)
A white crystal, yield 49%, mp: 198.5–199.5 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.69 (s, 1H), 7.80 (s, 1H), 7.50 (d, J = 8.2 Hz, 1H), 7.35
(dd, J = 10.0, 5.3 Hz, 2H), 7.22–7.15 (m, 1H), 7.09 (dd, J = 11.1, 3.9 Hz,
1H), 7.04–6.93 (m, 4H), 5.19 (s, 2H). 13C NMR (100 MHz, DMSO‑d6) δ
161.7 (d, JC-F = 243.6 Hz, 1C), 138.2, 136.2, 133.7, 129.2, 129.1, 126.9,
126.7, 124.6, 122.0, 120.0, 119.3, 115.8, 115.7, 115.5, 112.3, 101.6,
48.4; HRMS (ESI) calcd for C18H13BrFN3 ([M+H]+) 370.0350, found
370.0345.
2.2.53. 3-(4-bromo-1-(2-fluorobenzyl)-1H-imidazol-5-yl)-1H-indole (5o)
A white solid, yield 73%, mp: 210.7–211.3 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.75 (s, 1H), 7.80 (s, 1H), 7.52 (d, J = 8.1 Hz, 1H),
7.43–7.36 (m, 2H), 7.32–7.25 (m, 1H), 7.20 (t, J = 7.6 Hz, 1H),
7.11–7.01 (m, 3H), 6.86–6.79 (m, 1H), 5.26 (s, 2H); 13C NMR (100
MHz, DMSO‑d6) δ 161.0, 158.6, 138.5, 136.4, 130.3 (d, J = 8.2 Hz),
129.3 (d, J = 3.7 Hz), 127.0, 126.8, 125.0 (d, J = 3.6 Hz), 124.9, 124.4
(d, J = 14.5 Hz), 122.1, 120.1, 119.4, 115.9, 115.7 (d, J = 20.7 Hz),
112.4, 101.5, 43.5 (d, J = 4.5 Hz). 19F NMR (376 MHz, DMSO‑d6) δ
ꢀ 118.5; HRMS (ESI) calcd for C18H13BrFN3 ([M+H]+) 370.0350, Found
370.0352.
2.2.48. 3-(4-bromo-1-(3-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (5j)
A white solid, yield 65%, mp: 156.0–156.6 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.54 (s, 1H), 7.92 (s, 1H), 7.47 (d, J = 8.1 Hz, 1H),
7.38–7.36 (m, 1H), 7.29 (d, J = 7.9 Hz, 1H), 7.20–7.13 (m, 1H), 7.10 (t,
J = 7.6 Hz, 1H), 7.05 (t, J = 7.5 Hz, 1H), 6.99 (d, J = 7.6 Hz, 1H), 6.71
(d, J = 7.7 Hz, 1H), 6.65 (s, 1H), 5.09 (s, 2H), 2.12 (s, 3H). 13C NMR
(100 MHz, DMSO‑d6) δ 138.3, 138.1, 137.6, 136.4, 128.9, 128.6, 127.9,
127.0, 126.9, 124.8, 124.3, 122.1, 120.0, 119.5, 115.8, 112.4, 101.8,
49.2, 21.3; HRMS (ESI) calcd for C19H16BrN3 ([M+H]+) 366.0600,
Found 366.0608.
2.2.54. 3-(4-bromo-1-(4-chlorobenzyl)-1H-imidazol-5-yl)-1H-indole (5p)
A white solid, yield 53%, mp: 209.9–219.9 ◦C. 1H NMR (400 MHz,
DMSO‑d6) δ 11.52 (s, 1H), 7.95 (s, 1H), 7.45 (d, J = 8.0 Hz, 1H), 7.34 (d,
J = 7.8 Hz, 1H), 7.27 (d, J = 7.9 Hz, 3H), 7.15 (t, J = 7.5 Hz, 1H), 7.04 (t,
J = 7.4 Hz, 1H), 6.89 (d, J = 8.1 Hz, 2H), 5.14 (s, 2H); 13C NMR (100
MHz, DMSO‑d6) δ 138.4, 136.7, 136.3, 132.5, 129.0, 128.9, 127.1,
126.8, 124.8, 122.1, 120.1, 119.4, 115.9, 112.5, 101.6, 48.6; HRMS
(ESI) calcd for C18H13BrClN3 ([M+H]+) 386.0054, Found 386.0041.
2.2.49. 3-(4-bromo-1-(2-methylbenzyl)-1H-imidazol-5-yl)-1H-indole (5k)
A white solid, yield 65%, mp: 198.4–199.2 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.65 (s, 1H), 7.62 (s, 1H), 7.50 (d, J = 8.1 Hz, 1H), 7.45
(d, J = 7.9 Hz, 1H), 7.33–7.31 (m, 1H), 7.23–7.07 (m, 5H), 6.85–6.79
(m, 1H), 5.18 (s, 2H), 2.07 (s, 3H). 13C NMR (100 MHz, DMSO‑d6) δ
138.4, 136.3, 135.8, 135.3, 130.5, 127.9, 126.8, 126.7, 126.6, 125.1,
122.1, 120.1, 119.5, 115.8, 112.4, 101.7, 47.3, 18.8; HRMS (ESI) calcd
for C19H16BrN3 ([M+H]+) 366.0600, Found 366.0599.
2.2.55. 3-(1-(4-bromobenzyl)-4-bromo-1H-imidazol-5-yl)-1H-indole (5q)
A yellow solid, yield 31%, mp: 231.4–232.5 ◦C; 1H NMR (400 MHz,
Acetone‑d6) δ 10.68 (s, 1H), 7.83 (s, 1H), 7.51 (d, J = 8.2 Hz, 1H),
7.44–7.35 (m, 3H), 7.34 (d, J = 8.2 Hz, 1H), 7.22–7.17 (m, 1H),
7.12–7.07 (m, 1H), 6.92 (d, J = 8.4 Hz, 2H), 5.20 (s, 2H); 13C NMR (100
MHz, DMSO‑d6) δ 138.4, 137.1, 136.3, 131.8, 129.3, 127.1, 126.8,
124.8, 122.1, 121.1, 120.1, 119.4, 115.9, 112.5, 101.6, 48.6; HRMS
(ESI) calcd for C18H13Br2N3 ([M+H]+) 429.9549, Found 429.9557.
2.2.50. 3-(4-bromo-1-(3-methoxybenzyl)-1H-imidazol-5-yl)-1H-indole
(5l)
A white solid, yield 74%, mp: 184.6–185.7 ◦C. 1H NMR (400 MHz,
Acetone‑d6) δ 10.70 (s, 1H), 7.81 (s, 1H), 7.52 (d, J = 8.2 Hz, 1H), 7.42
(d, J = 7.9 Hz, 1H), 7.37 (d, J = 7.6 Hz, 1H), 7.23–7.14 (m, 2H),
7.13–7.08 (m, 1H), 6.78 (dd, J = 8.3, 2.6 Hz, 1H), 6.60 (d, J = 7.6 Hz,
1H), 6.51 (t, J = 2.1 Hz, 1H), 5.18 (s, 2H), 3.63 (s, 3H); 13C NMR (100
MHz, DMSO‑d6) δ 159.7, 139.3, 138.4, 136.4, 130.1, 127.0, 126.8,
124.8, 122.1, 120.1, 119.5, 119.3, 113.6, 115.7, 112.7, 112.4, 101.8,
55.3, 49.1; HRMS (ESI) calcd for C19H16BrN3O ([M+H]+) 382.0550,
Found 382.0544.
2.2.56. 3-(4-bromo-1-(4-(trifluoromethyl)benzyl)-1H-imidazol-5-yl)-1H-
indole (5r)
A light yellow solid, yield 21%, mp: 229.3–230.1 ◦C; 1H NMR (400
MHz, Acetone‑d6) δ 10.67 (s, 1H), 7.89 (s, 1H), 7.58 (d, J = 8.1 Hz, 2H),
7.50 (d, J = 8.2 Hz, 1H), 7.38–7.33 (m, 2H), 7.21–7.15 (m, 3H),
7.10–7.05 (m, J = 8.0, 7.0, 1.1 Hz, 1H), 5.34 (s, 2H); 13C NMR (100
MHz, DMSO‑d6) δ 142.5, 138.6, 136.3, 128.4 (q, J = 32.0 Hz), 127.7,
127.1, 126.8, 125.8 (q, J = 3.6 Hz), 124.8, 123.2, 122.1, 120.1, 119.3,
116.1, 112.4, 101.5, 48.8. 19F NMR (376 MHz, Acetone‑d6) δ ꢀ 63.1 (s,
3F); HRMS (ESI) calcd for C19H13BrF3N3 ([M+H]+) 420.0318, Found
420.0309.
7

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
in Figure 5 and Figure 6. Copies of the data can be obtained free of
charge via http://www.ccdc.cam.ac.uk/, or on application to CCDC, 12
Union Road, Cambridge CB12 1EZ, UK (Fax + 44 1223 336,033 or E-
mail: deposit@ccdc.cam.ac.uk).
2.4. Biological assays
Antifungal activities test of the target compounds was carried out
using mycelia growth inhibitory rate methods (Figure 7). The com-
pounds were tested with the concentration of 50
μg/mL, Osthole,
Boscalid and Carbendazim were used as the positive control. The tested
fungi were provided by the Laboratory of Plant Disease Control, Nanjing
Agricultural University, and the experimental procedure of the anti-
fungal activity was performed according to the paper from Department
of Plant Pathology, Nanjing Agricultural University.24 The strains were
activated in PDA at 25 ◦C for 2–15 days to obtain new mycelia, the edge
of the mycelia was punched before the antifungal activity assay. The
results of the test on the target compounds against Botrytis cinrea,
Alternaria solani, Gibberella zeae, Rhizoctonia solani, Gibberella zeae, Col-
letotrichum lagenarium, Alternaria leaf spot were listed in Table 1.
Figure 5. Crystal structure of compound 3m.
3. Results and discussion
3.1. Synthetic chemistry
New streptochlorin analogues were synthesized as depicted in
Scheme 1. The synthesis started with indole (1), a cheap and readily
available building block, to prepare aldehyde 2 through the Vilsmeier-
Haack reaction25; then the substituted indole-imidazole derivatives
were synthesized by the Van Leusen imidazole synthesis, to afford
compound 3 smoothly, under an optimized reaction condition, CH3OH
and DME (v/v 1:1) as the solvent at 20 ◦C.26
The Van Leusen imidazole synthesis is a two-part reaction, in which
compound 2 and a primary amine were firstly reacted to produce the
corresponding aldimine intermediate, subsequent treatment with Tos-
MIC and base led to the 1,5-substituted imidazole via the intermediate 4-
tosyl-2-imidazoline. We found that the temperature of this imidazole
synthesis reaction could affect the yield of our products, different tem-
perature gradient has been tried in the same reaction condition
(Table 2), the result is that the highest yield would be achieved at the
temperature of 20 ◦C. Compound 3 was then chlorinated or brominated
with NCS or NBS in a mixed solvent of THF and CCl4 (v/v 1:1) under
50 ◦C, to afford the target molecules 4 and 5, respectively.
Figure 6. Crystal structure of compound 3o.
2.2.57. 3-(4-bromo-1-(pyridin-3-ylmethyl)-1H-imidazol-5-yl)-1H-indole
(5s)
A yellow solid, yield 67%, mp: 180.6–181.7 ◦C; 1H NMR (400 MHz,
Acetone‑d6) δ 10.72 (s, 1H), 8.41–8.39 (m, 1H), 8.19 (d, J = 7.8 Hz, 1H),
7.88 (s, 1H), 7.52 (d, J = 8.2 Hz, 1H), 7.38 (dd, J = 7.7, 1.7 Hz, 2H),
7.35–7.31 (m, 1H), 7.24–7.18 (m, 2H), 7.12–7.07 (m, 1H), 5.29 (s, 2H);
13C NMR (100 MHz, DMSO‑d6) δ 149.2, 148.6, 138.4, 136.3, 135.1,
133.1, 127.1, 126.7, 124.7, 124.0, 122.2, 120.2, 119.3, 116.0, 112.5,
101.6, 47.0; HRMS (ESI) calcd for C17H13BrN4 ([M+H]+) 353.0396,
Found 353.0405.
3.2. Antifungal activity and the structure-activity relationships (SAR)
The results of the biological testing against six phytopathogenic
fungi are given in Table 1. In order to analyze the structure-activity
relationships, compounds (3a-3s), (4a-4s) and (5a-5s) were tested in
comparison with lead compounds streptochlorin and pimprinine, and
commercial fungicides Osthole, Boscalid and Carbendazim were used as
the positive controls. In spite of the difficulties to find clear structure-
activity relationships from the biological data, some broad conclusions
2.3. X-ray diffraction analysis
The crystallographic data has been deposited with the Cambridge
Crystallographic Data Centre (CCDC) as supplementary publication
number: 1,986,013 (compound 3m), 1,986,028 (compound 3o), shown
A (Blank control)
B (Testing sample)
C (Positive control)
Figure 7. Antifungal activity test with mycelia growth inhibitory rate methods.
8

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
Table 1
Antifungal activity of the target compounds (50 μg/mL).
No.
R =
X =
Growth inhibition (%)
BOT
ALS
GIB
RHI
COL
ALL
3a
n-Propyl
n-Butyl
H
25.8
21.7
1.4
36.1
62.0
20.1
4.9
26.9
12.9
7.1
8.2
16.0
20.8
15.2
0.0
49.1
29.0
2.6
3b
H
48.9
4.1
3c
1-isobutyl
Methoxyethyl
Cyclohexyl
Bn
H
3d
H
1.1
35.4
21.6
26.0
29.8
24.0
20.2
7.7
4.8
10.8
54.5
85.1
97.5
70.0
74.4
38.2
21.6
5.2
3e
H
66.8
25.8
21.7
26.7
6.0
19.0
29.3
34.6
19.8
23.8
4.4
50.0
53.7
56.8
54.2
60.9
50.4
51.6
40.3
48.1
34.6
47.8
62.4
68.1
64.1
21.3
53.6
58.3
61.1
18.0
61.4
67.8
55.4
63.4
90.3
50.6
36.5
54.1
41.6
49.2
60.6
54.9
0.0
16.9
31.9
28.5
19.2
32.6
49.2
51.1
32.6
44.7
15.2
61.0
45.7
45.4
47.1
0.0
3f
H
3g
4-Me-Bn
4-MeO-Bn
4-F-Bn
H
3h
H
3i
H
3j
3-Me-Bn
2-Me-Bn
3-MeO-Bn
2-MeO-Bn
3-F-Bn
H
5.9
3k
H
25.1
17.0
34.9
2.4
10.7
4.3
30.2
37.3
40.2
15.4
15.8
42.2
44.2
36.4
14.5
35.5
62.3
37.3
12.8
76.4
68.6
40.2
62.3
49.9
26.3
12.5
23.5
23.4
26.9
30.8
20.2
4.8
3l
H
3m
H
54.4
15.1
10.1
36.2
40.2
38.6
11.8
48.9
62.8
24.3
10.1
73.9
60.5
66.4
54.4
61.7
33.5
0.3
17.1
7.4
3n
H
3o
2-F-Bn
H
16.8
21.9
36.2
25.1
8.2
20.5
28.3
29.0
32.5
6.7
3p
4-Cl-Bn
H
3q
4-Br-Bn
H
3r
4-CF3-Bn
pyridin-3-ylmethyl
n-Propyl
n-Butyl
H
3s
H
4a
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
Br
/
39.4
40.6
57.3
10.7
50.6
38.8
27.9
32.8
43.8
52.2
18.1
45.9
34.8
23.9
17.5
55.1
11.2
10.7
11.2
35.0
43.3
38.6
0.9
44.4
38.9
30.1
11.3
42.5
33.0
33.3
30.3
38.2
40.4
0.0
49.1
41.2
36.2
5.1
4b
4c
1-isobutyl
Methoxyethyl
Cyclohexyl
Bn
4d
4e
85.6
79.3
52.9
58.1
49.0
46.5
0.0
4f
4g
4-Me-Bn
4-MeO-Bn
4-F-Bn
4h
4i
4j
3-Me-Bn
2-Me-Bn
3-MeO-Bn
2-MeO-Bn
3-F-Bn
4k
4l
6.0
44.7
44.4
30.8
66.4
51.1
45.0
0.0
54.4
35.4
15.1
34.9
44.9
7.5
4m
15.9
27.2
41.0
13.3
0.0
4n
4o
2-F-Bn
4p
4-Cl-Bn
4q
4-Br-Bn
4r
4-CF3-Bn
pyridin-3-ylmethyl
n-Propyl
n-Butyl
1.6
5.5
45.1
9.9
8.7
4s
13.3
67.4
61.2
28.8
12.3
67.4
56.9
42.1
49.6
71.2
13.5
26.9
18.0
23.1
31.6
21.1
19.3
19.0
0.0
15.2
38.9
88.3
20.8
10.6
66.4
70.9
56.3
60.3
55.6
27.3
20.3
28.6
8.1
0.0
12.2
53.3
56.2
40.2
6.7
5a
56.6
67.1
48.5
0.0
40.3
32.6
53.6
0.0
5b
5c
1-isobutyl
Methoxyethyl
Cyclohexyl
Bn
5d
5e
29.5
41.5
33.0
30.2
45.1
39.3
29.6
50.6
35.4
65.3
50.8
52.9
7.6
57.5
75.4
54.6
58.6
86.5
51.0
47.8
39.7
58.2
66.5
61.0
48.0
40.4
0.0
43.5
38.2
33.1
26.6
37.5
37.6
59.2
36.9
46.5
63.1
43.3
55.7
40.5
11.5
0.0
43.3
60.4
61.3
60.9
53.6
47.0
17.5
27.3
39.1
54.0
16.2
40.0
16.3
24.9
6.8
5f
5g
4-Me-Bn
4-MeO-Bn
4-F-Bn
5h
5i
5j
3-Me-Bn
2-Me-Bn
3-MeO-Bn
2-MeO-Bn
3-F-Bn
5k
5l
5m
5n
9.0
5o
2-F-Bn
21.3
19.7
15.9
8.2
5p
4-Cl-Bn
5q
4-Br-Bn
5r
4-CF3-Bn
pyridin-3-ylmethyl
/
8.0
5s
1.4
0.0
12.5
59.3
85.5
39.5
26.0
6.4
0.0
Pimprinine
Streptochlorin
Osthole
Boscalid
Carbendazim
50.0
65.4
54.4
99.9
59.6
50.0
99.9
20.6
22.9
99.9
66.7
82.4
73.2
94.9
99.9
62.6
99.9
70.9
24.4
99.9
50.3
94.6
40.0
99.9
99.9
/
/
/
/
/
/
/
/
aBOT, Botrytis cinerea; ALS, Alternaria solani; GIB, Gibberella zeae; RHI, Rhizoctorzia solani; COL, Colletotrichum lagenarium; ALL, Alternaria Leaf Spot.
bAll the data was the average value of three replications, the bold means data equal to or above 55% control.
9

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
Scheme 1. Synthetic routes for the target compounds.
could still be drawn.
Table 2
Firstly, an additional halogen atom introduced at the imidazole ring
can also further improve the antifungal activity. The chlorinated and
brominated compounds (series 4 and 5) display more potent activities
and broader antifungal spectrum in the artificial media assays,
compared with series 3. Compound whose 4-position of the imidazole
ring were substituted by halogen atom (Cl, Br) generally showed better
antifungal activity than those were not halogenated, though compounds
3f and 3g also demonstrated 85.1%, 97.5% against Alternaria leaf spot,
respectively.
Conditions and yields for the synthesis of compounds.
Entry
Temperature
Timea
4 h
Yieldb
80%
86%
81%
74%
74%
70%
Secondly, bioscreening data of antifungal activity indicated that the
compound with n-Butyl, Cyclohexyl, Bn, 4-F-Bn or 4-Me-Bn substituent
at the imidazole ring exhibited more potent antifungal activity than
those with other substituents, and this is highlighted by compounds 3e,
3f, 3i, and their corresponding halogenated counterparts 4e, 4f, 4i and
5e, 5f, 5i. While, the effect on the antifungal activity of the other sub-
stituents at the imidazole ring was uncertain, due to the absence of
biological activity.
1
2
3
4
5
6
10 ◦
20 ◦
40 ◦
60 ◦
80 ◦
C
C
C
C
C
3 h
3 h
2.5 h
2.5 h
2 h
Reflux
a
Time to finish the reaction monitored by TLC.
Isolated yields.
b
Thirdly, the synthesized streptochlorin analogues seems more active
to inhibit the growth of Alternaria solani, Gibberella zeae, Rhizoctorzia
solani and Alternaria leaf spot, in particular 3f, 3g and 4e showed
effective control against Alternaria Leaf Spot, their growth inhibition
reach as high as 85.1%, 97.5% and 85.6%, respectively. Moreover, 22
compounds in the 59 target molecules showed growth inhibition above
55% against Rhizoctorzia solani, and this is highlighted by compounds 4i
and 5i, which displaying 90.3% and 86.5% growth inhibition, respec-
tively, even more active than those of lead compounds streptochlorin,
pimprinine, and positive control osthole.
Figure 8. Structures of some reported potent inhibitors of aaRS.
Figure 9. Superposition diagram of streptochlorin and AN2690-AMP with tLeuRS.
10

Y. Gao et al.
Bioorganic & Medicinal Chemistry 35 (2021) 116073
of these data are very close, especially ΔEbinding
.
4. Conclusions
Based on the natural product structure of streptochlorin, three series
of analogues have been effectively synthesized from starting material
indole, through Vilsmeier-Haack reaction, Van Leusen imidazole syn-
thesis and halogenation reaction in a sequential order. Bioassay showed
that target compounds with Cl or Br on the 4-position of imidazole ring
generally displayed more potent activities and broader antifungal
spectrum in the primary screening, and the compounds with n-Butyl,
Cyclohexyl, Bn, 4-F-Bn or 4-Me-Bn substituent at the imidazole ring
usually exhibited higher antifungal activity than those with other sub-
stituents. Meanwhile, some target molecules possessed excellent anti-
fungal activity, and this is highlighted by compounds 4g and 4i,
displaying 97.5% and 90.3% growth inhibition against Alternaria Leaf
Spot and Rhizoctorzia solani, respectively, both of them are superior to
the lead compounds streptochlorin, pimprinine, and commercial fungi-
cide osthole. The simulated models and scores indicated that strepto-
chlorin binds with Thermus thermophiles Leucyl-tRNA Synthetase in a
similar mode to AN2690, offering a perspective on the mode of action
study for antifungal activities of streptochlorin derivatives. Further
study on structural optimization and potential target are well under way
in our group, aiming to obtain novel streptochlorin analogues to
improve the antifungal activity and figure out the mode of action.
Figure 10. Simulated binding modes of streptochlorin with tLeuRS.
Table 3
Data of calculated binding affinity of streptochlorin and AN2690-AMP.
Molecule
AutoDock Scores (kcal/mol)
ΔEbinding
ΔEHbond
ΔEvdw
ΔEestat
ΔEdsolv
Streptochlorin
AN2690-AMP
ꢀ 5.81
ꢀ 7.55
ꢀ 0.80
ꢀ 2.31
ꢀ 7.78
ꢀ 0.05
ꢀ 0.20
2.52
5.82
Declaration of Competing Interest
ꢀ 12.35
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
3.3. Molecular modeling
The mode of action for the antifungal activities of streptochlorin and
its derivatives is still not clear, though it’s reported that pimprinine is a
potent inhibitor of monoamine oxidase,27,28 which is an important
target for the treatment of neurodegenerative diseases rather than
pathogen infection disease. Through structure comparison and literature
research, we found some reported indole alkaloids and analogues
(Figure 8), with similar or modified chemical structures of strepto-
chlorin, such as indolmycin is a naturally occurring antibiotic that acts
against Gram-negative bacteria, and indolmycin derivative shows
similar biological activity,29 chuangxinmycin exhibits in vitro an anti-
bacterial spectrum that includes a number of Gram-positive and Gram-
negative bacteria,30,31 they are potent and selective inhibitors of
aminoacyl-tRNA Synthetase (aaRS),32,33 which is an important enzyme
family for the discovery of antifungal drugs, in which Tavaborole
(AN2690), a novel boron-containing small molecule medication for the
treatment of fungal infection laughed by Anacor Pharmaceuticals in
2014,34 it inhibits fungal protein synthesis by the inhibition of Leucyl-
tRNA Synthetase (LeuRS), a proofreading aaRS.
Acknowledgments
We are grateful to the financial support for this work from the Na-
tional Natural Science Foundation of China (32061143045), the
Fundamental Research Funds and for the Central Universities
(KYLH201908), Jiangsu Provincial Science Foundation for Youths
(BK20160734), Anhui Key Research and Development Program
(201904b11020025), and Bayer Grants4 Ag Initiative. We also thank
Prof. Ge-Fei Hao and Miss Chen-Yang Jia from Central China Normal
University for their kind help on molecular modeling.
Appendix A. Supplementary material
Supplementary data to this article can be found online at https://doi.
org/10.1016/j.bmc.2021.116073.
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