Synthesis, nematicidal activity and docking study of novel chromone derivatives containing substituted pyrazole

Article abstract of DOI:10.1016/j.cclet.2017.10.011

A series of chromone derivatives containing substituted pyrazole were designed and synthesized. Preliminary bioassays showed that most of the synthesized compounds exhibited good nematicidal activity in vivo against Meloidogyne incognita at 10 mg/L. Among the tested compounds, A10 and A11 exhibited 100% inhibition rates. In addition, the molecular docking results indicated that both compound A10 and A11 interacts with amino acid residue Tyr121, Trp279, Tyr70, Trp84 and Phe330 of AChE via hydrogen bond and π–π stacking. This investigation suggested that the chromone containing substituted pyrazole scaffold could be further optimized to explore novel, high-bioactivity nematicidal leads.

Full text of DOI:10.1016/j.cclet.2017.10.011

Accepted Manuscript
Title: Synthesis, nematicidal activity and docking study of
novel chromone derivatives containing substituted pyrazole
Authors: Wei Li, Jiuhui Li, Hongfeng Shen, Jiagao Cheng,
Zhong Li, Xiaoyong Xu
PII:
DOI:
Reference:
S1001-8417(17)30428-X
https://doi.org/10.1016/j.cclet.2017.10.011
CCLET 4284
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11-7-2017
1-10-2017
11-10-2017
Please cite this article as: Wei Li, Jiuhui Li, Hongfeng Shen, Jiagao Cheng,
Zhong Li, Xiaoyong Xu, Synthesis, nematicidal activity and docking study of
novel chromone derivatives containing substituted pyrazole, Chinese Chemical
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Communication
Synthesis, nematicidal activity and docking study of novel chromone derivatives
containing substituted pyrazole

Wei Lia,1, Jiuhui Lia,1, Hongfeng Shena, Jiagao Chenga,b,*, Zhong Lia,b, Xiaoyong Xua,b,
a Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
b Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China
 Corresponding authors.
E-mail addresses: xyxu@ecust.edu.cn (X. Xu), jgcheng@ecust.edu.cn (J. Cheng).
1 These authors contribauted equally to this work.
Graphical Abstract
Synthesis, nematicidal activity and docking study of novel chromone derivatives containing substituted pyrazole
Wei Lia,1, Jiuhui Lia,1, Hongfeng Shena, Jiagao Chenga,b,*, Zhong Lia,b, Xiaoyong Xua,b,*
a Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology,
Shanghai 200237, China
b Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, China
A series of chromone derivatives containing substituted pyrazole were designed and synthesized. Preliminary bioassays
showed that most of the synthesized compounds exhibited good nematicidal activity in vivo against Meloidogyne incognita at
10 mg/L.
ABSTRACT
A series of chromone derivatives containing substituted pyrazole were designed and synthesized. Preliminary bioassays showed that most of the synthesized
compounds exhibited good nematicidal activity in vivo against Meloidogyne incognita at 10 mg/L. Among the tested compounds, A10 and A11 exhibited 100%
inhibition rates. In addition, the molecular docking results indicated that both compound A10 and A11 interacts with amino acid residue Tyr121, Trp279, Tyr70,
Trp84 and Phe330 of AChE via hydrogen bond and π-π stacking. This investigation suggested that the chromone containing substituted pyrazole scaffold could
be further optimized to explore novel, high-bioactivity nematicidal leads
Keywords
Chromone
Substituted pyrazole

Meloidogyne incognita
Nematicidal activity
Molecular docking
Root-knot nematodes (RKNs) are soil worms belonging to the plant-parasitic nematodes that feed on the roots of different crops
such as tomato, pepper, watermelons and onions, resulting in an annual crop loss of about 100 billion USD around the world [1,2]. At
present, fosthiazate and abamectin are the most commonly used nematocides in the market. Avermectin is a broad-spectrum, highly
effective pesticide. It is widely used in the prevention and control of harmful insects, mites and nematodes in agriculture [3,4].
Fosthiazate is an organophosphorus nematicide, which has the advantages of non-cross resistance of most organophosphorus
compounds and easy to be degraded [5-7]. Although recently some new stars of nematocide industry like fluensulfone and tioxazafen
have entered the pesticide market [8-10], such as tioxazafen, a new type of broad-spectrum nematocide, mainly used for seed treatment,
has a good control effect. The search for novel chemotypes of nematicides, which are safer, environmentally friendly, and
nematode-specific, is still urgent [11].
Chromones are a group of naturally occurring compounds that are ubiquitous in nature, especially in plants. Both of synthetic and
natural origin have been recognized to display valuable antibacterial, antifungal and antirhinoviral activity (Fig. S1 in Supporting
information) [12,13]. More importantly, Lee et al. [14]. reported that chromone derivatives are active nematicidal compounds (Fig. S1).
It is well known that pyrazole exhibited diversity biological activities, such as antimicrobial, xanthine oxidase inhibitory activity,
herbicidal [15-19]. What’s more, Badische Anilin-und-Soda-Fabrik (BASF) crop science reported in 2007 that the pyrazole derivative
1–1 can be used as a nematicide (Fig. S2 in Supporting information) [20]. In our group’s previous study, Li et al. [21] and Chen et al.
[22] reported that pyrazole derivative containing a diphenylacetylene scaffold (1-2) and pyrazole derivative containing a 1,2,3-triazole
scaffold (1-3) exhibited good inhibition rates against Meloidogyne incognita (Fig. S2). Liu et al. [23,24] also synthesized some
pyrazole derivatives 1-4 and 1-5 (Fig. S2).
In this study, our design stratege is to construct a novel structure scaffold which was combined chromone and substituted pyrazole
by flexible chiain. In 2014, Syngenta and Bayer crop science announced a series of aromatic/heterocyclic carboxamides, which have
good nematocidal activity [25,26]. (Fig. S3 in Supporting information). With all this in mind, we introduced amide and alkyl ester
flexible chain into chromone structure as linker to investigate the nematicidal bioactivity, and designed two series of novel chromone
derivatives (Scheme 1, A and B). The chromone derivatives containing substituted pyrazole were synthesized and their biological
activities in vivo against M. incognita were measured.
The general synthetic routes (Schemes S1and S2) and experimental data for synthesis of compounds A1-A14 and B1-B4 were listed
in Supporting information. The second-stage juveniles (J2) of M. incognita used in all tests were cultured by Huzhou Modern
Agricultural Biotechnology Innovation Center, Chinese Academy of Sciences, China. Assay of nematicidal activity can be found in
Supporting information.
The in vivo nematocidal activity of compounds A1-A14 and B1-B4 against M.incognita are listed in Table 1. Fenamiphos and
Avermectin were used as controls. As shown in Table 1, the preliminary bioassays indicated that almost all of the target compounds had
exceed 90% inhibition rates against M. incognita at 25.0 mg/L.
Based on the data in Table 1, when we fixed chromone and substituted pyrazole two parts, and focus our attention on the effect of
the linker type on the nematicidal bioactivity, it was found that R5 and R6 were hydrogen (compound A1, 100% ) displayed good
inhibitory activities against M. Incognita. However, when R6 was hydrogen and methyl, ethyl and phenyl were introduced into R5 as
flexible chain, the nematicidal activities of compound A2 (95.5%), A3 (90.3%) , A4 (91.4%) were weaker than that of A1, which
indicated that R5 and R6 of flexible chain without substitutes are in benefit for increasing nematocidal activity. When chromone and
flexible chain were fixed, the substituents of pyrazole were changed further. Compared with pyrazole substituted by benzene and
pyridine, it was found that the bioactivity of compounds A6 (90.3%) was higher than that of compounds A1 (86.6%) at 10.0 mg/L. In
order to identify pyridine group is benefit for increasing nematicidal activity, compound A5, A7, A8, and A9 were synthesized,
compounds A5 (70.3%), A8 (70.3%) and A9 (80.4%) had higher nemoticidal activities than compounds A3 (65.6%), A2 ( 65.7%) and
A4 ( 60.0%), respectively. Meanwhile, when R6 of flexible chain was methyl, the nematicidal activity of compound A7 (75.9%) was
also lower than that of A6 (90.3%), which suggested further that no substitute on both R5 and R6 of flexible chain are benefit for
increasing nematocidal activity once again. Furthermore, the influence of substitutes position of nitrogen atom of pyrazole ring were
investigated, which was shown in Scheme 1. When the substitutes were R1, compound A1-A14, correspondingly, the substitutes were
R2 in compound B1-B4. Analyzing the activity of these compounds, it was found that the nematicidal activities of B1 (50.3%), B2
(60.5%) , B3 (50.4%) and B4 (55.0%) decreased compared to that of compounds A5 (70.3%), A6 (90.3%), A7 (75.9%) , A8 (70.3%) at
10.0 mg/L. It suggest that the R1 of pyrazole is important to the nemoticidal activity.
In some papers, it was reported that CF3 group can increase nematocidal activity [29,30]. So we tried to introduce CF3 group, and
also introduce CN and Br group into pyrazole. It was found that A10 (100%), A11 (100%), A12 (96.7%) and A13 (100%) displayed
excellent nematicidal activity against M. Incognita at 25.0 mg/L, respectively. Among the tested compounds, A10 and A11 still

exhibited 100 % inhibition rates at 10.0 mg/L. It demostrated the introduction of CF3 group is really benefit for increasing nematocidal
activity. Compared with the structure reported by Liu et al. [23,24], when pyrazole carboxamide kept the same, the highest inhibition
rates of compound 1-5 (Fig. S2) and 1-4 (Fig. S2) was 59.4% at 10.0 mg/L and 100% at 40.0 mg/L, our compounds A11 reached 100%
inhibition rates at 10.0 mg/L under the same test condition. It indicated that chromone and ester flexible chain might increase the
nemoticidal activities of our compounds.
As shown in Table 2, to determine the strength of activity of title compounds, the nematicidal evaluation of the compounds in 100%
inhibitory activity at 10.0 mg/L, such as A10 and A11, was continued at lower concentrations of 5.0 mg/L and 1.0 mg/L. However, it
was found that the inhibitory activities decreased very quickly with the decreasing of the treatment concentration. The nemoticidal
bioactivity of compound A10 was 21.4% at the treatment concentration 5.0 mg/L; that of positive control tioxazafen exhibited 92.9%.
The reason why the inhibitory rates decreased so quickly still needs to be investigated further. When the treatment concentration
decreased to 1.0 mg/L, compound A11 had 14.3% inhibitation rate, meanwhile, tioxazafen exhibited 28.6 % inhibition rates at 1.0
mg/L. Although the data is not very good, it still means that compound A11 is valuable to modify further based on that of tioxazafen.
Some literatures has reported that AChE is one of the target of nematicides [31,32]. Our high active compound was also tried to
investigate the mode with AChE, the binding modes between AChE (PDB:1odc) and the active compound A6 were selected as
exemplified in the case of representative compound. First of all, we did the docking poses of A6 with the AChE, and then did the
compound A10 and A11. Performed on Maestro 10.2 software, the most likely binding conformation was selected based on the glide
score and the binding mode, which was shown in Fig. S4 (Supporting information). From the docking result, one hydrogen bond and
four π-π stacking interactions were observed between the target and the compound A6. The H atom of amide group in alkyl chain of the
compound A6 can form tightly interaction with the OH group of Tyr121 in the hinge domain of the target via a H-bond. Meanwhile, the
benzene ring of the compound A6 formed the π-π stacking interaction with the Trp279 and Tyr70 residue. The pyridine ring of the
compound A6 formed the π-π stacking interaction with the Phe330 and Trp84 residue. All of these interactions contributed the stability
of the complex between AChE and the compound A6. It is different from the mode reported by Liu et al. [25,26]. Their docking results
indicated that compound 1-4 (Fig. S2) interact with amino acid residue Tyr 121, Trp 279 (compound 1-5 (Fig. S2) interact with amino
acid residue Tyr 121) of AChE via hydrogen bond. In order to verify the effect of hydrogen of CH2CH2 of flexible chain, we selected
A5 and A8 to make a docking. The comparison of the docking A5, A6 and A8 (Fig. S4) suggests that, as the hydrogen on the flexible
chain was replaced by methyl and ethyl, the number of hydrogen bonds on the flexible chain dispeared, this also explained the
experimental result that when the hydrogen of CH2CH2 of flexible chain was replaced by methyl and ethyl groups, the nematicidal
activity decreased. We also made the molecular docking of A10 and A11 with the AChE (Fig. S5 in Supporting information), both
compound A10 and A11 interacts with amino acid residue Tyr121, Trp279, Tyr70, Trp84 and Phe330 of AChE via hydrogen bond and
π-π stacking. It is the same as that of compound A6. The docking results also indicated that all the active compounds had similiar
binding mode.
In conclusion, a novel series of chromone derivatives containing substituted pyrazole were designed and synthesized. The
nematocidal activity results showed some of them possessed good activity against M. incognita at 10.0 mg/L. The docking results
indicated that both compound A10 and A11 interacts with amino acid residue Tyr121, Trp279, Tyr70, Trp84 and Phe330 of AChE via
hydrogen bond and π-π stacking. It implied that chromone containing substituted pyrazole was a potential active structure to be worth
studying further.
Acknowledgments
This work was financial supported by the National Natural Science Foundation of China (No. 21672061), National Key Research
Program of China (No. 2017YFD0200505), and Fundamental Research Funds for the Central Universities (No. 222201718004).
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Scheme 1. The design strategy of title compounds.

Table 1
Nematicidal activities of compounds A1–A14, B1–B4 against J2 of M. incognita in test tubes.
Compound
R1
R2
R3
R4 R5
-Cl -H
R6
-H
Inhibition rate against J2 of M. Incognita (%)a
25.0 mg/L
100
10.0 mg/L
86.6
A1
-phenyl
-CH3
-CH3
-CH3
-CH3
-CH3
-CH3
-CH3
-CH3
-CH3
-CF3
-CF3
-CN
－
－
－
－
－
－
－
－
－
－
－
－
－
－
A2
-phenyl
-Cl -CH2CH3 -H
95.5
90.3
91.4
100
65.7
65.6
60.0
70.3
90.3
75.9
70.3
80.4
100
A3
-phenyl
-Cl -CH3
-Cl -phenyl
-Cl -CH3
-Cl -H
-H
-H
-H
-H
A4
-phenyl
A5
-3-Chloropyridin-2-yl
-3-Chloropyridin-2-yl
-3-Chloropyridin-2-yl
-3-Chloropyridin-2-yl
-3-Chloropyridin-2-yl
-phenyl
A6
100
A7
-Cl -H
-CH3 90.8
A8
-Cl -CH2CH3 -H
100
100
100
100
96.7
100
pt
A9
-Cl -phenyl
-H
-H
-H
-H
-H
-H
-H
A10
A11
A12
A13
A14
B1
-H
-H
-H
-H
-H
-H
-H
-H
-H
-H
-3-Chloropyridin-2-yl
-3-Chloropyridin-2-yl
-phenyl
100
72.8
95.3
60.7
50.3
-CN
-3-Chloropyridin-2-yl
-Br
-3-Chloropyridin-2- -CH3
yl
-Cl -CH3
100
－

B2
B3
B4
-3-Chloropyridin-2- -CH3
yl
-3-Chloropyridin-2- -CH3
yl
-3-Chloropyridin-2- -CH3
yl
-Cl -H
-Cl -H
-H
100
60.5
50.4
55.0
－
－
－
-CH3 90.8
-Cl -CH2CH3 -H
91.4
AVM
Fenamiphos
Tioxazafen
100
100
100
100
100
92.9
-: no substitute.AVM: Avermectin.
pt: phytotoxic.
a Average of three experiments.
Table 2
Nematicidal activities of compounds A10 and A11 against J2 of M. incognita in test tubes.
Compound
Inhibition rate (%)
5.0 mg/L
21.4
-
100
100
1.0 mg/L
A10
A11
AVM
Fenamiphos
Tioxazafen
0
14.3
100
100
28.6
92.9
-: no data because of abnormal experiment.