Design and synthesis of novel deoxybenzoin derivatives as FabH inhibitors and anti-inflammatory agents

Article abstract of DOI:10.1016/j.bmcl.2010.01.032

β-Ketoacyl-acyl carrier protein synthase III (FabH) catalyzes the initial step of fatty acid biosynthesis via a type II fatty acid synthase in most bacteria. The important role of this essential enzyme combined with its unique structural features and ubiq

Full text of DOI:10.1016/j.bmcl.2010.01.032

Bioorganic & Medicinal Chemistry Letters 20 (2010) 2025–2028
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design and synthesis of novel deoxybenzoin derivatives as FabH inhibitors
and anti-inflammatory agents
*
*
Huan-Qiu Li, Yin Luo, Peng-Cheng Lv, Lei Shi, Chang-Hong Liu , Hai-Liang Zhu
State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, People’s Republic of China
a r t i c l e i n f o
a b s t r a c t
Article history:
b-Ketoacyl-acyl carrier protein synthase III (FabH) catalyzes the initial step of fatty acid biosynthesis via a
type II fatty acid synthase in most bacteria. The important role of this essential enzyme combined with its
unique structural features and ubiquitous occurrence in bacteria has made it an attractive new target for
the development of new FabH inhibitors. The synthesis and biological evaluation halide-deoxybenzoins
derivatives are described in this Letter. Potent FabH inhibitory and selective anti-Gram-negative bacteria
activities were observed in deoxybenzoin derivatives. Furthermore, compound 19 was able to reduce the
ECE-induced IL-8 production in gastric mucosal cells significantly. Based on the biological data and
molecular docking, compound 19 is a potential FabH inhibitor and anti-inflammatory agent deserving
further research.
Received 30 September 2009
Revised 10 December 2009
Accepted 13 January 2010
Available online 20 January 2010
Keywords:
Halide-deoxybenzoins
Escherichia coli FabH
Anti-inflammatory
ECE-induced IL-8
Ó 2010 Elsevier Ltd. All rights reserved.
Although several classes of antibacterial agents are presently
available, resistance in most of the pathogenic bacteria to these
drugs constantly emerges. In order to prevent this serious medical
problem, the elaboration of new types of antibacterial agents is a
very important task.1 Recent 10 years, different targets in key areas
of the bacterial cell cycle have been studied that would be a new
weapon against the problem of acquired resistance. One of the
most attractive biochemical pathways to be used as the target
for new antibacterial agents is the fatty acid biosynthesis (FAS).
This pathway has been demonstrated to be essential for bacteria
cell survival, and differs considerably from human FAS pathway.2,3
While in humans fatty acid synthesis occurs in a homodimeric
multifunctional enzyme,4 in bacteria the pathway is composed of
various discrete enzymes and each one can be considered a puta-
tive molecular target. Those features make the type II FAS pathway
a potential target for new antimicrobial agents.
A key enzyme in this pathway is the b-ketoacyl-acyl carrier pro-
tein synthase III (FabH), which is the enzyme responsible for the first
reaction in the pathway and plays an important regulatory role.
FabH has also been demonstrated to be essential for organismal sur-
vival and is present in a large number of important human patho-
gens. Furthermore, some chemical compounds had shown to
inhibit FabH from diverse microorganisms, including multi-drug
resistant strains.5,6 These facts support the idea that FabH can be
used as an effective molecular target for the development of new
antimicrobial agents. In our previous reports, isoflavone derivatives
displayed potent antimicrobial, Escherichia coli FabH inhibitory7 and
anti-inflammatory activities.8 Deoxybenzoins, intermediates in the
synthesis of isoflavone, and their structural similarities with isoflav-
one led us to study the biological activity of the latter. The hypothe-
sis is supported by the fact that deoxybenzoins exhibit a broad
variety of biological activities including antibacterial9 andHelicobac-
ter pylori urease inhibitory activity10 in our previous study. In this
Letter, a novel series of haloid deoxybenzoin derivatives were de-
signed for their E. coli FabH inhibitory activity. Docking simulations
were performed using the X-ray crystallographic structure of the
FabH of E. coli complexed with an inhibitor to explore the binding
modes of these compounds at the active site. Moreover, the ECE
(E. coli water extract) IL-8 expression inhibitory activity evaluation
was also determined.
A series of new deoxybenzoin Schiff bases 7–36 were synthe-
sized by the route outlined in Scheme 1. The synthesis started from
phenols and phenylacetic acids. The dihydric phenols, resorcinols,
and substituted resorcinols reacted with variously substituted
phenylacetic acids,11 giving excellent yields of deoxybenzoins cat-
alyzed by BF3ꢀOEt2. Then compounds 7–36 were obtained in high
yield using appropriately substituted anilines as the amine, and
TiCl4 as the carbonyl activator.12,13 All new compounds (Table 1)
were fully characterized by spectroscopic methods and elemental
analysis.
All of the deoxybenzoins 1–6 and new deoxybenzoin Schiff bases
(7–36) were evaluated for their antimicrobial activities against four
bacteria strains (Bacillus subtilis ATCC 6633, E. coli ATCC35218, Pseu-
domonas aeruginosa ATCC 2785, and Staphylococcus aureus ATCC
6538), three fungi (Aspergillus niger ATCC 16404, Candida albicans
ATCC 10231, and Trichophyton rubrum ATCC 10218). The Schiff bases
showed potent selective inhibitory activities against Gram-negative
* Corresponding author. Tel.: +86 25 8359 2672; fax: +86 25 8359 2572.
E-mail address: zhuhl@nju.edu.cn (H.-L. Zhu).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.01.032

2026
H.-Q. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2025–2028
Scheme 1. The synthetic routes of compounds 1–36.
Table 1
(MIC = 1.562 and 1.562 lg/mL) showed comparable activities to
Chemical structures of Schiff bases 7–36
the positive control kanamycin. Compounds 17–26 with the resor-
cinol skeleton displayed higher activity than other compounds (cat-
echol skeleton). Thus, the two meta hydroxyl groups on aromatic
ring of deoxybenzoin may be responsible for inhibitory activity.
The E. coli FabH inhibitory potency of the selected compounds
16–25 was examined and the results were summarized in Table
3. As shown in Table 3, among the tested compounds, compounds
19 and 24 showed potent inhibitory activity with IC50 = 1.8 and
Compd R1
R2
R3 R4 R5
Compd R1
R2 R3
R4 R5
7
8
9
OH OH
OH OH
OH OH
OH OH
OH OH
OH OH
OH OH
OH OH
OH OH
OH OH
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
Cl
Cl
Cl
Cl
Cl
F
F
F
F
F
Cl
Cl
Cl
Cl
Cl
Me
Br
Cl
22
23
24
OH
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
F
F
F
F
F
Me
Br
Cl
NO2
OH
Me
Br
OH
OH
OH
OH
H
10
11
12
13
14
15
16
17
18
19
20
21
NO2 25
OH
Me
Br
26
27
28
29
OH Cl
OH Cl
OH Cl
OH Cl
OH Cl
OH
OH
OH
OH
OH
H
H
3.9
l
M, respectively. Other tested compounds displayed moderate
M. It also
Cl
Cl
NO2 30
H
NO2
OH
Me
Br
Cl
NO2
OH
inhibitory activity with IC50 ranging from 8.3 to 63.4
l
OH
Me
Br
31
32
33
34
H
H
H
H
can be seen from Table 3 that the selected compounds displayed
low hemolytic activity. These biological assays indicate that com-
pounds 19 and 24 are potent inhibitors of E. coli FabH as antibacte-
rial agents. In addition, molecular docking of compound 19 and
E. coli FabH was performed on the binding model based on the
E. coli FabH–CoA complex structure (1HNJ.pdb).14 The FabH active
site generally contains a catalytic triad tunnel consisting of Cys-
His-Asn, which is conserved in various bacteria. This catalytic triad
plays an important role in the regulation of chain elongation and
substrate binding. Since the alkyl chain of CoA is broken by Cys
of the catalytic triad of FabH, interactions between Cys and
substrate appear to play an important role in substrate binding.
( Fig. 1) Qiu et al. have refined three-dimensional structure of
E. coli FabH in the presence and absence of malonyl-CoA by X-ray
spectroscopy. Since malonyl moiety is degraded by E. coli FabH,
molecular docking studies for FabH and malonyl-CoA was carried
OH
OH
OH
OH
OH
H
H
H
H
H
F
F
F
F
F
Cl
NO2 35
OH 36
H
H
E. coli and P. aeruginosa, but none of the compounds showed signif-
icant inhibitory activity against fungi, supported by the fact that
their MICs were all high than 50 lg/mL (data not shown). Deoxy-
benzoins 1–6 showed no activity (MIC >50) while deoxybenzoin
Schiff bases 7–36 displayed well antimicrobial activities. As shown
in Table 2, the MIC values of the compounds differed greatly, ranging
from 0.78 to 50
lg/mL, and compounds 18, 19, 23, and 24 exhibited
excellent activities against Gram-negative E. coli and P. aeruginosa.
Especially, compounds 19 (MIC = 0.78 and 1.562
l
g/mL) and 24
Table 2
Antimicrobial activity of the synthesized compounds
Compd
MIC (lg/mL)
Compd
MIC (lg/mL)
Ea
P
B
S
E
P
B
S
7
8
9
50
50
25
25
50
50
50
25
12.5
25
50
12.5
3.125
1.562
6.25
12.5
25
50
50
50
50
50
25
50
50
50
25
25
50
50
50
25
50
25
50
25
50
12.5
25
25
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
25
25
6.25
1.562
12.5
25
25
50
50
50
50
50
25
50
25
50
25
25
25
50
25
25
50
50
50
25
50
25
50
12.5
50
12.5
50
25
50
50
12.5
12.5
50
25
50
25
12.5
25
3.125
1.562
6.25
12.5
25
12.5
6.25
25
25
25
12.5
6.25
25
10
11
12
13
14
15
16
17
18
19
20
21
50
12.5
6.25
25
50
50
25
6.25
25
25
12.5
3.125
0.78
6.25
6.25
12.5
25
25
12.5
>50
25
50
50
Kanamysin B
3.125
3.125
0.39
1.56
Penicillin G
6.25
6.25
1.562
1.562
a
B, Bacillus subtilis ATCC 6633; E, Escherichia coli ATCC 35218; P, Pseudomonas fluorescens ATCC 13525; S, Staphylococcus aureus ATCC6538.

H.-Q. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2025–2028
2027
Table 3
stimulate human gastric epithelial cancer cell line AGS to stimulate
IL-8 expression, and the affect of compound 19 on IL-8 levels were
assessed by ELISA assay. Fortunately, we found that compound 19
exhibited a strong attenuation of IL-8 production induced by E. coli
water extract in AGS cells. Inactive compound 12 was also been
evaluated as the negative control.
E. coli FabH inhibitory activity of the selected compounds 16–25
a
Compound
E. coli FabH IC50
(lM)
Hemolysis LC30 (mg/mL)
16
17
18
19
20
21
22
23
24
25
63.4 7.2
15.1 2.3
9.1 1.8
1.8 0.4
8.7 1.6
20.5 2.4
35.3 4.7
8.3 1.5
3.9 0.8
28.7
>10
>10
>10
>10
>10
>10
>10
>10
>10
>10
As shown in Figure 3, compound 19 showed well inhibitory activ-
ity against IL-8 levels which stimulated by E. coli. ECE (E. coli water
extract) alone stimulated gastric mucosal cells to produce IL-8 as
much as 1143.5 pg mLꢁ1. However, different dose-dependent atten-
uations of ECE-induced IL-8 production were seen with the addition
of compound 19 and the reference compound genistein. Different
dose-dependent attenuations of E. coli-induced IL-8 production
were observed with the addition of aspirin and compound 19. Com-
pound 19 significantly reduced the IL-8 level in a dose-dependent
a
Lytic concentration 30%.
out to identify a plausible malonyl-binding mode.14 Enlightened by
these facts, compound 19 with the most potent inhibitory activity
was hit by pharmacophore map I mentioned above. The binding
model of compound 19 and E. coli FabH is depicted in Figure 2.
In the binding model, amino hydrogen of Cys112 and Gly306 forms
hydrogen bonds with 3-hydroxy of compound 19. The 30-Cl aniline
ring in compound 19 projects into a hydrophobic interaction re-
gion, which is comprised of the side chains of His244, Asn247,
Asn274, and Phe157. The hydrophobic interaction between 19
and FabH was important for the potent inhibitory activity of 19.
In general, gram-negative bacterial infections rapidly induce an
inflammatory response in which the cytokine network plays a
major role. Lipopolysaccharides (LPS) released from these bacteria
may be a major immunogen contributing to the cytokine burst by
the LPS LPS binding protein (BP) CD14 complex formation. IL-8
is a cytokine implicated in some cancers and a wide range of
chronic inflammatory conditions, including rheumatoid arthritis
heart and gastritis.15,16 In addition, IL-8 has been shown previously
to be derived after stimulation with E. coli in transformed epithelial
cell-lines.17 Here, Gram-negative bacteria E. coli was used to
way at concentrations of 15, 30, and 60
IL-8 production was observed when the concentration of compound
19 was 60
mol Lꢁ1. Interestingly, compound 19 showed a more po-
tent inhibitory activity against ECE-induced IL-8 production than
genistein at the concentration of 30
mol Lꢁ1 (P <0.05) and
60
mol Lꢁ1 (P <0.01). However, the negative control compound
l
mol Lꢁ1, and the lowest
l
l
l
12 at the same concentration could only reduce the IL-8 level
slightly. In addition, cell viability was assessed using the MTT (3-
(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide) assay
to determine whether compound 19 and aspirin affect cell viability
at the concentrations tested (15, 30, and 60
were incubated with aspirin or compound 19 at serial concentra-
tions of 15, 30, and 60
mol Lꢁ1. Then MTT assay was performed
l
mol Lꢁ1). AGS cells
l
48 h later. The result shown in Figure 4 demonstrated that com-
pound 19 and aspirin did not affect cell viability at the concentra-
tions tested (15, 30, and 60 l
mol Lꢁ1). Based on the data obtained
in this study, it can be concluded that compound 19 would be a po-
tential and promising anti-inflammatory agent.
In summary, a series of haloid deoxybenzoin derivatives were
synthesized for the first time and evaluated for E. coli FabH inhib-
Figure 1. FabH-catalyzed initiation reaction of fatty acid biosynthesis.
Figure 2. Binding model of compound 19 and E. coli FabH.

2028
H.-Q. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2025–2028
19 into the E. coli FabH active site to determine the probable bind-
ing conformation. Furthermore, compound 19 was able to reduce
the ECE-induced IL-8 production in gastric mucosal cells signifi-
cantly. Based on the data obtained from this study, we conclude
that compound 19 is a potential FabH inhibitor and anti-inflamma-
tory agent worth of further study.
Acknowledgments
This work was supported by National Basic Research Program
(973) of China (No. 2008CB418004), China Postdoctoral Science
Foundation (No. 20080441043) and Jiangsu Provincial Fund for
Hi-Tech Research (No. BG2007330).
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2010.01.032.23
Figure 3. Inhibitory activities of compound 19 on IL-8 production induced by E. coli
water extract in gastric mucosal cells. Results are means SEM of 3–5 experiments.
Comparison 15, 30, and 60 l
mol Lꢁ1 of all agents versus control: *P <0.05, **P <0.01,
References and notes
and ***P <0.001; comparison compound 19 versus aspirin: #P <0.05, ##P <0.01, and
###P <0.001.
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