Design, synthesis, antibacterial evaluation and docking study of novel 2-hydroxy-3-(nitroimidazolyl)-propyl-derived quinolone

Article abstract of DOI:10.1111/cbdd.12395

A novel series of 2-hydroxy-3-(nitroimidazolyl)-propyl-derived quinolones 6a-o were synthesized and evaluated for their in vitro antibacterial activity. Most of the target compounds exhibited potent activity against Gram-positive strains. Among them, moxifloxacin analog 6n displayed the most potent activity against Gram-positive strains including S. epidermidis (MIC = 0.06 μg/mL), MSSE (MIC = 0.125 μg/mL), MRSE (MIC = 0.03 μg/mL), S. aureus (MIC = 0.125 μg/mL), MSSA (MIC = 0.125 μg/mL), (MIC = 2 μg/mL). Its activity against MRSA was eightfold more potent than reference drug gatifloxacin. Finally, docking study of the target compound 6n revealed that the binding model of quinolone nucleus was similar to that of gatifloxacin and the 2-hydroxy-3-(nitroimidazolyl)-propyl group formed two additional hydrogen bonds. A novel series of 2-hydroxy-3-(nitroimidazolyl)-propyl derived quinolones 6a-o were synthesized and tested for their antibacterial activity. Moxifloxacin analog 6n showed potent activity against all tested strains (MIC = 0.03-2 μg/mL).

Full text of DOI:10.1111/cbdd.12395

Chem Biol Drug Des 2014
Research Article
Design, Synthesis, Antibacterial Evaluation and
Docking Study of Novel 2-Hydroxy-3-(nitroimidazolyl)-
propyl-derived Quinolone
1
1
2
Qing Li , Junhao Xing , Haibo Cheng ,
Increasing prevalence of bacterial resistance to antibiotics
represents a serious medical and economical challenge (1–
3
2
2
Hui Wang , Jing Wang , Shuai Wang ,
Jinpei Zhou and Huibin Zhang *
2
1,
3
). Infections caused by drug-resistant bacteria are often
associated with considerable morbidity and mortality (4). Of
particular concern are multidrug resistant (MDR) bacteria,
such as methicillin-resistant aureus (MRSA), vancomycin-
resistant Staphylococcus aureus (VRSA) and vancomycin-
resistant Enterococcus faecalis (VRE), which are exhibiting
increasing levels of resistance to commonly used antibiotics
1
Center of Drug Discovery, China Pharmaceutical
University, Nanjing 210009, China
2
Department of Medicinal Chemistry, China
Pharmaceutical University, 24 Tongjia Xiang, Nanjing
2
10009, China
3
School of Life Science and Technology, China
Pharmaceutical University, 24 Tongjia Xiang, Nanjing
(5,6). Among them, MRSA is the leading cause of nosocomial
and community-acquired infections worldwide, and it has
been estimated that MRSA infection leads to 19 000 deaths
annually in the United States (4). Thus, it is urgent for devel-
opment of new antibacterial agents with the ability to extermi-
nate these drug-resistant bacterial strains.
2
10009, China
*Corresponding author: Huibin Zhang,
zhanghb80@cpu.edu.cn
A novel series of 2-hydroxy-3-(nitroimidazolyl)-propyl-
derived quinolones 6a–o were synthesized and evalu-
ated for their in vitro antibacterial activity. Most of the
target compounds exhibited potent activity against
Gram-positive strains. Among them, moxifloxacin ana-
log 6n displayed the most potent activity against
Quinolones, such as enoxacin (1), lomefloxacin (2) and cip-
rofloxacin (3) (Figure 1), which exert their antibacterial
action by inhibition of DNA-gyrase and topoisomerase IV
(7), are important antibacterial agents widely used in treat-
Gram-positive
strains
MIC = 0.06 lg/mL), MSSE (MIC = 0.125 lg/mL), MRSE
MIC = 0.03 lg/mL), S. aureus (MIC = 0.125 lg/mL),
including
S. epidermidis
ment of both Gram-positive and Gram-negative bacterial
infections (8). Quinolones also possess exceptional anti-
bacterial activity against Mycobacterium tuberculosis
(
(
MSSA (MIC = 0.125 lg/mL), (MIC = 2 lg/mL). Its activ-
ity against MRSA was eightfold more potent than refer-
ence drug gatifloxacin. Finally, docking study of the
target compound 6n revealed that the binding model
of quinolone nucleus was similar to that of gatifloxacin
and the 2-hydroxy-3-(nitroimidazolyl)-propyl group
formed two additional hydrogen bonds.
(MTB), gatifloxacin (4) and moxifloxacin (5) (Figure 1) are
undergoing evaluation in phase III trial for drug-susceptible
MTB (9). The SAR studies of quinolones have revealed that
basic group at the C-7 position is the most adaptable site
for regulating physicochemical property and an area that
greatly influences their potency, spectrum and safety
(10,11). Moreover, increasing bulk at C-7 position is toler-
Key words: antibacterial activity, docking study, nitroimidaz-
ole, quinolone
ated (12). Thus, much effort has been made on the struc-
tural modification of C-7 position in quinolones by
incorporating several bioactive moieties including macro-
lides (13,14), oxazolidinones (15), triazoles (16), 5-(nitroa-
ryl)-1,3,4-thiadiazoles (17,18) and sulfonamides (19,20).
This led to obtaining quinolone hybrids as a new class of
antimicrobial agents (21). Several quinolone hybrids dis-
played enhanced antibacterial activity against both Gram-
positive and Gram-negative organisms (13–20). Recently,
chemometric studies coupled with 3D structure-based
molecular modeling approaches were conducted to
explore the possibilities for the optimization of quinolone
compounds, which also revealed that several novel frag-
ments attached at 1 and 7 positions of those quinolones
Abbreviations: 3D, three dimension; MDR, multidrug resis-
tant; MIC, minimum inhibitory concentration; MRSA, methicil-
lin-resistant Staphylococcus aureus; MRSE, methicillin-
resistant Staphylococcus epidermidis; MSSA, methicillin-sensi-
tive Staphylococcus aureus; MSSE, methicillin-sensitive
Staphylococcus epidermidis; MTB, Mycobacterium tuberculo-
sis; PDB, protein data bank; VRE, vancomycin-resistant
Enterococcus faecalis; VRSA, vancomycin-resistant Staphylo-
coccus aureus.
Received 21 February 2014, revised 11 June 2014 and
accepted for publication 3 July 2014
ª 2014 John Wiley & Sons A/S. doi: 10.1111/cbdd.12395
1

Li et al.
Figure 1: Structures of quinolones and
design of target compounds 6a–o.
could provide a good accommodation for binding of the
active site (22,23). All these stimulated us with great inter-
est to focus on further structural modification at the C-7
position of quinolone in order to find novel quinolone deriv-
atives with potential activity against bacterial strains includ-
ing drug-resistant microorganisms.
were recorded with a Bruker AV-300 or ACF 500 spec-
trometer (Beijing, China) in the indicated solvents (TMS as
internal standard): the values of the chemical shifts are
expressed in d values (ppm) and the coupling constants
(J) in Hz. High-resolution mass spectra were recorded
using an Agilent QTOF 6520 (Beijing, China).
In this study, we introduced 2-hydroxy-3-(nitroimidazolyl)-
propyl group which may severe as new hydrogen bond
donors and receptors to increase binding affinity to the
enzymes at C-7 position of quinolone. Thus, a series of
novel compounds including 3-(2-chloro-4-nitro-1H-imi-
dazol-1-yl)-2-hydroxypropyl-derived quinolones 6a–i and
Synthesis of 2-chloro-4-nitroimdazole (10)
4-Nitroimidazole (22.6 g, 0.2 mol) was mixed with acetic
anhydride (200 mL) in 500-mL three-neck round-bottomed
flask. Fuming nitric acid (13.6 mL, 0.3 mol) was slowly
added the well-stirred mixture at a rate such that the inter-
nal temperature is maintained at 0 °C. After addition was
completed, the reaction mixture was warmed to 23–25 °C
and stirred for 4 h. The mixture was poured into ice water
(800 mL) and extracted with dichloromethane (200 mL 9
3). The combined organic layers was washed with brine,
dried over anhydrous Na SO and evaporated in vacuo to
2-hydroxy-3-(2-methyl-5-nitro-1H-imidazol-1-yl)propyl-derived
quinolones 6j–o were designed and synthesized (Figure 1).
All of the target compounds 6a–o were evaluated for their
in vitro activity against both Gram-positive and Gram-neg-
ative pathogens. Furthermore, the molecular docking was
performed by inserting compound 6n into the active site
of the topoisomerase II DNA-gyrase to investigate binding
model of the target compounds.
2
4
afford 1,4-dinitro-1H-imidazole (8) as white solid (23.0 g,
73%).
The suspension of 1,4-dinitro-1H-imidazole (23.0 g, 0.15
mol) in toluene (200 mL) was refluxed for 16 h. After TLC
analysis indicated the completed consumption of starting
materials, the mixture was cooled to room temperature
and a gradual formation of precipitate was observed. The
precipitate was collected by filtration to afford 2,4-dinitro-
1H-imidazole as yellowish solid (18.5 g, 80%).
Methods and Materials
General chemistry
All reagents were purchased from Shanghai Chemical
Reagent Company (Shanghai, China) and used without
further purification. Melting points were measured on capil-
lary tube and were uncorrected. IR spectra (in KBr pellets)
were taken using Shimadzu FT-IR-8400S spectrophotom-
eter (Nishinokyo-Kuwabara-cho, Nakagyo-ku, Kyoto,
2,4-dinitro-1H-imidazole (7.81 g, 0.05 mol) was mixed with
concentrated hydrochloric acid (75 mL) and refluxed for
2 h. Then the mixture was cooled to room temperature,
1
13
6 3
Japan). H NMR and C NMR spectra (DMSO-d , CDCl )
2
Chem Biol Drug Des 2014

2-Hydroxy-3-(nitroimidazolyl)-propyl-derived Quinolone
addition of water (10 mL) afforded a white precipitate
which was collected by filtration, dried in vacuo to give 2-
chloro-4-nitro-1H-imidazole as white solid (3.61 g, 50%).
General procedure for the preparation of
compounds 6a–i
A
mixture of 2-chloro-4-nitro-1-(oxiran-2-ylmethyl)-1H-
+
1
m.p. 219–219.5 °C; ESI-MS m/z 148.3 [M + H] ; H NMR
DMSO-d , 300 MHz, ppm): d 14 (brs, 1H), 8.45 (s, 1H).
imidazole 13 (3.7 mmol) and quinolones (2.7 mmol) in eth-
anol (25 mL) was refluxed for 16 h. The solution was
cooled to room temperature and evaporated under
reduced pressure. The residues were purified by silica gel
(
6
Synthesis of 2-chloro-4-nitro-1-(oxiran-2-
ylmethyl)-1H-imidazole (13)
column
chromatography
(dichloromethane/methanol,
100:1) to afford compounds 6a–i as yellow solid.
To
5 mmol) in anhydrous ethanol (100 mL) was added glyc-
idol (2.5 mL, 38 mmol) and K CO (0.7 g, 5 mmol), then
the mixture was heated to reflux for 16 h. The solvent was
removed and the residue was dissolved in water (20 mL)
and extracted with ethyl acetate/methanol (20/1,
a solution of 2-chloro-4-nitro-1H-imidazole (3.7 g,
2
2
3
7-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
hydroxypropyl)-3-methylpiperazin-1-yl)-1-
cyclopropyl-6-fluoro-8-methoxy-4-oxo-1,
4-dihydroquinoline-3-carboxylic acid (6a)
Gatifloxacin(1 g, 2.7 mmol), yield 50%; m.p. 210–212 °C;
30 mL 9 3). The combined organic layers were dried over
+
+
anhydrous Na SO and concentrated under reduced pres-
2
4
ESI-MS m/z 579.3[M + H] , 601.3 [M + Na] ; IR (vmax/cm):
sure to give yellow oil, The resulting crude oil was purified
by silica gel column chromatography (dichloromethane/
methanol, 20:1) to afford 3-(2-chloro-4-nitro-1H -imidazol-
3410 (COOH), 1727 and 1618 (C=O), 1443 and 1316
1
(N=O); H NMR (DMSO-d
6
, 500 MHz, ppm): d 14.92 (br s,
1H, COOH), 8.70 (s, 1H, H -quinolone), 8.53 (s, 1H,
2
1
-yl)propane-1,2-diol (11) as a yellow solid (3.2 g, 63%).
5 F 5
H -imidazole), 7.75 (d, J H, = 12 Hz, H -quinolone),
5.28–5.18 (m, 1H, HO-propyl), 4.32–3.93 (m, 5H, propyl,
+
1
ESI-MS m/z 222.1 [M + H] ;
H
NMR (DMSO-d
6
,
3
00 MHz, ppm): d 8.40 (s, 1H, H -imidazole), 5.26 (d,
and CH-cyclopropyl), 3.74 (s, 3H, CH O), 3.40–3.33 (m,
5
3
J = 5.4 Hz, 1 H, OH), 4.91 (t, J = 5.4 Hz, 1H, CH
2
O),
3H, piperazine), 3.04–2.96 (m, 2H, piperazine), 2.75–2.61
(m, 2H, piperazine), 2.46–2.30 (m, 1H, propyl), 1.03–1.12
4
.19 (dd, 1H, J = 3.3, 14.1 Hz, NCH ), 3.97 (dd, 1H,
2
J = 8.4, 14.1 Hz, NCH
2
), 3.76–3.82 (m, 1H, CHO), 3.42–
(m, 5H, cyclopropyl, and CH
2H, cyclopropyl); C NMR (DMSO-d , 300 MHz, ppm): d
3
-piperazine), 0.81–0.85 (m,
13
3
.45 (m, 1H, CH O), 3.27–3.31 (m, 1H, CH O).
2
2
6
1
76.74, 166.07, 157.57, 154.30, 150.91, 146.18, 144.84,
To a solution of resulting compound 11 (5.52 mg, 25 mmol)
in pyridine (25 mL) maintained at 10 °C, methanesulfonyl
chloride (3.4 mg, 30 mmol) was slowly added. After addi-
tion was completed, DMAP (0.28 mg, 2.5 mmol) was
added and stirred for 2 h. The reaction mixture was poured
into water (100 mL) and pH value was adjusted to 4–5 and
extracted with ethyl acetate (30 mL 9 3). The combined
organic layers was wash with brine, dried over anhydrous
Na SO and concentrated under reduced pressure to afford
139.50, 134.57, 132.54, 124.89, 121.22, 106.98, 67.49,
66.75, 63.40, 58.08, 57.46, 57.14, 56.97, 55.88, 55.50,
52.64, 52.44, 52.26, 51.65, 50.88, 41.19, 15.71, 14.83,
9.45, 9.29; HR-MS (ESI) m/z: calculated for
+
C
25
H
29ClFN
6
O
7
[M + H] : 579.1765, found: 579.1762.
7-((4aS,7aS)-1-(3-(2-chloro-4-nitro-1H-imidazol-1-
yl)-2-hydroxypropyl)hexahydro-1H-pyrrolo[3,4-b]
pyridin-6(2H)-yl)-1-cyclopropyl-6-fluoro-8-methoxy-
4-oxo-1,4-dihydroquinoline-3-carboxylic acid (6b)
2
4
compound 12 as yellow oil. The resulting crude oil was
directly used in the next step without purification. ESI-MS
+
+ 1
m/z 300.0 [M + H] , 322.0 [M + Na] ; H NMR (DMSO-d
6
,
Moxifloxacin hydrochloride (1.18 g, 2.7 mmol), yield 42%;
+
5
1
00 MHz, ppm) d: 8.48 (s, 1H, H
H, CHOH), 4.09–4.25 (m, 5H, propyl), 3.23 (s, 3 H, CH
5
-imidazole), 5.76 (br s,
).
m.p. 203–206 °C; ESI-MS m/z 605.2 [M + H] ; IR (vmax
/
3
cm): 3411 (COOH), 1727 and 1620 (C=O), 1436 and 1343
1
(
6
N=O); H NMR (DMSO-d , 500 MHz, ppm): d 15.18 (br s,
The obtained crude compound 12 was dissolved in ethyl
acetate (100 mL), DBU (40 mmol) was added and stirred
at room temperature for 2 h. After TLC analysis indicated
the completed consumption of starting materials, the
reaction mixture was washed with brine and dried over
1H, COOH), 8.64 (s, 1H, H -quinolone), 8.39 (s, 1H, H -
2
5
imidazole), 7.64 (d, 1H, JH, F = 14 Hz, H
5
-quinolone), 5.21
(m, 1H, HO-propyl), 4.19–4.11 (m, 2H, propyl), 3.97–3.96
(m, 1H, cyclopropyl), 3.82–3.75 (m, 2H, propyl), 3.71(br s,
1H, pyrrolo[3,4-b]pyridine), 3.56 (s, 3H, CH O), 3.49–3.42
3
anhydrous Na
crude product was purified by silica gel column chroma-
tography (ethyl acetate/petroleum ether, 1:1) to yield
2
SO
4
. After evaporation of solvent, the
(m, 1H, pyrrolo[3,4-b]pyridine), 3.10 (s, 1H, pyrrolo[3,4-b]
pyridine), 3.50–3.47 (m, 1H, pyrrolo[3,4-b]pyridine), 2.54–
2.53 (m, 1H, pyrrolo[3,4-b]pyridine), 2.92–2.90 (m, 1H,
2-chloro-4-nitro-1-(oxiran-2-ylmethyl)-1H-imidazole (13) as
pyrrolo[3,4-b]pyridine), 2.39–2.25 (m, 3H, propyl
,
and
brown oil, two steps yield 36%. ESI-MS m/z 242.2
pyrrolo[3,4-b]pyridine), 1.77–1.53 (m, 4H, pyrrolo[3,4-b]
+
1
13
[M + K] ; H NMR (DMSO-d
6
, 500 MHz, ppm): d 8.51
pyridine), 1.17–0.93 (m, 4H, cyclopropyl);
C NMR
(
1H, s, H -imidazole), 4.48 (dd, 1H, J = 3.5, 14.5 Hz,
5
(DMSO-d , 300 MHz, ppm): d 176.33, 166.30, 155.50,
6
NCH ), 4.19 (dd, 1H, J = 5.5, 14.5 Hz, NCH ), 3.39–3.41
151.71, 150.51, 144.76, 141.08, 137.50, 134.96, 132.24,
124.74, 117.30, 106.95, 67.07, 62.05, 61.64, 59.05,
53.80, 53.40, 51.42, 50.34, 41.12, 37.05, 23.42, 22.21,
2
2
(m, 1H, CHO), 2.86–2.88(m, 1H, CH
2
O), 2.62–2.63(m,
1
H, CH O).
2
Chem Biol Drug Des 2014
3

Li et al.
.76, 9.00; HR-MS (ESI) m/z: calculated for
9
(d, 1H, J = 20.1 Hz, HO-propyl), 4.59 (q, 2H, J = 6 Hz,
CH -ethyl), 4.32–4.20 (m, 1H, propyl), 4.07–3.89 (m, 2H,
+
C
27
H
31ClFN
6
O
7
[M + H] : 605.1921, found: 605.1930.
2
propyl), 3.42–3.36- (m, 3H, piperazine), 3.08–2.91 (m, 2H,
piperazine), 2.73–2.55- (m, 2H, piperazine), 2.45–2.31 (m,
7
-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
2H, propyl), 1.44 (t, 3H, J = 6.6 Hz, CH
3
-piperazine), 1.06
NMR (DMSO-d6,
d 175.49, 165.51, 156.16, 152.87,
13
hydroxypropyl)piperazin-1-yl)-1-ethyl-6-fluoro-4-
oxo-1,4-dihydroquinoline-3-carboxylic acid (6c)
(t, 3H, J = 6 Hz, CH -ethyl);
C
3
300 MHz, ppm):
Norfloxacin (0.86 g, 2.7 mmol), yield 46%; m.p. 210–
151.10, 147.50, 144.30, 133.62, 132.08, 127.25, 124.36,
120.35, 106.96, 68.48, 67.09, 66.36, 63.50 57.54, 57.06,
56.80, 56.43, 55.25, 54.86, 53.78, 53.57, 52.12, 51.95,
+
2
12 °C; ESI-MS m/z 523.3 [M + H] ; IR (vmax/cm): 3426
(
COOH), 1719 and 1628 (C=O), 1474 and 1340 (N=O);
1
H NMR (DMSO-d , 300 MHz, ppm): d 15.34 (br s, 1H,
51.45, 50.67, 46.60, 15.91, 14.76, 13.81; HR-MS (ESI) m/
6
+
COOH), 8.95 (s, 1H, H
2
-quinolone), 8.51 (s, 1H, H
5
-imid-
z: calculated for C23
found: 555.1575.
H
2
26ClF N
6
O
6
[M + H] : 555.1565,
azole), 7.91(d, 1H, JH,F = 13.2 Hz, H -quinolone), 7.16 (d,
5
1
H,
J
H,F = 7.2 Hz,
H
8
-quinolone), 5.29 (d, 1H,
-ethyl),
.23–4.26 (d, 1H, propyl ), 4.09–3.97 (m, 2H, propyl ),
J = 5.1 Hz, OH), 4.59 (q, 2H, J = 7.2 Hz, CH
4
2
7-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
hydroxypropyl)piperazin-1-yl)-6,8-difluoro-1-(2-
fluoroethyl)-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid (6f)
,
,
3
.30 (s, 4H, piperazine), 2.60–2.72(m, 4H, piperazine),
2
.43 (d, 2H, J = 5.7 Hz, propyl), 1.42 (t, 3H, J = 7.2 Hz,
1
3
CH
3
-ethyl);
6
C NMR (DMSO-d , 300 MHz, ppm): d
1
1
6
76.10, 166.07, 154.47, 151.17, 148.41, 145.30, 144.39,
37.15, 132.19, 124.40, 119.08, 111. 05, 106.78, 66.10,
Fleroxacin (1 g, 2.7 mmol), yield 42%; m.p. 191–192 °C;
+
ESI-MS m/z 559.3 [M + H] ; IR (vmax/cm): 3415 (COOH),
1
1.22, 52.97, 51.96, 49.10, 48.88, 14.27; HR-MS (ESI)
1720 and 1626 (C=O), 1474 and 1335 (N=O); H NMR
+
m/z: calculated for C H ClFN O6 [M + H] : 523.1503,
(DMSO-d , 300 MHz, ppm): d 14.76 (br s, 1H, COOH),
22
25
6
6
found: 523.1509.
8.86 (s, 1H, H
2 5
-quinolone), 8.51 (s, 1H, H -imidazole),
7
.87 (d, 1H, JH,F = 6.9 Hz, H -quinolone), 5.25 (d, 1H,
5
J = 2.7 Hz, HO-propyl), 4.98–4.84 (m, 4H, fluoroethyl),
4.25–4.22 (m, 1H, propyl), 4.06–3.99 (m, 2H, propyl),
3.33–3.32(m, 4H, piperazine), 2.63–2.52 (m, 4H, pipera-
zine), 2.43 (d, 2H, J = 3 Hz, propyl); C NMR (DMSO-
d6, 300 MHz, ppm): d 175.66, 165.37, 156.20, 152.88,
152.33, 144.38, 133.75, 132.19, 127.35, 124.42,
120.15, 107.10, 106.78, 83.00, 80.84, 65.98, 61.49,
7
-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
hydroxypropyl)piperazin-1-yl)-1-ethyl-6-fluoro-4-
oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic
acid (6d)
13
Enoxacin (0.86 g, 2.7 mmol), yield 15%; m.p. 220–
+
2
22 °C; ESI-MS m/z 524.3 [M + H] ; IR (vmax/cm): 3447
1
(
COOH), 1724 and 1628 (C=O), 1472 and 1371 (N=O); H
NMR (DMSO-d , 300 MHz, ppm): d 15.30 (br s, 1H,
COOH), 8.97 (s, 1H, H -quinolone), 8.52 (s, 1H, H -imid-
azole), 8.06 (d, 1H, JH,F = 13.8 Hz, H -quinolone), 5.29
d, 1H, J = 4.8 Hz, OH), 4.49 (q, 2H, J = 7.2 Hz, CH2-
ethyl), 4.24 (d, 1H, propyl), 4.04–3.97 (m, 2H, propyl
.82–3.79 (m, 4H, piperazine), 2.56–2.69 (m, 4H, pipera-
zine), 2.43 (d, 2H, J = 5.7 Hz, propyl), 1.39 (t, 3H,
57.83, 53.79, 51.98, 50.35; HR-MS (ESI) m/z: calculated
+
6
for
C
22
H
23ClF
3
N
6
O
6
[M + H] :
559.1314,
found:
2
5
559.1319.
5
(
)
,
7-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
3
hydroxypropyl)piperazin-1-yl)-1-cyclopropyl-6-
fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic
acid (6g)
13
J = 7.2 Hz, CH
3 6
-ethyl); C NMR (DMSO-d , 300 MHz,
ppm): d 176.26, 165.78, 149.80, 147.63, 145.10, 144.77,
Ciprofloxacin (0.89 g, 2.7 mmol), yield 31%; m.p. 193–
+
1
6
44.39, 132.25, 124.37, 119.20, 112.56, 108.02, 66.09,
194 °C; ESI-MS m/z 535.1 [M + H] ; IR (vmax/cm): 3415
1
1.07, 53.02, 51.92, 47.13, 46.65, 14.61; HR-MS (ESI)
(COOH), 1721 and 1629 (C=O), 1472 and 1339 (N=O); H
+
m/z: calculated for C21
found: 524.1462.
H
24ClFN
7
O
6
[M + H] : 524.1455,
6
NMR (DMSO-d , 300 MHz, ppm): d 14.94 (br s, 1H,
COOH), 8.66 (s, 1H, H -quinolone), 8.53 (s, 1H, H -imid-
2
5
azole), 7.90 (d, 1H, JH,F = 13.2 Hz, H
5
-quinolone), 7.55
(d, 1H,
JH,F = 7.8 Hz,
8
H -quinolone), 5.30 (d, 1H,
7
-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
hydroxypropyl)-3-methylpiperazin-1-yl)-1-ethyl-
,8-difluoro-4-oxo-1,4-dihydroquinoline-3-
J = 4.5 Hz, HO-propyl), 4.27–4.23 (m, 1H, propyl), 4.05–
3.98 (m, 2H, propyl), 3.84–3.82 (m, 1H, cyclopropyl),
3.32–3.30 (m, 4H, piperazine), 2.73–2.61 (m, 4H, pipera-
zine), 2.48–2.46 (m, 2H, propyl), 1.33–1.19 (m, 4H, cyclo-
6
carboxylic acid (6e)
Lomefloxacin (1.05 g, 2.7 mmol), yield 42%; m.p. 215–
13
propyl); C NMR (DMSO-d , 300 MHz, ppm): d 176.74,
6
+
2
16 °C; ESI-MS m/z 555.1 [M + H] ; IR (vmax/cm): 3411
166.36, 155.07, 151.77, 148.40, 145.60, 144.85, 139.58,
132.66, 124.50, 119.95, 111.19, 107.16, 66.53, 61.72,
1
(COOH), 1722 and 1624 (C=O), 1470 and 1329 (N=O); H
NMR (DMSO-d , 300 MHz, ppm): d 14.91 (br s, 1H,
53.40, 52.44, 49.83, 36.24, 7.97; HR-MS (ESI) m/z: cal-
6
+
COOH), 8.93 (s, 1H, H
2
-quinolone), 8.52 (s, 1H, H
5
-imid-
culated for C23
535.1508.
H
25ClFN
6
O
6
[M + H] : 535.1503, found:
azole), 7.76 (d, 1H, JH,F = 12 Hz, H -quinolone), 5.23
5
4
Chem Biol Drug Des 2014

2-Hydroxy-3-(nitroimidazolyl)-propyl-derived Quinolone
7
-(4-(3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
the crude 6j–l, then purification was achieved by silica gel
column chromatography (dichloromethane/methanol, 50:1)
to afford compounds 6j–l as yellow solid.
hydroxypropyl)piperazin-1-yl)-1-cyclopropyl-6-
fluoro-4-oxo-1,4-dihydro-1,8-naphthyridine-3-
carboxylic acid (6h)
1
8
4
-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydro-1,
-naphthyridine-3-carboxylic acid (0.89 g, 2.7 mmol), yield
1-cyclopropyl-6-fluoro-7-(4-(2-hydroxy-3-(2-
methyl-5-nitro-1H-imidazol-1-yl)propyl)-3-
methylpiperazin-1-yl)-8-methoxy-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid (6j)
+
6%; m.p. 211–212 °C; ESI-MS m/z 536.1 [M + H] ; IR
(
v
max/cm): 3404 (COOH), 1724 and 1628 (C=O), 1472 and
1
1
342 (N=O); H NMR (DMSO-d
6
, 300 MHz, ppm): d 14.98
-quinolone), 8.52 (s, 1H,
= 13.8 Hz, H -quinolone),
(br s, 1H, COOH), 8.53 (s, 1H, H
2
Gatifloxacin (1 g, 2.67 mmol), yield 93%; m.p. 225–
+
H -imidazole), 8.00 (d, 1H, J
229 °C; ESI-MS m/z 559.3[M + H] ; IR(v /cm): 3497
5
H,F
5
max
1
5
3
3
.30 (m, 1H, HO-propyl), 4.27–4.23 (m, 1H, propyl),
.98–4.05 (m, 2H, propyl), 3.79 (s, 4H, piperazine),
.61–3.53 (m, 1H, cyclopropyl), 2.67–2.54 (m, 4H, pipera-
(COOH), 1700 and 1620 (C=O), 1433 and 1377 (N=O); H
NMR (DMSO-d , 500 MHz, ppm): d 14.55 (br s, 1H,
6
COOH), 8.69 (s, 1H, H
azole), 7.72 (d, 1H, JH,
2
-quinolone), 8.02 (s, 1H, H
4
-imid-
zine), 2.43–2.41 (m, 2H, propyl), 1.17–1.01 (m, 4H, cyclo-
propyl); C NMR (DMSO-d , 300 MHz, ppm): d 176.35,
F
= 14.5 Hz, H -quinolone), 5.07
5
1
3
(d, 0.5H, J = 5.0 Hz, HO-propyl), 5.03 (d, 0.5H,
J = 5.0 Hz, HO-propyl), 4.73 (d, 0.5H, J = 14 Hz, propyl),
4.59 (d, 0.5H, J = 14 Hz, propyl), 4.17–3.92 (m, 3H, pro-
6
1
1
5
65.66, 149.66, 148.58, 147.05, 146.60, 145.14, 144.40,
32.24, 124.36, 119.20, 112.18, 107.56, 66.09, 61.15,
3.16, 53.93, 46.65, 34.85, 6.79; HR-MS (ESI) m/z: calcu-
pyl, and cyclopropyl), 3.76 (s, 3H, CH
3H, piperazine), 3.05–2.96 (m, 2H, piperazine), 2.81–2.61
(m, 2H, piperazine), 2.49 (s, 3H, CH -imidazole), 2.44–
.34 (m, 2H, propyl), 1.09–1.06 (m, 3H, CH -piperazine),
C NMR (DMSO-d6,
176.78, 166.12, 157.64, 154.32,
3
O), 3.43–3.34 (m,
+
lated for C H ClFN O [M + H] : 536.1455, found:
2
2
24
7 6
536.1453.
3
2
1
3
13
.12–0.99 (m, 4H, cyclopropyl);
7
-(3-((3-(2-chloro-4-nitro-1H-imidazol-1-yl)-2-
300 MHz, ppm): d
hydroxypropyl)(methyl)amino)piperidin-1-yl)-1-
cyclopropyl-6-fluoro-8-methoxy-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid (6i)
152.74, 150.96, 146.28, 139.50, 138.94, 134.63, 133.45,
121.20, 107.02, 68.33, 67.65, 63.44, 58.30, 57.63, 57.43,
55.73, 55.57, 52.54, 51.91, 51.25 51.08, 50.03, 41.17,
Balofloxacin (1.05 g, 2.7 mmol), yield 44%; m.p. 202–
16.00, 15.04, 14.97, 9.50, 9.30; HR-MS (ESI) m/z: calcu-
+
+
2
03 °C; ESI-MS m/z 593.3 [M + H] ; IR (vmax/cm): 3411
lated for C26
581.2143.
H
31
N
6
O
7
FNa [M + Na] : 581.2136, found:
1
(
COOH), 1727 and 1618 (C=O), 1434 and 1315 (N=O); H
NMR (DMSO-d , 300 MHz, ppm): d 14.98 (br s, 1H,
COOH), 8.70 (s, 1H, H -quinolone), 8.48 (d, 1H,
6
2
J = 2.1 Hz, H
quinolone), 5.17 (d, 1H, J = 3.6 Hz, HO-propyl), 4.25–4.15
m, 2H, propyl, and cyclopropyl), 3.94–3.88 (m, 2H, pro-
pyl), 3.74(s, 3H, CH O), 3.57–3.37 (m, 2H, piperidine),
.12–2.99 (m, 2H, piperidine), 2.72–2.61 (m, 1H, piperi-
5
-imidazole), 7.74 (d, 1H, J H,F = 12 Hz, H
5
-
1-cyclopropyl-6-fluoro-7-((4aS,7aS)-1-(2-hydroxy-
3-(2-methyl-5-nitro-1H-imidazol-1-yl)propyl)
hexahydro-1H-pyrrolo[3,4-b]pyridin-6(2H)-yl)-8-
methoxy-4-oxo-1,4-dihydroquinoline-3-carboxylic
acid (6k)
(
3
3
dine), 2.56–2.52 (m, 2H, piperidine), 2.34 (d, 3H,
Moxifloxacin hydrochloride (1.16 g, 2.67 mmol), yield 87%,
m.p. 128–131 °C; ESI-MS m/z 585.0 [M + H] ; IR(vmax/
+
J = 3 Hz, CH N-piperidine), 1.98–1.77(m, 2H, propyl),
3
1
pyl);
.71–1.41 (m, 2H, piperazine), 1.17–0.97(m, 4H, cyclopro-
cm): 3428 (COOH), 1717 and 1616 (C=O), 1437 and 1362
1
3
1
C NMR (DMSO-d
6
, 300 MHz, ppm): d 176.30,
(N=O); H NMR (CDCl
1H, COOH), 8.76 (s, 1H, H
3
, 500 MHz, ppm): d 14.97 (br s,
-quinolone), 7.93 (s, 1H, H
imidazole), 7.75 (d, 1H, J H, = 14 Hz, H -quinolone),
1
1
6
2
65.64, 157.30, 153.39, 150.40, 145.68, 144.34, 139.60,
34.11, 132.00, 124.40, 120.50, 106.48, 67.15, 62.70
0.48, 57.53, 53.10, 51.93, 50.79, 40.77, 26.47, 25.98,
2
4
-
F
5
4.55 (dd, 1H, J = 12.0, 21.5 Hz, HO-propyl), 4.05–3.99
(m, 4H, propyl, pyrrolo[3,4-b]pyridine, and cyclopropyl),
3.82–3.80 (m, 2H, propyl), 3.56 (d, 3H, J = 11.5 Hz,
5.39, 9.02, 8.77; HR-MS (ESI) m/z: calculated for
+
C H ClFN O [M + H] : 593.1921, found: 593.1926.
2
6
31
6 7
CH
.70 (m, 3H, pyrrolo[3,4-b]pyridine), 2.50 (d, 3H,
J = 32.5 Hz, CH -imidazole), 2.60–2.39 (m, 2H, propyl),
1.82–1.57 (m, 5H, pyrrolo[3,4-b]pyridine), 1.25–0.93 (m,
3
O), 3.50–3.42 (m, 2H, pyrrolo[3,4-b]pyridine), 3.16–
2
General procedure for the preparation of
compounds 6j–l
3
13
A
mixture of quinolone (2.67 mmol), ornidazole
4H, cyclopropyl); C NMR (CDCl , 500 MHz, ppm): d
3
(
2.67 mmol) and KOH (6.9 mmol) in ethanol (20 mL) and
176.89, 167.00, 154.60, 152.51, 152.00, 149.60, 140.80,
138.36, 137.37, 134.45, 133.22, 118.42, 107.77, 67.79,
66.99, 62.79, 61.81, 61.06, 58.96, 58.07, 55.30, 53.89,
53.60, 51.19, 50.37, 50.02, 49.36, 48.17, 40.40, 37. 41,
H O (20 mL) was refluxed for 12 h. After TLC analysis
2
indicated the completed consumption of starting materials,
the solvent was evaporated in vacuo, and the resulting
residues were dissolved in water (20 mL) and the pH value
was adjusted to 4–5 with aqueous 50% HCl, a yellow
precipitate was formed and collected by filtration to give
36.94, 24.19, 23.37, 23.22, 22.00, 14.69, 9.88, 9.02; HR-
+
MS (ESI) m/z: calculated for C28
607.2292, found: 607.2300.
H
33FN
6
O
7
Na [M + Na] :
Chem Biol Drug Des 2014
5

Li et al.
-cyclopropyl-6-fluoro-7-(3-((2-hydroxy-3-(2-
methyl-5-nitro-1H-imidazol-1-yl)propyl)(methyl)
amino)piperidin-1-yl)-8-methoxy-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid (6l)
+
1
culated for C26
581.2142.
31 6 7
H N O FNa [M + Na] : 581.2136, found:
Balofloxacin (1.0 g, 2.67 mmol), yield 91%, m.p. 112–
1-cyclopropyl-6-fluoro-7-((4aS,7aS)-1-((R)-2-
hydroxy-3-(2-methyl-5-nitro-1H-imidazol-1-yl)
propyl)hexahydro-1H-pyrrolo[3,4-b]pyridin-6(2H)-
yl)-8-methoxy-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid (6n)
+
1
16 °C; ESI-MS m/z 573.2 [M + H] ; IR (vmax/cm): 3411
1
(
COOH), 1727 and 1618 (C=O), 1434 and 1345 (N=O); H
NMR (CDCl , 300 MHz, ppm): d 14.77 (br s, 1H, COOH),
.79 (s, 1H, H -quinolone), 7.94 (s, 1H, H -imidazole),
.80 (d, 1H, JH,F = 12 Hz, H -quinolone), 4.58 (d, 1H,
3
8
7
2
4
5
Moxifloxacin hydrochloride (1.16 g, 2.67 mmol), yield 88%;
+
J = 13.2 Hz, HO-propyl), 4.09–3.99 (m, 3H, cyclopropyl,
propyl, and piperidine), 3.76 (d, 3H, J = 1.8 Hz, CH O),
.67–3.43 (m, 3H, propyl, and piperidine), 3.12–3.01 (m,
H, piperidine), 2.80–2.75 (m, 2H, piperidine), 2.56–2.48
-imidazole), 2.40 (d,
H, J = 4.8 Hz, CH N-piperidine), 2.09–1.49 (m, 4H,
m.p. 128–130 °C; ESI-MS m/z 585.0 [M + H] ; IR(vmax/
3
cm): 3361 (COOH), 1708 and 1619 (C=O), 1443 and 1259
1
3
2
(N=O); H NMR (CDCl , 500 MHz, ppm): d 14.95 (br s,
3
1H, COOH), 8.76 (s, 1H, H
2
-quinolone), 7.93 (s, 1H, H
4
-
(m, 1H, piperidine), 2.56 (s, 3H, CH
3
imidazole), 7.79 (d, 1H J H, F = 14 Hz, H
5
-quinolone), 4.57
3
(d, 1H, J = 12.0 Hz, HO-propyl), 3.99–4.07 (m, 4H, propyl,
3
piperidine, and propyl), 1.24–0.84 (m, 4H, cyclopropyl);
pyrrolo[3,4-b]pyridine, and cyclopropyl), 3.84 (s, 1H, pro-
1
3
C NMR (CDCl , 300 MHz, ppm): d 176.02, 165.74,
pyl), 3.58 (s, 3H, CH O), 3.49–3.44 (m, 3H, pyrrolo[3,4-b]
3
3
1
1
5
3
57.00, 153.66, 151.15, 148.83, 144.47 138.80, 137.43,
32.95, 132.30, 120.80, 106.90, 66.35, 61.49, 60.12,
8.85, 56.46, 56.01, 52.67, 52.33, 50.38, 49.30, 39.60,
pyridine), 2.87–2.76 (m, 3H, pyrrolo[3,4-b]pyridine), 2.54
(s, 3H, CH -imidazole), 2.58–2.46 (m, 2H, pyrrolo[3,4-b]
3
pyridine), 1.84–1.57 (m, 5H, pyrrolo[3,4-b]pyridine, and
13
7.28, 36.84, 26.58, 25.95, 24.80, 13.80, 8.66, 8.38; HR-
propyl), 1.27–0.90 (m, 4H, cyclopropyl); C NMR (CDCl
500 MHz, ppm): 176.66, 166.00, 154.69, 152.69,
152.00, 149.62, 140.92, 138.40, 137.30, 134.44, 133.28,
3
,
+
MS (ESI) m/z: calculated for C H FN O [M + H] :
d
27
34
6 7
5
73.2468, found: 573.2488.
1
4
18.63, 107.87, 67.78, 62.85, 61.11, 58.97, 55.35, 50.34,
9.25, 48.04, 40.40, 36.94, 24.24, 23.41, 14.73, 9.85,
General procedure for the preparation of
compounds 6 m-o
9.07; HR-MS (ESI) m/z: calculated for C H FN O Na
28 33 6 7
+
[M + Na] : 607.2292, found: 607.2301.
A
(
H
mixture of quinolone (2.3 mmol), (S)-ornidazole
2.53 mmol) and KOH (6.9 mmol) in ethanol (20 mL) and
O (20 mL) was refluxed for 12 h. After TLC analysis
2
1-cyclopropyl-6-fluoro-7-(3-(((R)-2-hydroxy-3-(2-
methyl-5-nitro-1H-imidazol-1-yl)propyl)(methyl)
amino)piperidin-1-yl)-8-methoxy-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid (6o)
indicated the completed consumption of starting materials,
the solvent was evaporated in vacuo, and the resulting
residues were purified as in method for preparation of
compounds 6j–l.
Balofloxacin (1.0 g, 2.67 mmol), yield 68%, m.p. 112–
+
1
15 °C; ESI-MS m/z 573.2 [M + H] ; IR (vmax/cm): 3410
1
(COOH), 1727 and 1617 (C=O), 1435 and 1342 (N=O); H
1
-cyclopropyl-6-fluoro-7-(4-((R)-2-hydroxy-3-(2-
NMR (CDCl , 300 MHz, ppm): d 14.73 (br s, 1H, COOH),
3
methyl-5-nitro-1H-imidazol-1-yl)propyl)-3-
methylpiperazin-1-yl)-8-methoxy-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid (6m)
8.74(s, 1H, H -quinolone), 7.92 (s, 1H, H -imidazole), 7.81
2
4
(d, 1H, J = 12 Hz, H
5
-quinolone), 4.60 (s, 1H, HO-propyl),
4.12–3.98 (m, 3H, cyclopropyl, propyl, and piperidine),
3.76 (s, 3H, CH O), 3.68–3.42 (m, 3H, propyl, and piperi-
Gatifloxacin (1 g, 2.67 mmol), yield 87%; m.p. 224–
3
+
2
26 °C; ESI-MS m/z 559.3 [M + H] ; IR(vmax/cm): 3408
dine), 3.14–3.02 (m, 2H, piperidine), 2.81–2.74 (m, 2H,
(
COOH), 1733 and 1598 (C=O), 1433 and 1314 (N=O);
piperidine), 2.56 (s, 3H, CH -imidazole), 2.41 (d, 3H,
3
1
H NMR (DMSO-d
6
, 500 MHz, ppm): d 14.55 (br s, 1H,
J = 4.8 Hz, CH
3
N-piperidine), 2.10–1.49 (m, 4H, piperi-
COOH), 8.69 (s, 1H, H -quinolone), 8.02(s, 1H, H -imid-
dine, and propyl), 1.25–1.17(m, 3H, piperidine, and cyclo-
2
4
13
azole), 7.72 (d, J H,
F
= 14.5 Hz, H
5
-quinolone), 5.07 (d,
propyl), 1.01–0.94 (m, 2H, cyclopropyl); C NMR (CDCl
3
,
1
H, J = 5 Hz, HO-propyl), 4.67 (d, 1H, J = 14 Hz, pro-
300 MHz, ppm): 175.98, 165.64, 156.99, 153.69,
d
pyl), 4.17–4.01 (m, 3H, propyl, and cyclopropyl), 3.77 (s,
151.15, 148.83, 144.52, 138.90, 137.45, 132.95, 132.28,
120.75, 107.12, 66.33, 61.45, 58.90, 56.42, 52.36, 50.33,
49.25, 39.59, 37.25, 36.80, 26.60, 25.97, 24.82, 13.80,
3
2
3
H, CH
H, piperazine), 2.82–2.63 (m, 2H, piperazine), 2.49 (s,
H, CH -imidazole), 2.49–2.35 (m, 2H, propyl) 1.09–1.06
3
O), 3.41–3.34 (m, 3H, piperazine), 3.05–2.96 (m,
3
8.65, 8.36; HR-MS (ESI) m/z: calculated for C27
H
34FN
6
O
7
+
(
m, 3H, CH -piperazine), 1.14–1.03 (m, 4H, cyclopropyl);
C NMR (DMSO-d , 300 MHz, ppm): d 176.78, 166.12,
6
[M + H] : 573.2468, found: 573.2486.
3
1
3
1
1
5
1
57.64, 154.32, 152.74, 150.96, 146.28, 139.50,
38.94, 134.63, 133.45, 121.20, 107.02, 67.65, 63.38,
8.30, 57.36, 57.63, 55.57, 52.52, 51.25 50.03, 41.25,
6.00, 14.97, 14.92, 9.50, 9.30; HR-MS (ESI) m/z: cal-
Minimum inhibitory concentration measurement
The minimum inhibitory concentration (MIC) was performed
by agar dilution method according to Clinical and Labora-
6
Chem Biol Drug Des 2014

2-Hydroxy-3-(nitroimidazolyl)-propyl-derived Quinolone
a
b
c
d
Scheme 1: Synthesis of the target
compounds 6a–i. Reagents and
conditions: (a) Fuming nitric acid, Ac
2
O,
0
°C, 4 h; (b) toluene, reflux, 16 h; (c)
e
f
g
2 3
con.HCl, reflux, 2 h; (d) Gycidol, K CO ,
EtOH, reflux, 16 h; (e) pyridine, MsCl,
DMAP, 10 °C, 2 h; (f) EtOAc, DBU, r.t.,
h; (g) quinolones, EtOH, reflux, 16 h.
2
tory Standards Institute guidelines (24). A series of twofold
dilutions of the test compounds 6a–o and gatifloxacin were
prepared in DMSO (1 mL). Each dilute was added to mol-
ten Mueller-Hinton Agar (MHA) media at 56 °C to obtain
the desired final concentrations ranging from 1280 to
favorable free energy of binding were selected as the
resultant complex structures.
Results and Discussion
0.031 lg/mL. The turbidity of bacterial suspensions were
adjusted to approximately 0.5 McFarland standard (approx-
Chemistry
8
imately 1.5 9 10 CFU/mL) and further diluted to give
The synthetic routes adopted to obtain the target com-
pounds 6a–o were diagramed in Schemes 1 and 2. The
structures of target compounds were confirmed by IR,
NMR and MS spectral data. As depicted in Scheme 1,
2-chloro-4-nitroimdazole 10 was synthesized using the
reported procedure (27). Nitration of commercially available
8
1
0 CFU/mL. Plates were inoculated with 1 lL of the
appropriate bacterial suspension and incubated at 35 °C
for 16 h. The MICs were the lowest concentration of the
test compound at which no growth was observed on the
plate. Media without any drugs was made as control.
4
-nitiroimidazole 7 with fuming nitric acid in acetic anhy-
dride to give 1,4-dinitroimidazole 8, which was subse-
quently undergone thermal rearrangement in toluene to
obtain 2,4-dinitroimidazole 9. Compound 9 was then halo-
genated with concentrated hydrochloric acid to afford
2-chloro-4-nitroimdazole 10. According to the reported
procedure (28,29), ring-opening reaction of compound 10
with glycidol gave compound 11, then sulfonating of com-
pound 11 with Msyl chloride/pyridine and cyclization with
1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) at room temper-
ature gave key intermediate 2-chloro-4-nitro-1-(oxiran-
2-ylmethyl)-1H-imidazole 13. Condensation of compounds
13 with commercially available quinolones provided target
compounds 6a–i (Table 1).
Docking study
The automated docking studies were carried out using
AutoDock version 4.2 (25). The 3.5 A crystal structure of to-
ꢀ
poisomerase II DNA-gyrase (PDB ID: 2XCT) (26) was
derived from PDB. The Discovery Studio 2.5 (Accelrys, Inc.,
San Diego, CA, USA) package was used to prepare the
docking files. The protein targets were prepared by remov-
ing water molecules and bound ligands. Polar hydrogens
were added. The manganese ion at the active site was
retained and the charge was set to +2 e (26). For the
ligands, the protonation state was adjusted to physiological
pH, specifically, carboxylic acid moieties were deprotonated
and amino groups were protonated. Conjugate gradient
minimizations with CHARMm forcefield were performed.
The synthesis of compounds 6j–o (Table 1) was depicted
in Scheme 2. Compounds 6j–l were synthesized by
the condensation of quinolones with ornidazole (4) in
The grid size was set to 40 9 50 9 60 points in the x, y
ꢀ
and z dimensions, with a grid spacing of 0.375 A centered
on the original ligand in crystal structure complex. Then
automated docking studies were carried out to evaluate
the binding free energy of the three selected compounds
within the macromolecules. The Lamarckian genetic algo-
rithm was chosen to search for the best conformers. The
parameters were set using the software ADT (AutoDock-
Tools package, version 1.5.4) (La Jolla, CA, USA). Default
settings were used with an initial population of 50 ran-
domly placed individuals,
a
maximum number of
6
7
2
.5 9 10 energy evaluations, and a maximum number of
.7 9 10 generations. A mutation rate of 0.02 and a
4
crossover rate of 0.8 were chosen. Simulations were
ranked according to the docked energy between the pro-
ꢀ
tein and the ligand and clustered together by <2 A in root-
Scheme 2: Synthesis of the target compounds 6j–o. Reagents
mean-square deviation (RMSD). The results of the most
2
and conditions: (a), quinolones, KOH, H O/EtOH, reflux, 12 h.
Chem Biol Drug Des 2014
7

Li et al.
Table 1: Structures and calculated physicochemical parameters of the target compounds 6a–o
O
O
O
O
O
O
F
F
Cl
F
A
OH
N
OH
N
OH
OH
N
OH
OH
O2N
N
A
X
N
R
N
A
X
N
R
N
X
N
R
O2N
O2N
6a-6i
6j-l
6m-o
a
b
b
ꢀ
2b
Compound
A
X
R
clogP
solubility
TPSA A
6
a
q
q
C-OCH
3
Cyclopropyl
À0.70
À4.13
157.1
N
N
n
n
H
6
b
N
C-OCH3
Cyclopropyl
À0.39
À4.65
157.1
N
H
q
q
6
6
6
6
6
6
6
c
d
e
f
CH
N
Ethyl
Ethyl
Ethyl
À1.08
À1.55
À0.66
À1.21
À0.96
À1.43
À0.79
À3.27
À3.52
À3.96
À3.66
À3.73
À3.99
À4.37
147.9
160.8
147.9
147.9
147.9
160.8
157.1
N
N
N
N
N
N
N
n
n
n
n
n
N
N
N
N
N
q
q
q
q
CF
CF
CH
N
2 2
FCH CH -
g
h
i
Cyclopropyl
Cyclopropyl
Cyclopropyl
n
n
C-OCH
3
3
N
q
N
6
6
6
j, 6m
k, 6n
l, 6o
q
q
C-OCH
Cyclopropyl
Cyclopropyl
Cyclopropyl
À1.15
À0.83
À1.24
À3.25
À3.77
À3.49
157.1
157.1
157.1
N
N
H
n
n
N
C-OCH3
N
H
C-OCH
3
N
q
n
N
Gatifloxacin
–
–
–
À1.27
À3.72
82.11
a
q is quinolone nucleus; n is 2-hydroxy-3-(nitroimidazolyl)-propyl.
clogP, solubility and TPSA (topological polar surface area) were calculated by OSIRIS Property Explorer Version 2.
b
H
2
O/ethanol (1/1) in the presence of KOH at reflux tem-
The presence of a 2-hydroxy-3-(nitroimidazolyl)-propyl
perature. (R)-2-hydroxy-3-(2-methyl-5-nitro-1H-imidazol-1-
yl)propyl-derived quinolones 6m–o were synthesized in
the same condition by using enantiomerically pure (S)-
ornidazole (14) as starting material to determine the influ-
ence of the geometries for activity.
group in C-7 position of quinolones could influence the
physicochemical properties of quinolone compounds. Their
physicochemical parameters were calculated and pre-
sented in Table 1. From the parameters, it was observed
that all the target compounds exhibited high TPSA values
8
Chem Biol Drug Des 2014

2-Hydroxy-3-(nitroimidazolyl)-propyl-derived Quinolone
Table 2: In vitro antibacterial activity of the target compounds 6a–o
MIC (lg/mL)
Gram-positive
Gram-negative
a
b
c
d
e
f
g
h
Compound
S.e.
MSSE
MRSE
S. a.
MSSA
MRSA
E. c.
K. p.
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
a
b
c
d
e
f
0.03
0.125
32
4
0.25
16
2
2
0.5
1
0.125
0.25
0.25
0.25
>32
2
2
16
2
2
0.5
1
0.25
0.5
0.03
0.125
>32
4
0.125
2
2
0.125
0.25
1
0.125
0.125
1
0.5
>32
>32
16
>32
8
0.5
0.5
>32
16
4
16
4
4
0.5
1
0.5
0.5
32
0.125
1
0.125
8
16
>32
32
32
32
32
16
8
32
8
8
16
2
32
16
4
2
>32
>32
4
>32
16
16
4
8
4
4
32
2
>32
>32
>32
>32
32
>32
>32
>32
>32
>32
8
g
h
i
8
0.5
32
0.25
0.5
32
0.125
1
0.125
j
k
l
2
32
1
16
m
n
o
16
32
0.125
1
32
0.03
0.25
0.06
0.03
0.25
0.06
8
0.06
Gatifloxacin
0.06
1
a
Staphylococcus epidermidis ATCC 12228.
Methicillin-sensitive Staphylococcus epidermidis clinical isolates.
Methicillin-resistant Staphylococcus epidermidis clinical isolates.
S. a., Staphylococcus aureus ATCC 29213.
b
c
d
e
f
Methicillin-sensitive Staphylococcus aureus clinical isolates.
Methicillin-resistant Staphylococcus aureus clinical isolates.
g
E. c., Escherichia coli ATCC 700603.
K. p., Klebsiella pneumoniae ATCC 25922.
h
when compared to gatifloxacin and similar lipophilicity
more potent than reference drug gatifloxacin. The MIC val-
ues of compounds 6a–o against S. aureus indicated some
compounds possessed a comparable or better activity in
comparison with reference drug. Moxifloxacin analog 6n
showed the most potent activity (MIC = 2 mg/mL) against
MRSA, and its activity was eightfold more than that of
gatifloxacin. In addition, compounds 6a, i, k and l
exhibited potent activity (MIC = 8 mg/mL) against MRSA,
which were twofold more potent than gatifloxacin. For
Gram-negative pathogens, compounds 6a–b, 6e, 6i–6l
and 6n–o had respectable in vitro activity against E. coli
(MIC = 2–8 lg/mL), but were less active than reference
drug (MIC = 0.06 lg/mL). All synthesized compounds
showed poor or no activity (MIC > 32 lg/mL) against
K. pneumoniae except compounds 6l and 6n, with MIC of
2 and 1 lg/mL, were equipotent to the standard gatifloxa-
cin (MIC = 1 lg/mL).
(
clogP around À1) and solubility (solubility around À3.5) to
reference drug gatifloxacin.
Antibacterial evaluation
The target compounds 6a–o were tested for their in vitro
antibacterial activity against eight bacterial strains including
Staphylococcus epidermidis ATCC 12228, Staphylococcus
aureus ATCC 29213, Escherichia coli ATCC 700603,
Klebsiella pneumonia ATCC 25922, methicillin-sensitive
Staphylococcus epidermidis (MSSE), methicillin-resistant
Staphylococcus epidermidis (MRSE), methicillin-sensitive
Staphylococcus aureus (MSSA) and MRSA. The minimum
inhibitory concentration values (MICs) were determined by
a standard agar dilution method (24) using gatifloxacin as
reference drug. The results of MIC values were listed in
Table 2.
Among synthesized compounds, moxifloxacin analog 6n
displayed the most potent activity against Gram-positive
strains including S. epidermidis (MIC = 0.06 lg/mL),
MSSE (MIC = 0.125 lg/mL), MRSE (MIC = 0.03 lg/mL),
S. aureus (MIC = 0.125 lg/mL), MSSA (MIC = 0.125 lg/
mL), MRSA (MIC = 2 lg/mL), compared with other syn-
thesized compounds and reference drug gatifloxacin. Its
inhibitory activity against K. pneumoniae (MIC = 1 mg/mL)
The MIC values of compounds 6a–o against S. epidermi-
dis strains indicated that most compounds displayed
potent activity against both standard strains and clinical
isolates with respect to gatifloxacin. Gatifloxacin analog 6a
and moxifloxacin analog 6n exhibited the most potent
inhibitory activity against S. epidermidis and MRSE with
the same MIC value of 0.03 mg/mL, which were twofold
Chem Biol Drug Des 2014
9

Li et al.
(
a)
(b)
(
c)
(d)
Figure 2: The binding model of docked compounds with topoisomerase II DNA-gyrase. The enzyme is shown as cartoon, while residues
(
(
(
white) in the active site and docked compounds are shown as sticks. H-bonding interactions are shown in orange dotted lines.
A) ciprofloxacin (orange) and original X-ray structure of ciprofloxacin (green), (B) gatifloxacin (cyan) and original X-ray structure ciprofloxacin
green), (C) compound 6n (yellow), (D) compound S-6n (magenta). This figure was made using PyMol.
was equal to reference drug. The results were in accor-
dance with the reported finding that one of the promising
hits originated from moxifloxacin chemical class (22,23).
Docking analysis
With the aim to investigate binding model and understand
the potent activity observed, compound 6n with the most
potent antibacterial activity was selected for docking study
by using AutoDock 4.2 software (25). Gatifloxacin and (S)-
isomer of compound 6n (S-6n) were also docked into the
active site for comparison. To evaluate the docking accu-
racy of AutoDock 4.2, the cocrystallized ligand ciprofloxa-
cin was redocked within the active site of topoisomerase II
DNA-gyrase (26). As shown in Figure 2, Autodock was
successful in reproducing the binding position for cipro-
Structurally, the C-8 methoxy group substituted com-
pounds except 6m were statistically better than the
remaining tested compounds in antibacterial activity, dem-
onstrating that introduction of the methoxy group at the
C-8 position of quinolone seems to contribute to the anti-
bacterial activity. The naphthyridine derivatives 6d and 6h
were more potent than its corresponding quinolone cong-
eners 6c and 6g, Thus, replacement of CH at 8-position
with N increased the antibacterial activity. The comparison
of the MIC values of 2-chloro-4-nitroimidazole derivatives
ꢀ
floxacin, showing a RMSD of 0.62 A for all atoms in com-
parison with original poses of X-ray structure complexes
(30). The binding models of gatifloxacin, compound 6n
and S-6n with DNA-gyrase were depicted in Figure 2.
6
a–b, 6i and corresponding 2-methyl-5-nitroimidazole
derivatives 6l–o revealed that the substitution position of
nitro group at imidazole has no prominent effect on activ-
ity. (R)-isomers 6m–o displayed dramatically dissimilar anti-
bacterial activity with their racemate 6j–l, which suggested
that the stereochemistry of 2-hydroxy at the propyl group
may play an important role for the binding of the target
compounds with DNA-gyrase.
As shown in Figure 2, gatifloxacin in binding model nearly
took the same pose with that observed in the X-ray struc-
ture of DNA-gyrase ciprofloxacin complexes (Figure 2B).
The docked gatifloxacin formed two coordination bonds
2+
with Mn ion by the carbonyl and carboxylate groups of
ꢁ
ꢁ
ꢀ
ꢀ
quinolone scaffold with 1.5 A and 2.0 A distance, respec-
1
0
Chem Biol Drug Des 2014

2-Hydroxy-3-(nitroimidazolyl)-propyl-derived Quinolone
tively, and two p-p stacks between quinolone ring and
pyrimidine rings in DG-8 and DG-9. The nitrogen atom of
piperazine ring formed two hydrogen bonds with Arg 456
Acknowledgments
Authors are really grateful to Prof. Wenbin Shen, China
pharmaceutical University for providing H NMR &
ꢁ
ꢁ
ꢀ
ꢀ
1
13
(
2.3 A) and DC-13 (2.4 A). The docking binding model of
C
compound 6n indicated that compound 6n was well filled
in the active site (Figure 2C). The binding model of quino-
lone nucleus of compound 6n was similar with that of cip-
rofloxacin and gatifloxacin. Two strong p–p stacks were
formed between the quinolone moiety of compound 6n
and the purine rings of DG-8 and DG-9. The carbonyl and
carboxylate groups of quinolone scaffold formed two coor-
NMR spectra. This study was supported by the China
National Key Hi-Tech Innovation Project for the R&D of
Novel Drugs (No. 2013ZX09301303-002).
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