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Article history: Metronidazole has a broad-spectrum antibacterial activity. Hereby a series of novel metronidazole deriv-
Received 22 January 2014 atives were designed and synthesized based on nitroimidazole scaffold in order to find some more potent
Revised 3 March 2014 antibacterial drugs. For these compounds which were reported for the first time, their antibacterial activ-
Accepted 4 March 2014
ities against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus were
Available online 13 March 2014
tested. These compounds showed good antibacterial activities against Gram-positive strains. Compound
4m represented the most potent antibacterial activity against S. aureus ATCC 25923 with MIC of 0.003 lg/
Keywords:
mL and it showed the most potent activity against S. aureus TyrRS with IC50 of 0.0024 lM. Molecular
Metronidazole derivatives
Antibacterial activities
docking of 4m into S. aureus tyrosyl-tRNA synthetase active site were also performed to determine the
S. aureus TyrRS probable binding mode.
Molecular docking Ó 2014 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmc.2014.03.004
0968-0896/Ó 2014 Elsevier Ltd. All rights reserved.
2410 S.-F. Wang et al. / Bioorg. Med. Chem. 22 (2014) 2409–2415
O
CH 3 N N
Cl O O
Cl N a
N S Cl N S
OH O
O O
Cl O2 N O2 N
N N
N Cl N 1 2
N N
O O O N
OH R
N
Cl Cl O 2N N
O O b N
Ketoconazole Miconazole Metronidazole HN N R N N
N S
O
O NO2
O2N
Scheme 1. Chemical structure of metronidazole.
2 3a-3o 4a-4o
especially ketoconazole, it also contains piperazine skeleton. This
promoted us to synthesize new derivatives of metronidazole with Scheme 2. Reagents and conditions: (a) CH2Cl2, TEA, 0 °C, 5 h; (b) K2CO3, DMF,
80 °C, 22–24 h.
piperazine skeleton for the sake of finding new efficacy antibacterial
agents. Hence, we synthesized a series of novel metronidazole zole and piperazine derivatives. The key compound MET-OTs (2-
derivatives owing piperazine skeleton (4a–4o). In our preliminary (2-methyl-5-nitro-1H-imidazol-1-yl)ethyl 4-methylbenzenesulfonate,
work, the molecular docking was performed to validate which anti- compound 1) was synthesized by the method in our previous
bacterial target protein the designed compounds can work, the paper.35 The research showed when the ratio of MET-OTs and piper-
compounds were fitted into the ATP binding site of FabH (PDB code: azine derivatives was 1:1.2, the reaction temperature was 80 °C, and
1HNJ), bacterial DNA gyrase (PDB code: 3G75), bacterial thymidyl- the reaction time was 24 h, compounds 4a–4o were obtained with
ate kinase (PDB code: 4HEJ) and S. aureus tyrosyl-tRNA synthetase the higher yield. The chemical structures of these metronidazole
(PDB code: 1JIJ).30–34 The results have been plotted as a line-scatter derivatives were summarized in Table 1. All of the synthetic com-
graph and presented in Figure 1. It showed that the interaction en- pounds were characterized by 1H NMR, elemental analysis and mass
ergy between the designed compounds and protein 1JIJ is the low- spectrum, and they gave satisfactory analytical and spectroscopic
est. It means that the designed compounds are likely to display data, which were in full accordance with their depicted structures.
more potent inhibitory activity against S. aureus tyrosyl-tRNA syn-
thetase. So we studied their antibacterial activities against Bacillus 2.2. Biological activity
subtilis (B. subtilis) and Staphylococcus aureus (S. aureus) Escherichia
coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), and S. aureus 2.2.1. Antibacterial activity
tyrosyl-tRNA synthetase (PDB code: 1JIJ) inhibitory activities. The The synthesized compounds were tested for their antibacterial
results showed that the compounds showed good activity against activity against two Gram-negative bacterial strains: E. coli and P.
Gram-positive bacterial but no activity against the Gram-negative aeruginosa and two Gram-positive bacterial strains: B. subtilis and
bacterial. Docking simulation was performed using the X-ray crys- S. aureus by MTT method with MH medium (Mueller-Hinton med-
tallographic structure of the TyrRS of S. aureus in complex with ium: casein hydrolysate 17.5 g, soluble starch 1.5 g, beef extract
the most potent inhibitor to explore the binding mode of the com- 1000 mL). The MICs (minimum inhibitory concentrations) of the
pound at the active site. compounds against these bacteria were reported in Table 2, the
activity of reference drugs Penicillin G and Chloramphenicol was
2. Results and discussion also included. The results revealed that those compounds showed
good activity against Gram-positive bacterial but inactive against
2.1. Chemistry Gram-negative bacterial.
Most of the new compounds exhibited good inhibitory activities
Compounds 4a–4o were synthesized by the routes outlined in against both B. Subtilis and S. Aureus. As shown in Table 2. Compounds
Scheme 2. They were first designed and synthesized from metronida- 4l and 4m showed most potent activities with MIC values of 0.033,
Figure 1. The CDOCKER_INTERACTION_ENERGY (kcal/mol) obtained from the docking study of all synthesized compounds by the CDOCKER protocol (Discovery Studio 3.5,
Accelrys, Co. Ltd).
S.-F. Wang et al. / Bioorg. Med. Chem. 22 (2014) 2409–2415 2411
3. Conclusion
4. Experiments
4.2. General method of synthesis of metronidazole derivatives 4.44–4.47 (t, J = 5.26 Hz, 2H, CH2), 3.51–3.63 (s, 4H, –CH2CH2–),
2.94–2.99 (s, 4H, –CH2CH2–), 2.50 (s, 3H, CH3). ESI-MS: 334.32
2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl 4-methylbenzene- (C16H21FN5O2, [M+H]+). Anal. Calcd for C16H20ClN5O2: C, 57.65; H,
sulfonate (2) was prepared according to our previous paper. Metro- 6.05; N, 20.01. Found: C, 57.60; H, 6.02; N, 20.02.
nidazole (3.14 g, 20 mmol) and Et3N (3.0 mL, 22 mmol) were
dissolved in CH2Cl2 (20 mL), and 4-methyl-benzenesufonyl chlo- 4.2.6. 1-(3-Methoxyphenyl)-4-(2-(2-methyl-5-nitro-1H-imidazol-
ride (3.83 g, 20.1 mmol) in CH2Cl2 (10 mL) was added. The reaction 1-yl)ethyl)piperazine (4f)
mixture was stirred at 0 °C for 5 h followed by the addition of Brown, yield: 61%, mp: 45–48 °C. 1H NMR (400 MHz, CDCl3): d
30 mL ice water, and then the layer was separated and the aqueous 7.96 (s, 1H), 7.16–7.20 (t, J = 8.04 Hz, 1H, ArH), 6.50–6.53
layer was extracted with ethyl acetate (2 30 mL). The organic (t, J = 5 Hz, 3H, ArH), 4.61–4.63 (t, J = 5.26 Hz, 2H, CH2), 4.43–4.46
layer was combined and washed with saturated NaHCO3, and dried (t, J = 5.28 Hz, 2H, CH2), 3.78 (s, 3H, CH3O-), 3.47–3.60 (s, 4H, –CH2-
with anhydrous Na2SO4 for 0.5 h. Removal of the solvent gave a CH2–), 3.09–3.13 (s, 4H, –CH2CH2–), 2.49 (s, 3H, CH3). ESI-MS:
slight-yellow crystal of compound 2 (MET-OTs). Compounds 346.36 (C17H24N5O3, [M+H]+). Anal. Calcd for C17H23N5O3: C,
4a–4o were synthesized by the following procedure. MET-OTs 59.12; H, 6.71; N, 20.28. Found: C: 59.11; H: 6.71; N, 20.2.
(2 mmol) and K2CO3 (2 mmol) were dissolved in DMF (20 mL),
and then one of those substituted piperazines was added. The reac- 4.2.7. 1-(3-Chlorophenyl)-4-(2-(2-methyl-5-nitro-1H-imidazol-
tion was stirred at 80 °C for 22–24 h. The reaction mixture was 1-yl)ethyl)piperazine (4g)
poured in water and extracted with ethyl acetate (3 50 mL). Brown, yield: 56%, mp: 66–68 °C. 1H NMR (400 MHz, CDCl3): d
The organic layer was combined and dried with anhydrous Na2SO4 7.96 (s, 1H), 7.15–7.19 (t, J = 8.12 Hz, 1H, ArH), 6.84–6.85 (d,
for 0.5 h. After the reaction mixture was vacuum distillated, the J = 6.48 Hz, 2H, ArH), 6.75–6.78 (m, 1H, ArH), 4.61–4.64 (t,
target product was separated by column chromatography. J = 5.28 Hz, 2H, CH2), 4.43–4.46 (t, J = 5.26 Hz, 2H, CH2), 3.47–3.59
(s, 4H, –CH2CH2–), 3.10–3.14 (s, 4H, –CH2CH2–), 2.49 (s, 3H, CH3).
4.2.1. 1-(2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl)-4-phenyl ESI-MS: 350.76 (C16H21ClN5O2, [M+H]+). Anal. Calcd for C16H20-
piperazine (4a) ClN5O2: C, 54.94; H, 5.76; N, 20.02. Found: C, 54.92; H,5.75; N,
Brown, yield: 47%, mp: 108–110 °C. 1H NMR (400 MHz, CDCl3): 20.02.
d 7.97 (s, 1H), 7.25–7.29 (m, 2H, ArH), 6.90–6.92 (d, J = 7.64 Hz, 3H,
ArH), 3.49–3.61 (s, 4H, –CH2CH2–), 3.09–3.13 (s, 4H, –CH2CH2–), 4.2.8. 1-(2-Methoxyphenyl)-4-(2-(2-methyl-5-nitro-1H-
2.49 (s, 3H, CH3), ESI-MS: 316.28 (C16H22N5O2, [M+H]+). Anal. Calcd imidazol-1-yl)ethyl)piperazine (4h)
for C16H21N5O2: C, 60.94; H, 6.71; N, 22.21. Found: C, 60.92; H, Yellow, yield: 52%, mp: 112–115 °C. 1H NMR (400 MHz, CDCl3):
6.72, N, 22.23. d 7.93 (s, 1H), 6.99–7.03 (m, 1H, ArH), 6.84–6.92 (m, 3H, ArH),
4.59–4.60 (d, J = 5.28 Hz, 2H, CH2), 4.41–4.44 (t, J = 5.22 Hz, 2H,
4.2.2. 1-(4-Fluorophenyl)-4-(2-(2-methyl-5-nitro-1H-imidazol- CH2), 3.85 (s, 3H, CH3O-), 3.49–3.61 (s, 4H, –CH2CH2–), 2.93–2.99
1-yl)ethyl)piperazine (4b) (s, 4H, –CH2CH2–), 2.47 (s, 3H, CH3). ESI-MS: 346.36 (C17H24N5O3,
Brown, yield: 51%, mp: 65–68 °C. 1H NMR (400 MHz, CDCl3) : d [M+H]+). Anal. Calcd for C17H23N5O3: C, 59.12; H, 6.71; N, 20.28.
7.93 (s, 1H), 6.93–6.97 (t, J = 8.34 Hz, 2H, ArH), 6.83–6.85 (m, 2H, Found: C, 59.12; H, 6.70; N, 20.27.
ArH), 4.41–4.45 (t, J = 6.26 Hz, 2H, CH2), 3.04–3.07 (t, J = 4.86 Hz,
4H, –CH2CH2–), 2.71–2.72 (t, J = 6.26 Hz, 2H, CH2), 2.63–2.65 (t, 4.2.9. 1-(2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethyl)-4-(3-
J = 4.86 Hz, 4H, –CH2CH2–,), 2.52 (s, 3H, CH3). ESI-MS: 334.27 (C16- (trifluoromethyl)phenyl)piperazine (4i)
H21FN5O2, [M+H]+). Anal. Calcd for C16H20FN5O2: C, 57.65; H, 6.05; Yellow, yield: 45%, mp: 98–101 °C. 1H NMR (400 MHz, CDCl3)
N, 21.01. Found: C, 57.62, H, 6.04; N, 21.03. d:7.96 (s, 1H), 7.34–7.38 (t, J = 7.94 Hz, 1H, ArH), 7.03–7.06 (m,
3H, ArH), 4.62–4.65 (t, J = 5.26 Hz, 2H, CH2), 4.44–4.46 (t,
4.2.3. 1-(2,3-Dichlorophenyl)-4-(2-(2-methyl-5-nitro-1H-imidazol- J = 5.28 Hz, 2H, CH2), 3.49–3.62 (s, 4H, –CH2CH2–), 3.14–3.18 (s,
1-yl)ethyl)piperazine (4c) 4H, –CH2CH2–), 2.50 (s, 3H, CH3). ESI-MS: 384.33 (C17H21F3N5O2,
Yellow, yield: 47%, mp: 90–93 °C. 1H NMR (400 MHz, CDCl3): d [M+H]+). Anal. Calcd for C17H20F3N5O2: C, 53.26; H, 5.26; N,
7.95 (s, 1H), 7.12–719 (m, 2H, ArH), 6.89–6.91 (m, 1H, ArH), 18.27. Found: C: 53.25; H, 5.27; N, 18.27.
4.61–4.64 (t, J = 5.26 Hz, 2H, CH2), 4.43–4.46 (t, J = 5.24 Hz, 2H,
CH2), 3.50–3.62 (s, 4H, –CH2CH2–), 2.92–2.97 (s, 4H, –CH2CH2–), 4.2.10. 1-(2,4-Dimethylphenyl)-4-(2-(2-methyl-5-nitro-1H-imid
2.49 (s, 3H, CH3). ESI-MS: 385.15 (C16H20Cl2N5O2, [M+H]+). Anal. azol-1-yl)ethyl)piperazine (4j)
Calcd for C16H19Cl2N5O2: C, 50.01; H, 4.98; N, 18.23. Found: C, Brown, yield: 55%, mp: 130–132 °C. 1H NMR (400 MHz, CDCl3)
49.98; H, 4.99; N, 18.22. d: 7.97 (s, 1H), 6.96–7.00 (t, J = 9.34 Hz, 2H, ArH), 6.86–6.88 (d,
J = 8.04 Hz, 1H, ArH), 4.61–4.64 (t, J = 5.24 Hz, 2H, CH2), 4.44–4.47
4.2.4. 1-(2-Chlorophenyl)-4-(2-(2-methyl-5-nitro-1H-imidazol- (t, J = 5.24 Hz, 2H, CH2), 3.46–3.59 (s, 4H, –CH2CH2–), 2.77–2.82
1-yl) ethyl)piperazine(4d) (s, 4H, –CH2CH2–), 2.51 (s, 3H, CH3), 2.26 (s, 3H, CH3), 2.27 (s, 3H,
Yellow, yield: 59%, mp: 120–122 °C. 1H NMR (400 MHz, CDCl3): CH3). ESI-MS: 344.38 (C18H26N5O2, [M+H]+). Anal. Calcd for
d 7.96 (s, 1H), 7.34–7.37 (m, 1H, ArH), 7.20–7.26 (m, 1H, ArH), C18H25N5O2: C, 62.95; H, 7.34; N, 20.39. Found: C, 62.92; H, 7.36;
6.98–7.02 (m, 2H, ArH), 4.62–4.64 (t, J = 5.26 Hz, 2H, CH2), N, 20.38.
4.44–4.47 (t, J = 5.26 Hz, 2H, CH2), 3.51–3.63 (s, 4H, –CH2CH2–),
2.94–2.99 (s, 4H, –CH2CH2–), 2.50 (s, 3H, CH3). ESI-MS: 350.76 4.2.11. 1-(3,4-Dichlorophenyl)-4-(2-(2-methyl-5-nitro-1H-imid
(C16H21ClN5O2, [M+H]+). Anal. Calcd for C16H20ClN5O2: C, 54.94; azol-1-yl)ethyl)piperazine (4k)
H, 5.76; N, 20.02. Found: C, 54.88; H, 5.75, N, 20.01. Yellow, yield: 61%, mp: 106–109 °C. 1H NMR (400 MHz, CDCl3):
d 7.98 (s, 1H), 7.29–7.31 (d, J = 8.6 Hz, 1H, ArH), 6.96–6.97 (d,
4.2.5. 1-(2-Fluorophenyl)-4-(2-(2-methyl-5-nitro-1H-imidazol- J = 2.76 Hz, 1H, ArH), 6.73–6.76 (m, 1H, ArH), 4.64–4.67 (t,
1-yl)ethyl)piperazine (4e) J = 5.26 Hz, 2H, CH2), 4.46–4.48 (t, J = 5.26 Hz, 2H, CH2), 3.50–3.62
Yellow, yield: 48%, mp: 125–127 °C. 1H NMR (400 MHz, CDCl3): (s, 4H, –CH2CH2–), 3.11–3.14 (s, 4H, –CH2CH2–), 2.52 (s, 3H, CH3).
d 7.96 (s, 1H), 7.34–7.37 (m, 1H, ArH), 7.20–7.26 (m, 1H, ArH), ESI-MS: 385.15 (C16H20Cl2N5O2, [M+H]+). Anal. Calcd for C16H19Cl2-
6.98–7.02 (m, 2H, ArH), 4.62–4.64 (t, J = 5.26 Hz, 2H, CH2), N5O2: C, 50.01; H, 4.98; N, 18.23. Found: C, 50.03; H, 4.97; N, 18.24.
2414 S.-F. Wang et al. / Bioorg. Med. Chem. 22 (2014) 2409–2415
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