Synthesis and in vitro antibacterial activity of a series of novel gatifloxacin derivatives

Article abstract of DOI:10.1016/j.ejmech.2011.06.032

A series of novel gatifloxacin (GTFX) derivatives were designed, synthesized and characterized by ¹H NMR, ¹³C NMR, MS and HRMS. These derivatives were evaluated for in vitro antibacterial activity against representative Gram-positive

Full text of DOI:10.1016/j.ejmech.2011.06.032

European Journal of Medicinal Chemistry 46 (2011) 4267e4273
Contents lists available at ScienceDirect
European Journal of Medicinal Chemistry
journal homepage: http://www.elsevier.com/locate/ejmech
Original article
Synthesis and in vitro antibacterial activity of a series of novel gatifloxacin
derivatives
1
,1
*
Yun Chai , Ming-Liang Liu , Kai Lv, Lian-Shun Feng, Su-Jie Li, Lan-Ying Sun, Shuo Wang, Hui-Yuan Guo
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China
a r t i c l e i n f o
a b s t r a c t
A series of novel gatifloxacin (GTFX) derivatives were designed, synthesized and characterized by 1H
NMR, 13C NMR, MS and HRMS. These derivatives were evaluated for in vitro antibacterial activity against
representative Gram-positive and Gram-negative strains. Our results reveal that most of the target
compounds show good potency in inhibiting the growth of Staphylococcus aureus including MRSA and
Staphylococcus epidermidis including MRSE. Compounds 8, 14 and 20 have useful activity against all of the
Article history:
Received 24 January 2011
Received in revised form
7 June 2011
Accepted 23 June 2011
Available online 1 July 2011
tested Gram-positive and Gram-negative strains (MICs: 0.06e4
a broad antimicrobial spectrum (MICs: 0.06e1 g/mL) was found to be 2e32-folds more potent than the
reference drug levofloxacin and parent GTFX against Pseudomonas aeruginosa.
Ó 2011 Elsevier Masson SAS. All rights reserved.
mg/mL). In particular, 20 possessing
m
Keywords:
Gatifloxacin derivatives
Synthesis
Antibacterial activity
1. Introduction
Gram-positive pathogens, including Staphylococci, Streptococci,
and Enterococci, is relatively moderate, which has not only limited
their use in infections caused by these strains, but is also believed to
be one of the reasons for the rapidly developing quinolone resis-
tance. Thus, recent efforts have been directed toward the synthesis
of new quinolones that can provide improved Gram-positive anti-
bacterial activity, while retaining the good Gram-negative activity
of early fluoroquinolones [7,8].
Recently, oxime-functionalized pyrrolidine derivatives as novel
C-7 substituents have attracted great attention and led to the
discovery of some new fluoroquinolones, such as gemifloxacin,
zabofloxacin (DW224a) and DW286. All of the three compounds
show excellent (especially Gram-positive) antibacterial activity and
pharmacokinetic profiles [9e11].
It was reported that linking a hydroxyl group to the nitrogen
atom of the C-7 side chain of norfloxacin or ciprofloxacin causes
increased in vitro and in vivo antibacterial activity [12,13]. More-
over, we had previously synthesized a series of MXFX derivatives
and found the compound with an 3-oxobutyl group on the nitrogen
atom of the C-7 side chain of MXFX, has better in vitro and in vivo
antibacterial activity than the corresponding hydroxyl analog [14].
These research results intensified our interest, it was decided to
make structural modifications on gatifloxacin (GTFX, Scheme 1), by
introduction of diversified substituents to the nitrogen atom of the
piperazine ring. These substituents include hydroxyl or methy-
lene-/ethylene-linked cyano, carbalkoxy, acyl, oxime, alkyloxime
and hydrazone. In order to clarify rationale of the design idea, we
also initially conducted molecular docking to predict the binding
Since the discovery of norfloxacin by Koga et al. in the early
1980s [1], fluoroquinolones have become an important class of
antibiotics for the treatment of various bacterial infections in both
community and hospital settings. These antibiotics exert their
antimicrobial effect by inhibition of two type II bacterial top-
oisomerase enzymes, DNA gyrase and topoisomerase IV, which are
essential cellular enzymes that catalyze the double strand breakage
of DNA to allow strand passage and thereby control the topology
and conformation of DNA [2e4].
Structureeactivity relationship (SAR) studies of fluoroquinolone
antibacterial agents showed that the basic group at the C-7 position
is the most adaptable site for chemical change and an area that
greatly influences their potency, spectrum and safety [5,6]. Piper-
azinyl and pyrrolidinyl type side chains have been proven to be the
optimal substituents. For example, many of the early fluo-
roquinolones (ciprofloxacin and ofloxacin), have a piperazinyl
group at the C-7 position, and introduction of the noted pyrrolidine
derivatives to the fluoroquinolones (trovafloxacin and moxi-
floxacin/MXFX) resulted in a dramatic improvement of Gram-
positive activity.
Considering that the activity of most fluoroquinolones currently
on the market or under development against clinically important
* Corresponding author. Tel.: þ86 010 63036965; fax: þ86 010 63047865.
E-mail address: lmllyx@yahoo.com.cn (M.-L. Liu).
1
These authors made equal contributions to the work.
0223-5234/$ e see front matter Ó 2011 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.ejmech.2011.06.032

4268
Y. Chai et al. / European Journal of Medicinal Chemistry 46 (2011) 4267e4273
Fig. 1. Surflex-Dock scores for the novel quinolones 1e21.
affinity of the target quinoloneeenzymeeDNA complexes [15]. The
scores (Fig. 1) reflecting the fitting quality of ligandereceptor
complexes show that all of the designed derivatives (1e21)
are much more potent than LVFX and GTFX against Streptococcus
pneumoniae. We report herein the synthesis of a series of novel
GTFX derivatives and their antibacterial activity. A SAR study is
also explored to facilitate the further development of the
fluoroquinolones.
the compound required to give complete inhibition of bacterial
growth. MICs of the synthesized compounds along with the stan-
dard drugs levofloxacin (LVFX) and GTFX for comparison are
reported in Table 2.
Generally, all of the target compounds 1e21 have potent anti-
bacterial activity against the tested strains. Compouds 8, 10, 12, 14,
20 and 21 show good potency in inhibiting the growth of Staphy-
lococcus aureus including methicillin-resistant S. aureus (MRSA)
and Staphylococcus epidermidis including methicillin-resistant
S. epidermidis (MRSE) (MICs: 0.06e0.5
mg/mL). Among them,
2. Results and discussion
compounds 8, 14 and 20 possess also useful activity against
the other Gram-positive strains including S. pneumoniae, Entero-
coccus faecalis and Enterococcus faecium and all of the tested
Gram-negative strains including Escherichia coli, Klebsiella pneu-
2.1. Chemistry
Synthetic pathways to the novel GTFX derivatives 1e21 are
depicted in Scheme 1. Nucleophilic substitution or addition of GTFX
with requisite chlorinated or propenyl reactants in the presence of
triethylamine gave the target compounds 1e6 (53e82%), and the
ketones 7, 8 were prepared as the same procedure. Condensation of
7, 8 with substituted amines formed Schiff’s bases 9e20 (52e91%)
in refluxing methanol, and as far as the amine hydrochlorides were
concerned, NaHCO3 was additionally acquired for neutralization.
Introduction of a hydroxyl group to the C-7 side chain of GTFX by
oxidation rearrangement of the ketone 8 in H2O2 (30%)eNaOH
(2 N) system yields 21 (63%). Table 1 shows structures, purities,
melting points and the toxicity (CC50) of the GTFX derivatives.
Since the imino moiety can exist in the E or Z configuration, it
was necessary to determine the geometries of the Schiff’s bases
9e20. However, it was a pity that we were not successful in
preparing X-ray quality single crystals.
moniae and Pseudomonas aeruginosa (MICs: 0.5e4
The most active compound 20 has a broad antimicrobial spec-
trum against all of the tested strains (MICs: 0.06e1 g/mL) which is
generally better than the reference drug LVFX and parent GTFX
mg/mL).
m
(MICs: 0.06e16 mg/mL). In particular, 20 (MICs: 0.25e0.5 mg/mL) is
Table 1
Structures, melting points, purities and cytotoxicity of GTFX derivatives 1e21.
O
O
F
COOH
F
COOH
N
N
NR2
N
N
R1
N
n
OCH3
N
n
OCH3
9-20
1-8, 21
2.2. Pharmacology
a
Compd.
R1
R2
n
m.p. (ꢀC)
Purities
(%)
CC50
(mg/mL)
The GTFX derivatives 1e21 were evaluated for their in vitro
antibacterial activity against representative Gram-positive and
Gram-negative strains using standard techniques [16]. Minimum
inhibitory concentration (MIC) is defined as the concentration of
1
2
3
4
5
6
7
8
CN
CN
COOCH3
COOCH3
COOC2H5
COOC2H5
COCH3
COCH3
e
e
1
2
1
2
1
2
1
2
1
1
1
1
1
1
1
2
2
2
2
2
0
181e183
180e182
195e197
152e153
184e186
141e142
146e148
134e136
151e153
144e146
216e218
205e207
178e180
161e163
211e213
198e200
180e182
177e179
181e183
176e178
227e229
99.41
99.45
98.11
94.08
99.37
99.45
97.33
96.63
96.54
99.96
93.31
95.85
95.54
96.56
97.56
95.67
96.95
97.82
93.56
96.54
97.12
353.55
500
500
>1000
1000
NTb
e
e
e
e
e
e
500
9.84
e
9
OCH3
OC2H5
49.61
31.25
500
707.11
250
11.05
176.78
44.19
157.49
88.39
31.25
62.5
10
11
12
13
14
15
16
17
18
19
20
21
e
e
NHCONH2
NHCOCH3
NHCOC5H4N
NHC6H5
OH
OH
OCH3
OC2H5
e
e
e
e
e
e
e
e
NHCONH2
NHC6H5
e
e
OH
19.69
a
CC50: The 50% cellular cytotoxic concentration.
Not tested.
b
Fig. 2. Predicted three-dimensional conformations of compound 20 docked in 3FOF.

Table 2
In vitro antibacterial activity of GTFX derivatives 1e21 against selected strains.
Strains
MIC(
1
m
g/mL)
2
3
4
5
6
7
8
9
10
11
12
0.25
13
14
15
16
17
18
19
0.5
2
1
1
20
21
0.125
0.25
0.25
0.25
0.25
0.25
LVFX GTFX
S.a.
1
1
1
0.25
0.25
0.25
8
1
2
4
4
2
8
128
32
8
4
4
4
128
0.25 0.06
0.5
>128
0.25
0.125
0.25
0.25
0.25
0.25
0.25
4
2
2
0.125
0.125 >128
0.125
0.25
0.25
2
32
32
0.25
0.25
0.25
0.5
64
16
0.06
0.25
0.125
0.06
0.25 0.125
0.06 0.125
0.25 0.06
MRSA
MSSA
MRSE
MSSEꢁ1
MSSEꢁ2
S.p.1
>128 >128
16
1
2
0.5
0.25
0.25
0.25
0.25
0.25
0.25
0.25
8
32
2
2
>128
4
4
4
4
>128
>128
>128
>128
>128
0.25
2
2
0.5
128
0.5
32 >128
32 >128
32 >128
0.5
0.5
4
2
2
1
64
2
0.25
0.25
0.25
0.5
0.25
0.25
0.25 0.25
0.25 0.25
0.25 0.25
0.25 0.25
32
4
64
64
128
128
16
128
64
16
32
4
4
128
32
0.5
0.5
0.25 0.06
0.25 0.25
0.06 0.25
2
32
4
1
>128
>128
>128
>128
>128
>128
128
>128
>128
>128
>128
128
2
16
4
8
4
0.25
>128 >128 >128 >128
>128 >128 >128
>128 >128 >128 >128
>128 >128 >128 >128
>128 >128 >128 >128
>128 >128 >128 >128 128
128 >128 128 128
>128 >128 >128 >128 128
>128 >128 >128 >128
128 >128 >128 >128
>128 >128 >128 >128
32
4
0.25
4
4
4
4
0.5
4
0.5
0.5
0.5
1
0.25
4
64
>128
2
0.25
0.25
4
4
4
4
0.5
4
0.25
0.25
0.125 >128
2
0.25
4
128
0.25
>128
>128
>128
>128
128
>128
>128
>128
32
128
8
2
8
8
8
8
2
8
4
1
2
4
0.5
0.25
0.5
0.5
0.5
1
0.25
1
1
16
S.p.2
4
2
32
32
32
2
>128
>128
>128
>128
64
>128
>128
>128
>128
32
0.25
4
64
64
>128
>128
>128
>128
>128
>128
>128
>128
128
>128
>128
128
>128
>128
2
16
16
16
16
4
16
16
2
16
4
2
32
4
E.fm.1
E.fm.2
E.fs.1
E.fs.2
E.co.1
E.co.2
E.co.3
K.p.1
8
8
8
8
4
8
8
2
32
32
64
32
16
32
64
32
32
8
>128
>128
>128
>128
128
>128
>128
>128
>128
>128
>128
>128
>128
>128 16
>128 16
>128 16
>128 16
>128
>128 16
>128 16
>128
>128
>128
64
>128 64
>128
4
2
8
4
>128
>128
16
8
4
8
2
8
8
2
2
64
64
64
8
8
4
8
4
32
16
2
4
4
0.25
4
4
0.25
0.5
1
0.5
16
8
4
16
8
1
0.125
K.p.2
P.a.1
2
2
2
1
8
4
1
128 >128
128 >128 >128 >128
128
128
8
2
32
32
P.a.2
0.25
4
64
128
>128
>128
0.25 0.5
16
2
P.a.3
P.a.4
32
2
128
16
128 >128 >128 >128 128
>128 >128 >128 >128 16
>128
>128
>128
>128
>128
8
0.5
0.25
0.5
2
0.25
LVFX: Levofloxacin; GTFX: Gatifloxacin.
S.a., Staphylococcus aureus ATCC25923; MRSA, Methicillin-resistant Staphylococcus aureus 08-1; MSSA, Methicillin-sensitive Staphylococcus aureus 08-1; MRSE, Methicillin-resistant Staphylococcus epidermidis 09-4; MSSE-1,
Methicillin-sensitive Staphylococcus epidermidis 09-3; MSSE-2, Methicillin-sensitive Staphylococcus epidermidis 09-6; S.p.1, Streptococcus pneumonia 08-2; S.p.2, Streptococcus pneumonia 08-4; E.fm.1, Enterococcus faecium
08-2; E.fm.2, Enterococcus faecium 08-7; E.fs.1, Enterococcus faecalis 08-10; E.fs.2, Enterococcus faecalis 08-12; E.co.1, Escherichia coli ATCC25922; E.co.2, Escherichia coli 08-21; E.co.3, Escherichia coli 08-22; K.p.1, Klebsiella
pneumoniae 09-22; K.p.2, Klebsiella pneumoniae 09-23; P.a.1, Pseudomonas aeruginosa ATCC27853; P.a.2, Pseudomonas aeruginosa 09-32; P.a.3, Pseudomonas aeruginosa 09-33; P.a.4, Pseudomonas aeruginosa 09-34.

4270
Y. Chai et al. / European Journal of Medicinal Chemistry 46 (2011) 4267e4273
2e32-folds more potent than the two reference drugs (MICs:
1e16 g/mL) against P. aeruginosa.
Some compounds were further examined for cytotoxicity (CC50
The 50% cellular cytotoxic concentration) in a mammalian Vero cell
line. After 72 h of exposure, viability was assessed on the basis of
cellular conversion of MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-
diphenyltetrazolium bromide) into a formazan product and the
results are reported in Table 1. The tested compounds showed CC50
4.2.1.1. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(cyanomethyl)-3-
methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
1. 71% yield. 1H NMR (400 MHz, CDCl3) dH 0.99e1.03 (2H, m,
cyclopropyl CH2), 1.19e1.25 (5H, m, CH3, cyclopropyl CH2),
2.88e2.98 (3H, m), 3.16e3.22 (1H, m), 3.44e3.61 (4H, m), 3.82 (3H,
s, OCH3), 3.97e4.05 (2H, m), 7.89 (1H, d, J ¼ 12.0 Hz, C5-H), 8.82 (1H,
m
:
s, C2-H), 14.68 (1H, s, COOH). 13C NMR (600 MHz, DMSO-d6)
d ppm:
8.90, 8.95, 15.95, 40.75, 41.79, 50.08, 52.20, 54.24, 56.54, 62.82,
106.48 (d, J ¼ 23 Hz), 106.52, 115.28, 120.98 (d, J ¼ 9 Hz), 134.06,
138.67 (d, J ¼ 12 Hz), 145.86, 150.51, 154.61 (d, J ¼ 247 Hz), 165.58,
176.21.FAB-MS: m/z 415 (M þ H)þ. HRMS-FAB: m/z Calcd. for
C21H24FN4O4 (M þ H)þ: 415.1782; Found 415.1795.
values ranging from 9.84 to >1000 mg/mL.
3. Conclusion and discussion
In summary, a series of novel GTFX derivatives were designed,
synthesized and evaluated for their in vitro antibacterial activity
against representative Gram-positive and Gram-negative strains.
Compounds 8, 14 and 20 have good activity against all of the tested
4.2.1.2. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(2-cyanoethyl)-3-
methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
2. 68% yield. 1H NMR (400 MHz, CDCl3) dH 0.10e1.22 (7H, m,
2 ꢂ cyclopropyl CH2, CH3), 2.55e3.45 (11H, m), 3.76 (3H, s, OCH3),
3.99e4.04 (1H, m), 7.84 (1H, d, J ¼ 12.0 Hz, C5-H), 8.80 (1H, s, C2-H),
14.75 (1H, s, COOH). FAB-MS: m/z 429 (M þ H)þ. HRMS-FAB: m/z
Calcd. for C22H26FN4O4 (M þ H)þ: 429.1938; Found 429.1924.
Gram-positive and Gram-negative strains (MICs: 0.06e4
is worth noting that the most active compound 20 (MICs:
0.25e0.5 g/mL) is 2e32-folds more potent than the two reference
mg/mL). It
m
drugs against P. aeruginosa.
Overall the tested activity of the GTFX derivatives (except for 14
and 20) against S. pneumoniae is not in agreement with what we
predicted based only on inhibition of topoisomerase IV. It suggests
that both of the topoisomerase IV and DNA gyrase in Gram-positive
bacteria could be the targets of the fluoroquinolones.
Antibacterial activity of the GTFX derivatives is dependant
mainly on the substituents on the nitrogen atom of the C-7 side
chain. The relative contribution of the substituents to antibacterial
activity is as follows: 1) phenylhydrazone > ketone > semi-
carbazone > oxime > methyloxime > ethyloxime, as for the 3-oxo/
imino butyl groups (n ¼ 2); 2) phenylhydrazone > acetylhydra
zone > ketone z ethyloxime > oxime > isonicotinoylhydrazone z
methyloxime > semicarbazone, as for 2-oxo/imino propyl grou
ps (n ¼ 1). In addition, antibacterial activity of the remaining groups
is in the order: hydroxy > cyanomethyl > cyanoethyl > (ethoxyl
carbonyl)methyl > (methoxylcarbonyl)methyl z (2-methoxylcarb
onyl)>ethyl > (2-ethoxylcarbonyl)ethyl.
4.2.1.3. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(2-methoxy-2-
oxoethyl)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 3. 79% yield. 1H NMR (400 MHz, CDCl3) dH 0.99e1.22
(7H, m, 2 ꢂ cyclopropyl CH2, CH3), 2.96e3.12 (4H, m), 3.41e3.53
(5H, m), 3.75, 3.77 (6H, 2s, 2 ꢂ OCH3), 4.00e4.03 (1H, m), 7.86 (1H,
d, J ¼ 12.0 Hz, C5-H), 8.80 (1H, s, C2-H),14.76 (1H, s, COOH). 13C NMR
(600 MHz, DMSO-d6)
d ppm: 8.88, 8.94, 15.87, 40.77, 50.55, 51.07,
51.84, 53.83, 54.14, 57.14, 62.87, 106.47 (d, J ¼ 9 Hz), 106.50, 120.74
(d, J ¼ 9 Hz), 134.12, 138.99 (d, J ¼ 12 Hz), 145.75, 150.47, 155.45
(d, J ¼ 248 Hz), 165.62, 170.92, 176.27. FAB-MS: m/z 448 (M þ H)þ.
HRMS-FAB: m/z Calcd. for C22H27FN3O6 (M þ H)þ: 448.1884; Found
448.1854.
4.2.1.4. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(3-methoxy-3-
oxopropyl)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 4. 82% yield. 1H NMR (400 MHz, CDCl3) dH 0.96e1.03
(2H, m, cyclopropyl CH2), 1.12e1.28 (5H, m, CH3, cyclopropyl CH2),
2.51e2.55 (3H, m), 2.64e2.79 (2H, m), 2.90e3.18 (3H, m),
3.37e3.42 (3H, m), 3.70, 3.74 (6H, 2s, 2 ꢂ OCH3), 4.00e4.03 (1H, m),
7.84 (1H, d, J ¼ 12.0 Hz, C5-H), 8.80 (1H, s, C2-H), 14.78 (1H,
4. Experimental protocols
4.1. Chemistry
;s, COOH). 13C NMR (600 MHz, DMSO-d6)
d ppm: 8.87, 8.97, 15.37,
Melting points were determined in open capillaries and are
uncorrected. 1H NMR and 13C NMR spectra were determined on
a Varian Mercury-400 or a Varian NMR-600 spectrometer in
DMSO-d6 or CDCl3 using tetramethylsilane as an internal standard.
Fast Atom Bombardment (FAB) mass spectra and high-resolution
mass spectra (HRMS) were obtained on a MICROMASS AutoSpec
Ultima-TOF mass spectrometer. Chemical purities were determined
by HPLC using Agilent Technologies 1200 Series HPLC system
consisting of a G1311A quaternary pump, G1329A auto sampler,
G1316A oven, and G1315D diode array detector. The reagents were
all of analytical grade or chemically pure. TLC was performed on
silica gel plates (Merck, ART5554 60F254).
30.80, 40.75, 48.40, 50.53, 50.70, 51.24, 54.36, 56.99, 62.88, 106.39,
106.47 (d, J ¼ 24 Hz), 106.48, 120.66 (d, J ¼ 9 Hz), 134.07, 139.00
(d, J ¼ 12 Hz), 145.68, 150.40, 155.32 (d, J ¼ 249 Hz), 165.57, 172.55,
176.22. FAB-MS: m/z 462 (M þ H)þ. HRMS-FAB: m/z Calcd. for
C23H29FN3O6 (M þ H)þ: 462.2040; Found 462.2047.
4.2.1.5. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(2-ethoxy-2-
oxoethyl)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 5. 53% yield. 1H NMR (400 MHz, CDCl3) dH 0.99e1.24
(7H, m, 2 ꢂ cyclopropyl CH2, CH3), 1.30 (3H, t, J ¼ 7.0 Hz, OCH2CH3),
2.98e3.13 (4H, m), 3.40e3.50 (5H, m), 3.77 (3H, s, OCH3), 4.01e4.03
(1H, m), 4.20 (2H, q, J ¼ 7.0 Hz, OCH2CH3), 7.84 (1H, d, J ¼ 12.0 Hz,
C5-H), 8.79 (1H, s, C2-H), 14.76 (1H, s, COOH). 13C NMR (400 MHz,
4.2. Synthesis
CDCl3) d ppm: 9.41, 9.51, 14.24, 16.17, 40.50, 50.82, 52.56, 54.61,
54.86, 57.40, 60.49, 62.53, 107.61, 108.02 (d, J ¼ 24 Hz), 121.57
(d, J ¼ 9 Hz), 133.89, 139.31 (d, J ¼ 11 Hz), 145.28, 149.76, 155.98
(d, J ¼ 252 Hz), 166.68, 170.55, 176.92. FAB-MS: m/z 462 (M þ H)þ.
HRMS-FAB: m/z Calcd. for C23H29FN3O6 (M þ H)þ: 462.2040; Found
462.2032.
4.2.1. General procedure for the preparation of compounds 1e8
A mixture of 1-cyclopropyl-6-fluoro-8-methoxyl-7-(3-methyl-
1-piperidin-1-yl)-1,4-dihydro-4-oxo-quinoline-3-carboxylic acid
(gatifloxacin, 10.0 mmol), chlorinated or propenyl reactants
(20.0 mmol) and triethylamine (20.0 mmol) in anhydrous ethanol
(25 mL) was stirred for 5e8 h at 50 ꢀC under an atmosphere of
nitrogen. The precipitate obtained was filtered and recrystallized
from methanol to give the title compounds 1e8 as off-white solids.
4.2.1.6. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(3-ethoxy-3-
oxopropyl)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 6. 61% yield. 1H NMR (400 MHz, CDCl3) dH 0.96e1.21

Y. Chai et al. / European Journal of Medicinal Chemistry 46 (2011) 4267e4273
4271
(7H, m, 2 ꢂ cyclopropyl CH2, CH3), 1.28 (3H, t, J ¼ 7.0 Hz, OCH2CH3),
2.51e2.52 (3H, m), 2.65e2.77 (2H, m), 2.92e3.15 (3H, m),
3.37e3.42 (3H, m), 3.74 (3H, s, OCH3), 4.00e4.03 (1H, m), 4.16 (2H,
q, J ¼ 7.0 Hz, OCH2CH3), 7.84 (1H, d, J ¼ 12.0 Hz, C5-H), 8.79 (1H, s,
0.96e1.23 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 1.26 (3H, t, J ¼ 7.0 Hz,
OCH2CH3), 1.92 (3H, s, CH3), 2.39e2.44 (1H, m), 2.63e2.66 (1H, m),
2.83e2.86 (2H, m), 3.08e3.13 (1H, m), 3.37e3.50 (4H, m), 3.76 (3H,
s, OCH3), 4.00e4.03 (1H, m), 4.10 (2H, q, J ¼ 7.0 Hz, OCH2CH3), 7.85
C2-H), 14.78 (1H, s, COOH). 13C NMR (400 MHz, CDCl3)
d
ppm: 9.44,
(1H, d, J ¼ 12.0 Hz, C5-H), 8.80 (1H, s, C2-H), 14.79 (1H, s, COOH). 13
C
9.59, 14.23, 15.82, 31.38, 40.48, 48.88, 50.81, 51.42, 55.11, 57.31,
60.56, 62.68, 107.80, 108.13 (d, J ¼ 23 Hz), 121.70, 133.95, 139.25,
145.21, 149.84, 155.95 (d, J ¼ 250 Hz), 166.72, 172.56, 177.00. FAB-
MS: m/z 476 (M þ H)þ. HRMS-FAB: m/z Calcd. for C24H31FN3O6
(M þ H)þ: 476.2197; Found 476.2181.
NMR (400 MHz, CDCl3) d ppm: 9.41, 9.54, 13.13, 14.63, 15.91, 40.50,
50.93 51.39, 55.91, 57.46, 57.70, 62.43, 68.98, 107.63, 108.08 (d,
J ¼ 23 Hz), 121.57, 133.89, 139.50, 145.25, 149.77, 155.48, 156.03 (d,
J ¼ 250 Hz), 166.70, 176.93. FAB-MS: m/z 475 (M þ H)þ. HRMS-FAB:
m/z Calcd. for C24H32FN4O5 (M þ H)þ: 475.2357; Found 475.2362.
4.2.1.7. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(2-oxopropyl)-3-
methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
7. 73% yield. 1H NMR (400 MHz, CDCl3) dH 0.97e1.00 (2H, m,
cyclopropyl CH2), 1.10 (3H, d, J ¼ 6.4 Hz, CCH3), 1.18e1.24 (2H, m,
cyclopropyl CH2), 2.20 (3H, s, COCH3), 2.67e2.90 (3H, m), 3.11e3.19
(2H, m), 3.40e3.59 (4H, m), 3.77 (3H, s, OCH3), 4.00e4.04 (1H, m),
7.86 (1H, d, J ¼ 12.0 Hz, C5-H), 8.80 (1H, s, C2-H), 14.77 (1H, s,
4.2.2.3. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(carbamoylhy-
drazono)propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquino-
line-3-carboxylic acid 11. 63% yield. 1H NMR (400 MHz, CDCl3) dH
0.97e1.26 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 1.91 (3H, s, CH3),
2.39e2.45 (1H, m), 2.64e2.89 (3H, m), 3.08e3.14 (1H, m),
3.38e3.57 (4H, m), 3.76 (3H, s, OCH3), 4.00e4.03 (1H, m), 7.51 (1H,
s, NH), 7.87 (1H, d, J ¼ 12.0 Hz, C5-H), 8.81 (1H, s, C2-H), 14.76 (1H, s,
COOH). 13C NMR (400 MHz, CDCl3)
d
ppm: 9.43, 9.56, 16.11, 27.80,
COOH). 13C NMR (600 MHz, DMSO-d6)
d ppm: 8.86, 8.95, 14.18,
40.50, 50.72, 52.97, 55.66, 57.29, 62.62, 63.90, 107.73, 108.13 (d,
J ¼ 23.5 Hz), 121.75, 133.92, 139.22, 145.30, 149.82, 155.98 (d,
J ¼ 252 Hz), 166.70, 176.99. FAB-MS: m/z 432 (M þ H)þ. HRMS-FAB:
m/z Calcd. for C22H27FN3O5 (M þ H)þ: 432.1935; Found 432.1905.
15.33, 40.75, 50.54, 51.14, 55.37, 57.00, 60.35, 62.88, 106.50, 106.62,
120.68 (d, J ¼ 9 Hz), 134.12, 139.03 (d, J ¼ 12 Hz), 145.72, 147.37,
150.47, 155.47 (d, J ¼ 247 Hz), 157.13, 165.63, 176.27. FAB-MS: m/z
489 (M þ H)þ. HRMS-FAB: m/z Calcd. for C23H30FN6O5 (M þ H)þ:
489.2262; Found 489.2250.
4.2.1.8. 1-Cyclopropyl-6-fluoro-8-methoxy-7-[4-(3-oxobutyl)-3-
methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
8. 77% yield. 1H NMR (400 MHz, CDCl3) dH 0.96e1.24 (7H, m,
2 ꢂ cyclopropyl CH2, CCH3), 2.20 (3H, s, COCH3), 2.48e2.68 (5H, m),
2.90e3.16 (3H, m), 3.37e3.42 (3H, m), 3.74 (3H, s, OCH3), 4.00e4.03
(1H, m), 7.83 (1H, d, J ¼ 12.0 Hz, C5-H), 8.78 (1H, s, C2-H), 14.77 (1H,
4.2.2.4. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(acetylhydrazono)
propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 12. 65% yield. 1H NMR (400 MHz, CDCl3) dH 0.97e1.24
(7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 1.91 (3H, s, CH3), 2.28 (3H, s,
COCH3), 2.45e2.49 (1H, m), 2.69e2.96 (3H, m), 3.08e3.13 (1H, m),
3.35e3.57 (4H, m), 3.77 (3H, s, OCH3), 4.02e4.03 (1H, m), 7.87 (1H, d,
J ¼ 12.0 Hz, C5-H), 8.28 (1H, s, NH), 8.81 (1H, s, C2-H), 14.77 (1H, s,
COOH). FAB-MS: m/z 488 (M þ H)þ. HRMS-FAB: m/z Calcd. for
C24H31FN5O5 (M þ H)þ: 488.2309; Found 488.2315.
br, COOH). 13C NMR (400 MHz, CDCl3)
d ppm: 9.42, 9.58, 15.73,
30.30, 40.36, 40.48, 47.96, 50.78, 51.44, 55.46, 57.32, 62.66, 107.72,
108.10 (d, J ¼ 23 Hz), 121.66, 133.94, 139.40, 145.23, 149.82, 155.96
(d, J ¼ 249 Hz), 166.70, 176.97, 207.78. FAB-MS: m/z 446 (M þ H)þ.
HRMS-FAB: m/z Calcd. for C23H29FN3O5 (M þ H)þ: 446.2091; Found
446.2089.
4.2.2.5. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(iso-
nicotinoylhydrazono)propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid 13. 52% yield. 1H NMR
(400 MHz, CDCl3) dH 0.97e1.30 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3),
2.18 (3H, s, CH3), 2.50e2.66 (1H, m), 2.95e3.28 (4H, m), 3.38e3.51
(3H, m), 3.63 (3H, s, OCH3), 3.75e3.81 (1H, m), 3.95e3.98 (1H, m),
7.89 (1H, d, J ¼ 11.6 Hz, C5-H), 7.77e7.78 (2H, m, pyridine-2H),
8.79e8.81 (2H, m, pyridine-2H), 8.82 (1H, s, C2-H), 13.42 (1H, s,
NH), 14.59 (1H, s, COOH). FAB-MS: m/z 551 (M þ H)þ. HRMS-FAB:
m/z Calcd. for C28H32FN6O5 (M þ H)þ: 551.2418; Found 551.2418.
4.2.2. General procedure for the preparation of compounds 9e20
To a stirring solution of 7, 8 (6.50 mmol) dissolved in methanol
(25 mL) was added dropwise a solution of substituted amine
hydrochlorides (10.0 mmol) and sodium bicarbonate (10.0 mmol)
in water (15 mL) at room temperature. The reaction mixture was
heated to refluxing and stirred for 2e3 h and concentrated under
reduced pressure. The residue was purified via silica gel column
chromatography (chloroform/methanol, 10:1, v/v) to give the title
compounds 9e11 and 15e19 as off-white solids.
A refluxing mixture of 7, 8 (2.32 mmol), substituted amines
(3.48 mmol) in methanol (6.50 mL) was stirred for 4e6 h and
concentrated under reduced pressure. The residue was purified via
silica gel column chromatography (chloroform/methanol, 10:1, v/v)
to give the title compounds 12e14 and 20 as off-white solids.
4.2.2.6. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(phenylhydrazono)
propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 14. 73% yield. 1H NMR (400 MHz, CDCl3) dH 0.95e1.27
(7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 1.97 (3H, s, CH3), 2.44e3.18 (5H,
m), 3.42e3.64 (4H, m), 3.78 (3H, s, OCH3), 3.99e4.04 (1H, m),
6.84e6.87 (1H, m, Ph-1H), 7.01e7.23 (2H, m, Ph-2H), 7.25e7.26 (2H,
m, Ph-2H), 7.89 (1H, d, J ¼ 12.0 Hz, C5-H), 8.81 (1H, s, C2-H), 14.79 (1H,
s, COOH). FAB-MS: m/z 522 (M þ H)þ. HRMS-FAB: m/z Calcd. for
C28H33FN5O4 (M þ H)þ: 522.2517; Found 522.2509.
4.2.2.1. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(methoxyimino)
propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 9. 70% yield. 1H NMR (400 MHz, CDCl3þD2O) dH
0.97e1.26 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 1.92 (3H, s, CH3),
2.39e2.43 (1H, m), 2.64e2.85 (3H, m), 3.08e3.13 (1H, m),
3.36e3.50 (4H, m), 3.76, 3.87 (6H, 2s, 2 ꢂ OCH3), 3.99e4.03 (1H, m),
7.87 (1H, d, J ¼ 12.0 Hz, C5-H), 8.81 (1H, s, C2-H), 14.79 (1H, s,
COOH). FAB-MS: m/z 461 (M þ H)þ. HRMS-FAB: m/z Calcd. for
C23H30FN4O5 (M þ H)þ: 461.2200; Found 461.2234.
4.2.2.7. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(hydroxyimino)
propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 15. 91% yield. 1H NMR (400 MHz, C5D5N) dH
0.97e1.03 (4H, m, 2 ꢂ cyclopropyl CH2), 1.16 (3H, d, J ¼ 6.0 Hz,
CCH3), 2.26 (3H, s, CH3), 2.52e2.66 (1H, m), 2.75e2.77 (1H, m),
3.00e3.25 (3H, m), 3.37e3.49 (4H, m), 3.73 (3H, s, OCH3), 3.97e3.98
(1H, m), 8.06 (1H, d, J ¼ 12.0 Hz, C5-H), 8.88 (1H, s, C2-H), 12.89 (1H,
4.2.2.2. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[2-(ethoxyimino)
propyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 10. 74% yield. 1H NMR (400 MHz, CDCl3) dH
br, COOH). 13C NMR (600 MHz, C5D5N)
d
ppm: 9.50, 9.60, 12.92,
15.64, 19.23, 41.00, 50.89, 51.77, 56.59, 57.31, 58.25, 62.83, 107.93,

4272
Y. Chai et al. / European Journal of Medicinal Chemistry 46 (2011) 4267e4273
108.14, 122.08, 134.40, 139.60, 146.05, 150.23, 154.07, 156.79 (d,
J ¼ 247 Hz), 166.70, 177.42. FAB-MS: m/z 447 (M þ H)þ. HRMS-FAB:
m/z Calcd. for C22H28FN4O5 (M þ H)þ: 447.2044; Found 447.2027.
4.2.2.11. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[3-(carbamoylhy-
drazono)butyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-
3-carboxylic acid 19. 68% yield. 1H NMR (400 MHz, C5D5N) dH
0.96e1.25 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 2.03 (3H, s, CH3),
2.81e3.42 (8H, m), 3.58e3.76 (3H, m), 3.83 (3H, s, OCH3), 3.95e3.98
(1H, m), 8.09 (1H, d, J ¼ 12.0 Hz, C5-H), 8.89 (1H, s, C2-H). FAB-MS:
m/z 503 (M þ H)þ. HRMS-FAB: m/z Calcd. for C24H32FN6O5
(M þ H)þ: 503.2418; Found 503.2425.
4.2.2.8. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[3-(hydroxyimino)
butyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 16. 70% yield. 1H NMR (400 MHz, C5D5N) dH
0.96e1.14 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 2.13 (3H, s, CH3),
2.49e2.65 (5H, m), 2.94e3.12 (3H, m), 3.12e3.40 (3H, m), 3.71 (3H,
s, OCH3), 3.96e3.99 (1H, m), 8.06 (1H, d, J ¼ 12.0 Hz, C5-H), 8.88 (1H,
s, C2-H), 12.47 (1H, s, NOH), 15.47 (1H, s, COOH). FAB-MS: m/z 461
(M þ H)þ. HRMS-FAB: m/z Calcd. for C23H30FN4O5 (M þ H)þ:
461.2200; Found 461.2210.
4.2.2.12. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[3-(phenyl-
hydrazono)butyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-
dihydroquinoline-3-carboxylic acid 20. 70% yield. 1H NMR
(400 MHz, CDCl3) dH 0.96e1.36 (7H, m, 2 ꢂ cyclopropyl CH2,
CCH3), 1.94 (3H, s, CH3), 2.67e3.51 (11H, m), 3.76 (3H, s, OCH3),
3.99e4.03 (1H, m), 6.82e6.86 (1H, m, Ph-1H), 6.99e7.04 (2H, m,
Ph-2H), 7.22e7.26 (2H, m, Ph-2H), 7.86 (1H, d, J ¼ 12.0 Hz, C5-H),
8.80 (1H, s, C2-H), 14.73 (1H, s, COOH). 13C NMR (400 MHz, CDCl3)
4.2.2.9. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[3-(methoxyimino)
butyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 17. 74% yield. 1H NMR (400 MHz, CDCl3) dH
1.01e1.64 (7H, m, 2 ꢂ cyclopropyl CH2, CCH3), 1.90 (3H, s, CH3),
2.73e3.01 (2H, m), 3.09e3.62 (7H, m), 3.83, 3.86 (6H, 2s, 2 ꢂ OCH3),
4.00e4.12 (2H, m), 4.26e4.49 (1H, m), 7.85 (1H, d, J ¼ 12.0 Hz, C5-
H), 8.82 (1H, s, C2-H), 14.53 (1H, s, COOH). 13C NMR (600 MHz,
d
ppm: 9.44, 9.59, 14.89, 15.81, 34.81, 40.49, 50.38, 50.40, 51.46,
55.06, 57.24, 62.72, 107.77, 108.12 (d, J ¼ 23 Hz), 112.88, 119.75,
121.63, 122.53, 129.17, 133.96, 139.28, 145.20, 145.68, 149.83, 155.93
(d, J ¼ 250 Hz), 166.73, 176.99. FAB-MS: m/z 536 (M þ H)þ. HRMS-
FAB: m/z Calcd. for C29H35FN5O4 (M þ H)þ: 536.2673; Found
536.2651.
CDCl3)
d ppm: 9.57, 9.67, 14.48, 15.16, 29.48, 40.37, 47.20, 49.30,
52.11, 54.56, 59.92, 61.59, 64.06, 108.25, 108.16, 122.84, 133.99,
137.45, 145.68, 150.17, 150.23, 153.50 (d, J ¼ 250 Hz), 166.32, 176.86.
FAB-MS: m/z 475 (M þ H)þ. HRMS-FAB: m/z Calcd. for C24H32FN4O5
(M þ H)þ: 475.2357; Found 475.2367.
4.2.3. 1-Cyclopropyl-6-fluoro-8-methoxy-7-(4-hydroxy-3-
methylpiperazin-1-yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic
acid 21
4.2.2.10. 1-Cyclopropyl-6-fluoro-8-methoxy-7-{4-[3-(ethoxyimino)
butyl]-3-methylpiperazin-1-yl}-4-oxo-1,4-dihydroquinoline-3-
carboxylic acid 18. 67% yield. 1H NMR (400 MHz, CDCl3) dH
1.00e1.64 (7H, m, 2 ꢂ cyclopropyl CH2, OCH2CH3), 1.62 (2H, d,
J ¼ 6.0 Hz, CCH3), 1.91 (3H, s, CH3), 2.73e2.99 (2H, m), 3.14e3.80
(7H, m), 3.79 (3H, s, OCH3), 4.01e4.05 (2H, m), 4.05e4.11 (2H, m,
J ¼ 7.0 Hz, OCH2CH3), 4.32e4.44 (1H, m), 7.76 (1H, d, J ¼ 12.0 Hz,
C5-H), 8.81 (1H, s, C2-H), 12.93 (1H, s, COOH). 13C NMR (600 MHz,
A suspension of 8 (1.0 g, 2.24 mmol) in water (10.0 mL) was
adjusted pH 9e10 with 2 N sodium hydroxide solution, and then
added 30% hydrogen peroxide (3.0 mL). The reaction mixture was
stirred for 12 h at room temperature and filtered. The resulting
precipitate was recrystallized from methanol to give the title
compound 21 as a white solid. 63% yield. 1H NMR (400 MHz, CDCl3)
dH 0.98e1.03 (2H, m, cyclopropyl CH2), 1.22e1.34 (5H, m, cyclo-
propyl CH2, CCH3), 2.90e3.19 (3H, m), 3.39e3.56 (4H, m), 3.79 (3H,
s, OCH3), 4.00e4.04 (1H, m), 7.89 (1H, d, J ¼ 12.4 Hz, C5-H), 8.82 (1H,
CDCl3)
d ppm: 9.58, 9.69, 14.47, 14.59, 15.33, 29.53, 40.38, 47.22,
49.31, 51.50, 53.68, 59.83, 64.09, 69.30, 108.13, 108.18 (d,
J ¼ 24 Hz), 122.81, 134.06, 137.46, 145.65, 150.17, 152.03, 156.83 (d,
J ¼ 249 Hz), 166.32, 176.85. FAB-MS: m/z 489 (M þ H)þ. HRMS-
FAB: m/z Calcd. for C25H34FN4O5 (M þ H)þ: 489.2513; Found
489.2524.
s, C2-H), 14.70 (1H, s, COOH). 13C NMR (600 MHz, DMSO-d6)
d ppm:
8.89, 8.93, 16.58, 40.78, 49.87, 55.90, 58.28, 61.55, 62.67, 106.50,
106.66, 120.86, 134.06, 138.50,145.75, 150.51, 155.41 (d, J ¼ 249 Hz),
165.62, 176.30. FAB-MS: m/z 392 (M þ H)þ. HRMS-FAB: m/z Calcd.
for C19H23FN3O5 (M þ H)þ: 392.1622; Found 392.1625.
O
O
N
O
N
F
COOH
F
COOH
F
COOH
b
c
N
N
N
O
NR2
N
HN
OCH3
N
n
OCH3
(n=1)
N
n
OCH3
7
GTFX
9-20
n=1, 2
8 (n=2)
R2=OH, OCH3, OC2H5, NHCONH2,
a
d
NHCOCH3, NHCOC5H4N, NHC6H5,
O
N
O
N
F
COOH
F
COOH
N
N
R1
N
n
OCH3
N
OCH3
HO
1-6
21
8
(from
)
R1=CN, COOCH3, COOC2H5
n=1, 2
Reagents and conditions: a: R1CH2Cl / CH2=CHR1, Et3N, EtOH (53-82%) b: CH3COCl / CH2=CHCOCH3, Et3N, EtOH (73-77%)
.
c: NH2R2 HCl, NaHCO3 / NH2R2 , MeOH (52-91%)
d: 30% H2O2, 2N NaOH (63%)
Scheme 1. Synthesis of GTFX derivatives 1e21.

Y. Chai et al. / European Journal of Medicinal Chemistry 46 (2011) 4267e4273
4273
4.3. Molecular modeling
harvested and cell viability was assessed by MTT assay. The CC50
values were calculated by Bliss analyses.
The target quinoloneeenzymeeDNA complexes were evaluated
by employing SYBYL X1.2 [16] software on a windows workstation.
The crystal structure data (3FOF) [4] was obtained from the protein
data bank. The surflex-dock module of the SYBYL software suite
was then implemented and the protomol was generated using
a ligand-based approach. The ligand was extracted from DNA-
bound crystal structure. For the purposes of these experiments,
“proto_thresh” was set to 0.5 and “proto_bloat” was left at the
default (0). Two factors “Multistart 5” and “Random 5” were
selected to help optimize ligand targeted docking. All other
parameters were left at the default values [17]. Surflex-dock returns
an affinity score reported as ꢁlog(Kd) that takes into account
hydrophobic, polar complementary, entropic, and solvation terms
and a “crash” score that represents “inappropriate” penetration of
a potential ligand into a binding site [16]. The predicted three-
dimensional conformation of compound 20 is shown in Fig. 2.
Acknowledgments
This work was supported by the key project of Major infectious
disease (No.2008ZX10003-006) and National S&T Major Special
Project on Major New Drug Innovation (No. 2009ZX09301-003).
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