Preparation and antibacterial evaluation of decarboxylated fluoroquinolones

Article abstract of DOI:10.1016/j.bmcl.2011.07.060

Decarboxylated ciprofloxacin (3) has been reported in the literature to have antibacterial activities against Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Bacillus subtilis, Enterobacter cloacae, Serratia marcescens and especially potent activity against Escherichia coli. Herein, we report our syntheses of 3 and five additional decarboxylated fluoroquinolones (FQs). We have re-evaluated the antibacterial activity of these FQs. In contrast to previously reported data, none of these decarboxylated fluoroquinolones showed significant antibacterial activity in our assays using both the broth dilution and agar methods. Our study confirmed that the presence of a carboxylic acid group at the 3-position of the fluoroquinolone scaffold is essential for antibacterial activity.

Full text of DOI:10.1016/j.bmcl.2011.07.060

Bioorganic & Medicinal Chemistry Letters 21 (2011) 5961–5963
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Preparation and antibacterial evaluation of decarboxylated fluoroquinolones
⇑
Son T. Nguyen, Xiaoyuan Ding, Michelle M. Butler, Tommy F. Tashjian, Norton P. Peet , Terry L. Bowlin
Microbiotix Inc., One Innovation Drive, Worcester, MA 01605, United States
a r t i c l e i n f o
a b s t r a c t
Article history:
Decarboxylated ciprofloxacin (3) has been reported in the literature to have antibacterial activities
against Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Bacillus subtilis,
Enterobacter cloacae, Serratia marcescens and especially potent activity against Escherichia coli. Herein,
we report our syntheses of 3 and five additional decarboxylated fluoroquinolones (FQs). We have re-eval-
uated the antibacterial activity of these FQs. In contrast to previously reported data, none of these decar-
boxylated fluoroquinolones showed significant antibacterial activity in our assays using both the broth
dilution and agar methods. Our study confirmed that the presence of a carboxylic acid group at the 3-
position of the fluoroquinolone scaffold is essential for antibacterial activity.
Received 24 June 2011
Accepted 18 July 2011
Available online 29 July 2011
Keywords:
Fluoroquinolone
Antibacterial
Decarboxylated
Ciprofloxacin
Norfloxacin
Ó 2011 Elsevier Ltd. All rights reserved.
Enrofloxacin
Fluoroquinolones represent an important class of antibiotics, and
are known for their activity against Gram-negative and -positive bac-
teria by inhibiting bacterial DNA gyrase.1 Structure–activity relation-
ship studies performed some years ago showed that modification of
the 3-carboxylic acid group was detrimental to the antibacterial
activities of quinolones unless the modified groups could be con-
verted to the carboxylic acid functionality in vivo.2 Substitution at
the 3-position with other functionalities, such as sulfonic acid, sul-
fonamide, carboxymethyl, hydroxamic acid or phosphonic acid,
led tomuchless active compounds.3 However, several recentreports
have disclosed that decarboxylated ciprofloxacin (3) displays anti-
bacterial activities againstStaphylococcus aureus,Staphylococcus epi-
dermidis, Enterococcus faecalis, Bacillus subtilis, Enterobacter cloacae,
Serratia marcescens and even more potent activity againstEscherichia
coli than ciprofloxacin.4 Should this finding be true, the decarboxyl-
ated fluoroquinolones might be acting via a new mechanism. For
example, Berge et al. reported that certain quinolones, which do
not contain a carboxylic acid functionality at the 3-position, are
methionyl t-RNA synthetase (MRS) inhibitors, and they were bacte-
ricidal.5 After an extensive literature search, we found that decar-
boxylated norfloxacin (7) has also been synthesized. In contrast to
3, compound 7 was reported to have no antibacterial activity.6 Be-
cause the biological profiles of decarboxylated fluoroquinolones
were limited and inconsistent, we decided to independently synthe-
size and examine the antibacterial activities of the decarboxylated
derivatives of ciprofloxacin (1), norfloxacin (5), enrofloxacin (8)
and 1-cyclopropyl-6,8-difluoro-7-(3-methylpiperazin-1-yl)-4-oxo-
quinoline-3-carboxylic acid (10).7
Following literature procedures, ciprofloxacin was treated with
KCN in DMSO in an attempt to prepare 3.4a,8 However, in our hands
this reaction gave a complex mixture containing the desired prod-
uct and unidentified components, which were difficult to separate
and isolate. However, when DMF was used as the solvent, a single
product was obtained, which was not 3 but rather its N-formyl
derivative 2, which has not been previously reported (Scheme 1).
Interestingly, in the absence of KCN, treatment of ciprofloxacin
with DMF at elevated temperature provided 4 in good yield. To
the best of our knowledge, this is a new method for the introduc-
tion of an N-formyl group to the piperazine ring of fluoroquino-
lones.9 Methanolysis of 2 in the presence of K2CO3 conveniently
provided compound 3.
Similar procedures were applied to norfloxacin to prepare its
decarboxylated derivatives 6 and 7. For enrofloxacin, because the
molecule does not contain a free NH group, its reaction with KCN
in either DMSO or DMF provided the same decarboxylated product
9. Interestingly, treatment of 10 with KCN in DMF provided the
decarboxylated product 11 in good yield; no formylation product
was observed. It is possible that steric hindrance of the methyl
group in the piperazine ring prevented the transamidation process.
The NMR data for our compounds were consistent with the data
reported by Park et al.4a and Koga et al.6 for compounds 3 and 7.
However, the data reported by Al-Hajjar et al.4b for 3 differed sig-
nificantly from ours. Upon inspecting the chemical shifts and cou-
pling patterns, we determined that the structure of the compound
prepared by Al-Hajjar et al.4b was misassigned. The 1H NMR spec-
trum of compound 3 should have four distinctive doublets (and no
singlet) in the aromatic region, two of which should share the same
coupling constant attributable to the C(2) and C(3) protons. The
data reported by Al-Hajjar lacked these two doublets and displayed
⇑
Corresponding author. Fax: +1 508 757 1999.
E-mail address: npeet@microbiotix.com (N.P. Peet).
0960-894X/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2011.07.060

5962
S. T. Nguyen et al. / Bioorg. Med. Chem. Lett. 21 (2011) 5961–5963
O
N
O
O
N
F
COOH
F
F
K2CO3, MeOH
70°C, 24 h
KCN, DMF
120°C,
N
N
N
N
24 h, 62%
HN
O
N
HN
37%, 2 steps
H
3
2
Ciprofloxacin (1)
O
O
F
OH
DMF
N
N
O
N
130°C, 24 h
74%
H
4
O
N
O
O
O
N
F
F
F
K2CO3, MeOH
KCN, DMF
OH
120°C, 24 h
95%
70°C, 24 h
73%
N
N
N
N
O
N
HN
HN
H
7
6
Norfloxacin (5)
O
O
N
F
COOH
F
KCN
DMF or DMSO
120°C, 24 h
N
N
N
N
N
65%
9
Enrofloxacin (8)
O
O
O
F
F
KCN, DMF
OH
120°C, 18 h
57%
N
N
N
N
HN
F
HN
F
10
11
Scheme 1. Synthesis of decarboxylated fluoroquinolones.
a singlet at 8.7 ppm.10 The singlet at low field is likely due to a C(2)
proton adjacent to C(3), which still bears a carboxylic acid moiety.
Seven compounds that we prepared were tested in vitro against
our panel of 16 bacterial strains using the standard broth dilution
method. To our disappointment, none of the decarboxylated fluo-
roquinolones displayed any antibacterial activity.11 To be consis-
tent with the Park4c report and to rule out the possibility that
the minimum inhibitory concentration (MIC) values might vary
due to different culture media, we reran the MIC assay using the
agar method and used the same strains of E. coli, S. aureus and E.
faecalis that Park et al.4a used. Again, none of the decarboxylated
compounds were active (Table 1). Among the seven compounds,
only 4, which still has the 3-carboxylic acid group, was active
but less potent than ciprofloxacin.12 Overall, our data consistently
showed that decarboxylated fluoroquinolones displayed no signif-
icant antibacterial activity against a variety of bacterial strains.
In conclusion, we prepared six decarboxylated fluoroquino-
lones, four of which are new. Our assays showed that none of these
compounds display significant antibacterial activity. It is possible
that the biological data reported by Park et al.4a, Al-Hajjar et al.4b
and Marks et al.4c for compound 3 arose from contaminated
samples,13 incorrectly assigned samples or MIC values that were
incorrectly recorded. Importantly, our study confirms that the
3-carboxylic acid group is essential for the antibacterial activity
of fluoroquinolones.
Table 1
Minimum inhibitory concentration (MIC) assay data
Supplementary data
Compound
MIC (
lg/mL)
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2011.07.060.
E. coli 29425
S. aureus 25923
E. faecalis 29212
Agar
Broth
Agar
Broth
Agar
Broth
2
3
4
6
7
9
11
>64
>64
0.5
>64
64
>64
>64
>80
>80
0.31
40
40
>80
>80
>64
>64
0.5
>64
>64
>64
>64
>80
>80
0.31
>80
>80
>80
>80
>64
>64
1
>64
32
>80
>80
0.63
>80
>80
>80
>80
References and notes
1. Ronald, A. R.; Low, D. E. Fluoroquinolone Antibiotics; Birkhauser Verlag: Basel,
2003; (b) Domagala, J. M.; Hanna, L. D.; Heifetz, C. L.; Huff, M. P.; Mich, T. F.;
Sanchez, P.; Solomon, M. J. Med. Chem. 1986, 29, 394.
2. Kondo, H.; Sakamoto, F.; Kawakami, K.; Tsukamoto, G. J. Med. Chem. 1998, 31,
221.
>64
>64
3. Chu, D. T. W.; Fernandes, P. B. Antimicrob. Agents Chemother. 1989, 33, 131.
4. (a) Park, C. H.; Lee, J.; Jung, H. Y.; Kim, M. J.; Lim, S. H.; Yeo, H. T.; Choi, E. C.;
Yoon, E. J.; Kim, K. W.; Cha, J. H.; Kim, S.-H.; Chang, D.-J.; Kwon, D.-Y.; Li, F.; Suh,
Y.-G. Bioorg. Med. Chem. 2007, 15, 6517; (b) Al-Hajjar, F. H.; Jabal Al-Hussain, A.
Ciprofloxacin
Norfloxacin
Enrofloxacin
<0.06
0.01
<0.06
<0.02
0.12
0.05
0.5
2.0
0.13
0.31
0.63
0.16
0.5
2.0
0.13
1.25
2.5
0.63

S. T. Nguyen et al. / Bioorg. Med. Chem. Lett. 21 (2011) 5961–5963
5963
EP1245566 A1, 2002.; (c) Marks, K. R.; Kerns, R. J. 240th ACS Meeting &
Exposition, Boston (MA), 2010, MEDI-325.; (d) Kerns, R. J.; Rybak, M. J.; Kaatz,
G. W.; Vaka, F.; Cha, R.; Grucz, R. G.; Diwadkar, V. U. Bioorg. Med. Chem. Lett.
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9. For a different method to prepare 4 see: Gau, W.; Kurz, J.; Petersen, U.;
Ploschke, H. J.; Wuensche, C. Arzneimittel Forschung 1986, 36, 1545.
10. Complete 1H NMR data (from Ref. 4b): (DMSO-d6) 8.7 (s), 7.9 (d), 7.5 (d), 4.2
(quint), 2.6-3.7 (m), 0.9–1.4 (m).
2003, 13, 2109; (e) Against S. aureus, ref4a reported MIC = 16
l
g/mL; ref4d
reported MIC > 16 lg/mL.
5. Berge, J. M.; Brown, P.; Elder, J. S.; Forrest, A. K.; Hamprecht, D. W.; Jarvest, R. L.;
McNair, D. J.; Sheppard, R. J. US 6320051 B1, 2001.
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1358.
7. For preparation and MIC values of 10 see: (a) Domagala, J. M.; Bridges, A. J.;
Culbertson, T. P.; Gambino, L.; Hagen, S. E.; Karrick, G.; Porter, K.; Sanchez, J. P.;
Sesnie, J. A.; Spense, G.; Szotek, D.; Wemple, J. J. Med. Chem. 1991, 34, 1142; (b)
Uno, T.; Okuno, T.; Kawakami, K.; Sakamoto, F.; Tsukamoto, G. J. Med. Chem.
11. See the Supplementary data for these data.
12. Ciprofloxacin, enrofloxacin and norfloxacin were included in the assays as
internal standards.
13. If the samples were contaminated with small amounts of fluoroquinolones the
MIC values could change significantly; see the Supplementary data for these
data.