Synthesis and in vitro antibacterial activity of oxazolidine LBM-415 analogs as peptide deformylase inhibitors

Article abstract of DOI:10.1016/j.bmcl.2010.12.097

The drug resistant bacteria pose a severe threat to human health. The increasing resistance of those pathogens to traditional antibacterial therapy renders the identification of new antibacterial agents with novel antibacterial mechanisms an urgent need.

Full text of DOI:10.1016/j.bmcl.2010.12.097

Bioorganic & Medicinal Chemistry Letters 21 (2011) 1541–1544
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and in vitro antibacterial activity of oxazolidine LBM-415 analogs
as peptide deformylase inhibitors
Linliang Yu a,b, , Weicheng Zhou a, Zhenyu Wang a
⇑
a State Key Lab of New Drug & Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1111 North Zhongshan Road, Shanghai 200437, PR China
b Department of chemistry, University of Kentucky, Lexington, KY 40506, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The drug resistant bacteria pose a severe threat to human health. The increasing resistance of those
pathogens to traditional antibacterial therapy renders the identification of new antibacterial agents with
novel antibacterial mechanisms an urgent need. In this study, a series of (2S)-N-substituted-1-[(form-
yhydroxyamino)methyl]-1-oxohexyl]-2-oxazolidinecarboxamides were designed, synthesized and eval-
uated for in vitro antibacterial activity. Most of these compounds displayed good activities against
Gram-positive organisms comparable to reference agent LBM-415.
Received 30 November 2010
Accepted 20 December 2010
Available online 24 December 2010
Keywords:
Bacterial peptide deformylase (PDF)
Enzyme inhibitors
LBM-415
Crown Copyright Ó 2010 Published by Elsevier Ltd. All rights reserved.
Antibiotic resistance is a serious global concern. The emergence
of superbugs, bacterial pathogens that are resistant to many
known antibiotics, is an imminent threat to public health.1 The
discovery of novel antibiotics with completely new mechanisms
of action are urgently desirable to circumvent the rapid rise of
resistance.2 In that essence, bacterial peptide deformylase (PDF)
is an attractive target for the exploration of a new antibiotic agent.3
In bacteria protein synthesis, PDF removes the formyl group of the
N-formyl methionine of the nascent protein in the press to afford
the mature protein, and it is essential for the bacterial growth.4,5
However, in mammalian cells, PDF was much less active compared
with its bacterial counterpart, which provided a sound basis for
selective inhibition.6 Additionally, given that PDF, encoded by def
gene, are essential to bacteria and it seems all bacterial PDF adopt
a similar overall tertiary structure,7,8 the inhibitors targeted at PDF
could lead to broad spectrum activity.
Based on the crystal structure of PDF in the cofactor and sub-
strate bound conformations,9–11 many bacterial PDF inhibitors
were designed and evaluated.12–15 The general structure was de-
rived and structure–activity relationship discussed. ( Fig. 1)16,17
LBM-415 (Fig. 1), with a pyrrolidine moiety at the P2 position, is
a potential PDF inhibitor progressed to clinical trial.18 In vitro drug
susceptibilities tests and in vivo characterization in infected ani-
mal mode showed that LBM-415 had a good antimicrobial activity
equivalent to the marketed antibiotic agents.19–22 In our previous
effort in searching for new antimicrobial agents,23–27 we investi-
gated the effects of substituent of P3 position of LBM-415, and ob-
tained several compounds with improved antimicrobial activity in
vitro.28 In this study, we focused on the modification of the P2
position of LBM-415. Oxazolidine moiety is an important building
block for many biological active agents.29,30 It is called pseudopro-
line to mimic the proline skeleton for investigation of peptide bio-
logical activity.31 With this in mind, we substituted the pyrrolidine
moiety of LBM-415 with oxazolidine at the P2 position. A series of
oxazolidinyl LBM-415 analogs (Fig. 2) were synthesized and their
in vitro antibacterial activities were evaluated.
H3C
CHO
N
P1
O
H
N
F
N
MBG
P3
HO
N
H
O
P2
O
N
H
N
O
O
General Structure
LBM-415
Figure 1. General structure of PDF inhibitor; structure of LBM-415.
H3C
O
CHO
N
R1
R2
N
HO
O
N
H
O
General Structure of 1a-1r
⇑
Corresponding author. Tel.: +1 859 257 0541; fax: +1 865 974 4115.
E-mail address: lyu4@uky.edu (L. Yu).
Figure 2. General structure of 1a–1r.
0960-894X/$ - see front matter Crown Copyright Ó 2010 Published by Elsevier Ltd. All
rights reserved.

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L. Yu et al. / Bioorg. Med. Chem. Lett. 21 (2011) 1541–1544
H3C
H3C
H3C
a
b
c, d, e
EtO
OEt
HO
OH
EtO
OH
HO
OH
O
O
O
O
O
O
3
4
2
f
H3C
H3C
O
g
h
H3C
H
H
N
N
N
MsO
HO
O
O
O
O
O
O
7
6
5
i
H3C
CHO
H3C
H
N
j, k
H
N
OH
N
OH
O
O
O
8
9
R1
HO
R1
O
R1
R1
O
N
n
m
O
N
l
O
H
H
OH
OH
N
N
R2
R2
H2N
N
H
O
Boc
O
Boc
O
10a, R1=H
10b, R1=CH3
11a-11p
12a-12p
o
H3C
CHO
H3C
r
O
O
CHO
N
R1
R1
R2
N
N
N
HO
O
R2
N
O
O
N
O
H
O
H
1a-1p
H3C
13a-13p
H3C
CHO
H3C
O
O
CHO
N
O
CHO
N
R1
p
R1
q
F
R1
F
F
N
N
N
O
N
O
HO
O
O
N
H
N
O
N
N
O
O
N
H
N
O
O
H
O
14a, R1=H
14b, R1=CH3
13i,13p
1q, 1r
Scheme 1. Reagents and conditions: (a) EtONa, n-C4H9Br, EtOH; (b) KOH, EtOH; (c) LiBH4, THF/i-PrOH; (d) (R)-1-phenylethanamine, EtOAc/i-PrOH; (e) HCl, EtOAc; (f) O-
benzylhydroxylamine hydrochloride, EDCI, NaOH, H2O; (g) MsCl, pyridine; (h) K2CO3, tetrabutylammonium bromide, THF; (i) LiOH, THF/CH3OH/H2O; (j) HCOOH/Ac2O; (k)
dicyclohexylamine, n-heptane; (l) HCHO, NaOH, (Boc)2O; (m) CDMT, R2NH2; (n) HCl/EtOAc; (o) 2-propane phosphonic acid anhydride, EtOAc; (p) urea hydrogen peroxide; (q)
10% Pd/C, HCOONN4, EtOH.
The synthesis of oxzaolidine formyl hydroxyamino derivatives
is outlined in Scheme 1. The general strategy relies on the coupling
of 9, bearing the protected formyl hydroxyl amine group in place,
with oxazolidinyl carboxamide (12) to form the amide linkage.
Compound 9 was prepared from dietheylmalonate according to
the literature.32,33
For the synthesis of 12, commercially available serine or threo-
nine was condensed with formaldehyde to construct the desired
oxazolidine ring, which is then N-protected with Boc anhydride,
and coupled with R2NH2 to give N-Boc protected oxazolidine deriv-
atives 11a–11p. Deprotection of 11a–11p with HCl in EtOAc,34,35
zylation of 13a–13p by Pd/C hydrogenation provide the desired
oxazolidine formyl hydroxyamino derivatives 1a–1p. For 13i and
13p, oxidation with urea hydrogen peroxide and debenzylation
afford the N-oxides 1q and 1r. These novel compounds were
characterized by 1H NMR and ESI-MS. The melting point and
optical rotation of the desired compounds were also measured
(Table 1).
The minimum inhibitory concentrations (MICs) of oxazolidine
formyl hydroxyamino derivatives against several Gram-positive
and Gram-negative bacterium were summarized in Table 2, along
with data of LBM-415 for comparison. MICs were determined by
the agar dilution method as outlined by the National Committed
for Clinical Laboratory Standards. The MIC was defined as the low-
followed by coupling with
9 in the presence of 2-propane
phosphonic acid anhydride gave the compounds 13a–13p. Deben-

L. Yu et al. / Bioorg. Med. Chem. Lett. 21 (2011) 1541–1544
1543
Table 1
Structure of 1a–1r
Compd
R1
R2
Compd
R1
R2
1a
1b
1c
1d
1e
1f
1g
1h
1i
H
H
H
H
H
H
H
H
H
Phenyl
4-Methylphenyl
4-Fluorophenyl
2,5-Difluorophenyl
1j
1k
1l
1m
1n
1o
1p
1q
1r
H
H
(2S)-Methyl-1-phenylmethyl
1-Phenylmethyl
4-Methylphenyl
CH3
CH3
CH3
CH3
CH3
H
4-Fluorophenyl
4-Methoxylphenyl
3-Fluoro-4-morpholinephenyl
3-Chloro-4-morpholinephenyl
5-Fluoro-2-pyridinyl
5-Fluoro-1-oxido-2-pyridinyl
5-Fluoro-1-oxido-2-pyridinyl
3-Fluoro-4-morpholinylphenyl
3-Chloro-4-morpholinylphenyl
4-Morpholinylphenyl
5-Fluoro-2-pyridinyl
CH3
Table 2
In vitro antibacterial activity of 1a-1r
Compd
MIC (lg/mL)
Gram-positive organism
Gram-negative organism
S. aureus 26003
0.39
S. pneumoniae 31002
S. albus 260101
S. boydii 51313
S. flexneri 92475
LBM-415
1a
1b
1c
1d
1e
1f
1g
1h
1i
1j
1k
1l
1m
1n
1o
1p
1q
1r
0.195
0.195
0.195
0.195
0.195
0.195
0.098
0.098
0.39
0.098
0.195
0.78
0.098
0.195
0.195
0.098
0.39
0.39
0.39
0.78
0.39
0.39
0.78
0.78
0.39
0.78
0.39
1.56
1.56
0.78
0.78
1.56
0.39
0.39
0.78
0.78
6.25
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
6.25
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
6.25
0.39
0.78
0.39
0.39
0.39
0.78
0.39
1.56
0.78
1.56
0.78
1.56
1.56
0.78
0.78
1.56
0.78
1.56
6.25
3.13
>6.25
3.13
>6.25
>6.25
>6.25
3.13
>6.25
>6.25
3.13
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
>6.25
0.195
0.195
3.13
>6.25
est concentration resulting in inhibition of visible bacterial growth
after incubation at 37 °C for 24 h.
‘New Drug Innovation 2009X09301-007’ from Ministry of Science
and Technology of China.
Shown in Table 2, all the oxazolidine formyl hydroxyamino
derivatives 1a–1r demonstrated significantly better antibacterial
activity against Gram-positive bacteria than Gram-negative. The
antibacterial spectrum was similar with LBM-415. Among the most
potent ones, 1a, 1c and 1d exhibited the same inhibitory effect on
the tested Gram-positive bacteria as LBM-415. On the other hand,
1g, 1i, 1m and 1q showed better activities than LBM-415 to the
Gram-negative bacteria. There are no substantial differences in
the activity against Streptococcus pneumoniae between the serine-
based oxazolidine derivatives and the threonine-based oxazoli-
dine. But against the Staphylococcus aureus, the serine-based
oxazolidine compounds showed better activities. Overall, the com-
pound 1g with (3-chloro-4-morpholinyl)phenyl substitution
exhibited highest activity and its potency is comparable to or even
slightly better than reference agent LBM-415.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2010.12.097.
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