Design, synthesis, and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives as novel peptide deformylase inhibitors

Article abstract of DOI:10.1016/j.bmcl.2010.04.123

The synthesis and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives are reported. The antibacterial activities of these derivatives were evaluated, and some of these derivatives showed better in vitro antibacterial activity than existing drugs, including penicillin, ciprofloxacin, vancomycin, and linezolid.

Full text of DOI:10.1016/j.bmcl.2010.04.123

Bioorganic & Medicinal Chemistry Letters 20 (2010) 3592–3595
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design, synthesis, and antibacterial activity of 2,5-dihydropyrrole formyl
hydroxyamino derivatives as novel peptide deformylase inhibitors
*
Wei Shi, Yuejiao Duan, Yu Qian, Ming Li, Liping Yang, Wenhao Hu
Department of Chemistry, East China Normal University, Shanghai 200062, China
a r t i c l e i n f o
a b s t r a c t
Article history:
The synthesis and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives are
reported. The antibacterial activities of these derivatives were evaluated, and some of these derivatives
showed better in vitro antibacterial activity than existing drugs, including penicillin, ciprofloxacin, van-
comycin, and linezolid.
Received 5 February 2010
Revised 23 April 2010
Accepted 27 April 2010
Available online 24 May 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
PDF inhibitor
Drug-resistant bacteria
Antibiotics
The rising morbidity caused by antibiotic-resistant Gram-posi-
tive pathogenic bacteria has become a major concern for clinicians
and the public health system. For example, the prevalence of meth-
icillin-resistant Staphylococcus aureus (MRSA) strains in U.S. hospi-
tals is presently in the range of 33–55% in 2006,1 and treatment for
infections caused by antibiotic-resistant bacteria has become com-
plex and costly. One worrisome trend is the high prevalence of
antibiotic-resistant bacteria strains in community-acquired infec-
tions.2 While vancomycin is an efficient therapeutic agent for most
antibiotic-resistant Gram-positive bacteria, vancomycin-resistant
S. aureus (VRSA) was reported in the U.S. in 2002.3 Therefore, it is
imperative to search for novel drug candidates with new modes
of action against drug-resistant bacteria, because antibacterial
drugs with a new mode of action are expected to have no pre-exist-
ing resistance.
Bacterial peptide deformylase (PDF), an iron-containing
metalloproteinase, is an attractive target for studies focusing on
developing new antibiotics for the following reason: while PDF
does not share close homology with any mammalian equivalent,
it catalyzes the removal of the N-formyl group from the N-terminal
methionine during bacterial protein synthesis.4 The proposed tran-
sition state structure corresponds to a formylmethionyl peptide
bound to a ferrous ion at the active site of the deformylase enzyme.
The transition state indicates that the generic inhibitor structure
should combine the characteristics of both the chelator and the
peptidomimetic backbone (Fig. 1).5 Actinonin (Fig. 2), a naturally
occurring antibiotic isolated in 1962 from an actinomycete,6 was
the first reported PDF inhibitor. It showed moderate antibacterial
activity against several Gram-positive and Gram-negative bacte-
ria,7 but did not show good in vivo antibacterial activity due to
poor pharmacokinetic properties, which could be attributed to
either poor absorption or quick clearance.8
Thus far, many pharmaceutical companies and academic insti-
tutions have focused on the development of novel PDF inhibitors.9
The first two PDF inhibitors that underwent human clinical trials
are BB83698 (Fig. 2, discovered by British Biotech, in collaboration
with Genesoft) and LBM415 (Fig. 2, discovered by Vicuron pharma-
ceuticals, in collaboration with Novartis).8 LBM415 was reported to
have better in vitro antibacterial activity than BB83698.8,10 Investi-
gations of the structure–activity relationships based on LBM415
modification have been reported.11
a,b-Dehydroamino acids were
found in many biologically active natural products, including ant-
rimycins, tentoxin, and the phosphatase inhibitors microcystin
and nodularin.12 In this study, we report our approach to the mod-
ification of LBM415, in which the pyrrolidine functionality at the
0
P2 position is replaced by 2,5-dihydropyrrole. A number of 2,5-
dihydropyrrole formyl hydroxyamino derivatives 1a–1r (Fig. 3)
were synthesized as novel PDF inhibitors, and their in vitro anti-
bacterial activities were evaluated.13
A general synthesis of 2,5-dihydropyrrole formyl hydroxyamino
derivatives (1a–1r) is illustrated in Scheme 1 and is similar to a
previously reported route.14 In the synthesis, dimethyl 2-butylmal-
onate was hydrolyzed with 30% aqueous sodium hydroxide to
afford 2-butylmalonic acid 2, which was converted to 2-methyl-
enehexanoic acid 3 by treatment with formaldehyde. Reaction of
3 with pivaloyl chloride gave an anhydride intermediate, which
was treated with the anion of (S)-4-benzyl-2-oxazolidinone to
* Corresponding author.
E-mail address: huwenhao@yahoo.com (W. Hu).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.04.123

W. Shi et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3592–3595
3593
O
N
O
Bu
(a)
Bu
Bu
Bu
O
(b)
Bu
(c)
EtO
OEt
HO
OH
OH
O
H
O
S
O
H
O
Fe
O
O
O
O
O
3
Ph
O
O
H
2
4
H
P3
X
N
R3
N
N
(d)
Bu
H
N
N
H
O
O
R2
H
H
O
P2
O
O
H
N
H
N
Bu
(f)
OH
N
(e)
PMBO
PMBO
N
OH
Figure 1. Generic PDF inhibitor structure.
PMBO
O
O
Ph
7
5
O
6
+
HO
(g)
O
O
N
Boc
8
N
OH
H
N
H
H
O
HO
N
O
O
F
O
O
O
N
9
H
N
N
HO
N
HO
N
(h)
H
N
O
H
O
N
O
H
O
O
H
O
Bu
Bu
(i)
Actinonin
LBM415
N
N
N
PMBO
PMBO
O
O
OH
O
O
O
10
11
OH
N
O
O
(j)
H
N
O
H
H
O
N
H
O
Bu
Bu
O
O
N
(k)
N
N
N
N
HO
PMBO
R1
R1
BB83698
Figure 2. Structures of Actinonin, LBM415 and BB83698.
O
O
N
N
O
O
1a-1r
R2
R2
12a-12r
Scheme 1. Reagents and conditions: (a) NaOH, H2O, reflux, 3–4 h, 89%; (b) 37%
HCHO, Et2NH, EtOH, reflux, 16 h, 84%; (c) i—3, pivaloyl chloride, Et3N, THF, ꢀ60 °C;
ii—LDA; (S)-4-benzyl-2-oxazolidinone, ꢀ60 °C; iii—ꢀ60 to 25 °C, 3 h, 63%; (d) i—
PMBONH2, 50 °C, 24 h; ii—PTSA, Na2CO3, EA/H2O, 58%; (e) LiOH, 30% H2O2, Na2SO3,
0 °C, 1 h, 58%; (f) HCO2Et, 60 °C, 16 h, 80%; (g) TFA/CH2Cl2, Et3N, 25 °C, 30 min,
quantity; (h) HOBt, EDCI, NMM, CH2Cl2, 25 °C, 16 h, 84%; (i) LiOH, dioxane/H2O,
25 °C, 5 h, 99%; (j) Et3N, ClCO2Et, R1R2NH, THF, 0–25 °C, 16 h, 60–81%; (k) TFA/
CH2Cl2, purified by chromatograph column, elute with CH2Cl2/MeOH 50:1, 35–45%.
H
O
N
N
HO
R1
O
N
O
R2
1a-1r
Figure 3. Generic structure of 1a–1r.
4–16 lg/ml) was observed when using aliphatic 1-phenylethylam-
0
ines that contain an aromatic ring at the P3 position (compounds
1c and 1d). Taking these results into account, we decided to replace
0
yield conjugated enone 4. The diastereoselective Michael addition
reaction of 4 with O-(4-methoxybenzyl)hydroxylamine15 afforded
5 as a single diastereomer with a yield of 58% after recrystallization
in t-butyl methyl ether. The chiral auxiliary was removed by LiOH
and H2O2 to give the corresponding carboxylic acid derivative 6.
Formylation of 6 using ethyl formate yielded 7.
The N-Boc protected 2,5-dihydropyrrole derivative 8 was pre-
pared in accordance with a previously described procedure.16 Suc-
cessful deprotection of 8 with trifluoroacetic acid afforded 9 in
quantitative yield. The coupling reaction between 7 and 9 was suc-
cessfully carried out using 1-hydroxy-benzotriazole monohydrate
the aliphatic amines at the P3 position with aromatic amines. Com-
pounds 1e–1m, each bearing aromatic amide moieties, were syn-
thesized, and they show moderate to good antibacterial activity
against the Gram-positive bacterial strains. Finally, heterocyclic
0
aromatic amines were introduced at the P3 position, resulting in
compounds 1n–1q. Good to excellent antibacterial activities were
observed with these compounds. Notably, compound 1q, which
contains a thiazolyl functionality, exhibited MIC values ranging
from 0.0625 to 0.25 lg/ml against Gram-positive bacterial strains
including S. aureus, MSSA, MRSA, and S. epidermidis. It is worth
mentioning that 1q also showed moderate antibacterial activity
(HOBt)
and
1-(3-dimethylaminopropyl)-3-ethylcarbodiimide
(MIC 16–32 lg/ml) against Gram-negative bacteria Escherichia coli.
hydrochloride (EDCI) in the presence of N-methylmorpholine
(NMM) to produce 10 with a yield of 84%. Hydrolysis of 10
followed by coupling with amines R1R2NH gave compounds 12a–
12r. Finally, removal of the PMB protecting group using trifluoro-
acetic acid successfully provided the desired 2,5-dihydropyrrole
formyl hydroxyamino derivatives 1a–1r. These compounds were
characterized by 1H NMR, 13C NMR and HR-MS(ESI), and HPLC pur-
ity of the compounds ranges from 90% to 97%.
The new compounds 1a–1r were screened against Gram-posi-
tive bacterial strains such as S. aureus and Staphylococcus epidermi-
dis and against the Gram-negative strain Escherichia coliform. The
screening results are summarized in Table 1. The compounds con-
taining aliphatic amines such as morpholine and cyclopropyl
amine (1a and 1b) exhibited unsatisfactory antibacterial activity
against all the tested strains. Moderate antibacterial activity (MIC
Because compound 1f, which contains an electron-withdrawing
group, showed favorable antibacterial activity, we incorporated
the electron-withdrawing trifluoromethyl group in a heterocyclic
amine to synthesize compound 1r. Unfortunately, a dramatic de-
crease in antibacterial activity was observed for compound 1r.
In summary, replacement of the pyrrolidine ring of LBM415
with a 2,5-dihydropyrrole backbone resulted in the synthesis of
novel compounds having in vitro antibacterial activity against
drug-resistant bacteria. The aliphatic amine derivatives 1a and
1b are poor antibacterial agents, but the aromatic amine deriva-
tives 1e–1m and heterocyclic amine derivatives 1n–1q are more
active against bacteria. Compound 1q showed excellent in vitro
antibacterial activity (MIC 0.0625–0.25 lg/ml) against Gram-posi-
tive bacterial strains, including drug-resistant bacteria MRSA. Fur-
ther in vivo studies of 1q are currently in progress in our lab.

3594
W. Shi et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3592–3595
Table 1
In vitro minimum inhibitory concentration (MIC,
l
g/ml) values of 1a–1r in various strainsa
Compound
–NR1R2
S. aureus
MSSA
MRSA
S. epidermidis
E. coli 1
E. coli 2
ATCC25923
ATCC29213
ATCC43300
ATCC12228
ATCC25922
ATCC35218
N
O
1a
1b
>64
64
>64
32
32
2
>64
4
>64
64
>64
32
HN
1c
4
4
16
16
8
2
8
4
>64
>64
>64
>64
N
H
1d
N
H
N
H
1e
1f
4
8
2
2
1
2
>64
>64
>64
64
32
N
H
NO2
0.5
0.5
0.5
1
0.5
2
N
H
OMe
1g
>64
H
N
1h
32
4
1
8
>64
>64
Br
N
H
1i
8
1
1
2
0.125
0.5
1
2
1
64
>64
>64
16
>64
64
Br
N
H
Br
1j
4
N
H
1k
0.5
0.25
Cl
N
H
Cl
F
1l
8
2
2
2
1
1
4
4
>64
>64
>64
64
N
H
1m
H
N
1n
1o
0.125
0.5
1
1
0.125
0.25
0.5
0.5
>64
>64
32
64
N
H
N
F
N
H
N
F
1p
0.5
1
0.5
1
>64
64
N
O
N
1q
1r
0.0625
32
0.25
16
0.125
8
0.25
16
32
16
N
H
S
N
N
N
>64
>64
CF3
S
H
LBM415
Linezolid
Penicillin
Ciprofloxacin
Vancomycin
0.25
2
0.0625
0.5
1
2
1
0.5
1
0.5
4
64
1
0.5
0.5
2
0.25
2
64
>64
>64
<0.03125
>64
64
>64
>64
<0.03125
>64
1
1
a
MIC was determined by the microbroth dilution technique. MSSA, methicillin-susceptible S. aureus; MRSA, methicillin-resistant S. aureus.
7. Chen, D. Z.; Patel, D. V.; Hackbarth, C. J.; Wang, W.; Yuan, Z., et al Biochemistry
2000, 39, 1256.
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This work was supported by the Science and Technology Com-
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of China (2009ZX09501-017).
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