Peptide deformylase inhibitors with non-peptide scaffold: Synthesis and structure-activity relationships

Article abstract of DOI:10.1016/j.bmcl.2010.11.056

Peptide deformylase (PDF), which removes the formyl group at the N-terminal methionine residue of nascent protein, has been recognized as a potent target for antibacterial therapy. We report herein the synthesis and structure-activity relationship studies

Full text of DOI:10.1016/j.bmcl.2010.11.056

Bioorganic & Medicinal Chemistry Letters 21 (2011) 133–136
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Peptide deformylase inhibitors with non-peptide scaffold: Synthesis
and structure–activity relationships
Seung Kyu Lee a,c, Kwang Hyun Choi a, Sang Jae Lee a, Jong Sun Lee a, Ji Yun Park a, B. Moon Kim b,
Bong Jin Lee a,c,
⇑
a Promeditech Ltd, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
b Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, Republic of Korea
c Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 599 Gwanak-Ro, Gwanak-Gu, Seoul 151-742, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 22 June 2010
Revised 27 October 2010
Accepted 10 November 2010
Available online 16 November 2010
Peptide deformylase (PDF), which removes the formyl group at the N-terminal methionine residue of
nascent protein, has been recognized as a potent target for antibacterial therapy. We report herein the
synthesis and structure–activity relationship studies of non-peptide PDF inhibitors.
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
PDF
SAR
Antibacterial
Non-peptide
Increasing antibacterial resistance poses a severe threat to
human health.1 As consequences, there is a growing need to iden-
tify new antibiotics that do not share the targets of existing anti-
bacterial drugs. Many novel and potentially useful targets are
discovered by analysis of microbial genomes, but only a few targets
succeed to yield active antibiotics.2,3 One of novel and potentially
useful targets that have recently received a particular attention is
peptide deformylase (PDF).4 The difference in protein synthesis be-
tween bacteria and mammalian cells stems from transformylation
and deformylation of initiating methionine. Protein synthesis in
bacteria is initiated with N-formylmethionine which is generated
by transformylation of methionine. PDF removes the formyl group
at the N-terminal methionine residue of nascent protein.5 The fact
that the peptide deformylase is essentially required for producing
mature protein in bacteria provides a rational basis to choose it
as a potential antibacterial target.
chiral alkyl chain and reverse hydroxamic acid, respectively, signif-
icantly increases antibacterial activity against S. aureus. Here, we
describe the synthesis of non-peptide PDF inhibitors 2 and corre-
0
sponding SAR around the P3 positions.
The synthesis of PDF inhibitors used in this study is outlined in
Schemes 1–3.7 Coupling of N-Boc amino acid 3 with Meldrum’s
acid in the presence of DCC and DMAP gave acyl Meldrum’s acid
and subsequent treatment with benzyl alcohol provided b-keto es-
ter 4.8 In this step tetramic acid, which was produced from unde-
sired cyclization reaction, was easily removed by silica-gel
column chromatography. Compound 5 was prepared from alkyl-
ation with butyl group at the a-position of the b-keto ester 4. Re-
moval of benzyl group by hydrogenolysis in the presence of 10%
Pd/C afforded a b-keto acid, which was treated with formaldehyde
and piperidine to give compound 6. Since the b-keto acid was eas-
ily decarboxylated at room temperature, storing the b-keto acid is
not recommended. Conjugate addition of benzylhydroxylamine
formed diastereomeric adducts (72:28, RS:SS diastereomeric ratio).
The desired (R)-diastereomer 7 was isolated from purification
through silica-gel column chromatography. Treatment of com-
pound 7 with formic acid and acetic anhydride provided com-
pound 8. Final compound 9 was obtained from removal of the
benzyl group through hydrogenolysis.
In a previous study, we have reported that PDF inhibitor 16 and
its analogs have potent antibacterial activity against Streptococcous
pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis
which are known to cause respiratory tract-associated infection
(Fig. 1). But PDF inhibitor 1 and analogs have lower antibacterial
activity against Staphylococcus aureus. During the course of our
PDF inhibitor program, we found that replacement of the N-alkyl
side chain and the hydroxamic acid moiety of compound 1 with
0
For the synthesis of PDF inhibitors with amide moiety at P3 po-
sition, compound 8b was treated with trifluoroacetic acid to afford
compound 10. Amine 10 was coupled with corresponding carbox-
ylic acid to provide compound 11. Removal of O-benzyl group with
hydrogenolysis gave final compound 12.
⇑
Corresponding author. Tel.: +82 2 880 7869; fax: +82 2 872 3632.
E-mail address: lbj@nmr.snu.ac.kr (B.J. Lee).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.11.056

134
S. K. Lee et al. / Bioorg. Med. Chem. Lett. 21 (2011) 133–136
Compounds were tested using a P. aeruginosa Ni-PDF enzyme
O
O
O
O
H
N
H
N
H
N
H
N
assay10 and primary in vitro antibacterial activity was tested
against S. pneumoniae, H. influenzae, M. catarrhalis and S. aureus.
The size of the amino acid side chain at P20 position appears to have
significant effect on the enzyme inhibition activity, and antibacte-
rial activity against S. aureus. From the assay data summarized in
R
HO
N
H
N
O
O
HO
O
1
2
0
Table 1, preferred side chain for P2 site appears to be an isopropyl
Figure 1. Structures of PDF inhibitor 1 and non-peptide PDF inhibitor 2.
group because valine derivative (9b) revealed potent inhibition
against enzyme and bacterial strains. The loss in activity of t-leu-
Compound 10 was treated with carbonyl diimidazole9 and the
resulting imidazolide 13 was coupled with the corresponding
amine in toluene to give compound 14. The final urea 15 was ob-
tained by deprotection of benzyl group using hydrogenolysis.
0
cine derivative (9c) against S. aureus shows that P2 binding pocket
is not suitable for binding with side chain bigger than isopropyl
group.
O
O
O
O
O
NHBoc
a
b
c
BnO
NHBoc
NHBoc
R1
O
HO
BnO
R1
R1
O
3
4
5
O
O
H
NHBoc
NHBoc
R1
NHBoc
d
e
f
BnOHN
N
BnO
R1
R1
6
7
8
O
O
NHBoc
H
N
HO
R1
9
Scheme 1. Reagents and conditions: (a) Meldrum’s acid, DCC, DMAP, rt, then toluene, BnOH, 80 °C, 30–50%; (b) K2CO3, NaI, n-BuBr, acetone, reflux, 18 h, 50–60%; (c) 10%
Pd/C, H2, EtOH, then CH2O, piperidine, 80 °C to rt, 55–65%; (d) BnONH2, 40 °C, 12 h, 55–60%; (e) HCO2H, Ac2O, EtOAc, rt, 1 h, 90–95%; (f) 10% Pd/C, H2, MeOH, rt, 2 h, 40–50%.
O
O
O
O
O
O
H
N
R2
NHBoc
NH2
a
b
H
N
H
N
H
N
BnO
BnO
BnO
O
10
11
8b
O
O
H
N
R2
c
H
N
HO
O
12
Scheme 2. Reagents and conditions: (a) TFA, dichloromethane, rt, 6 h, 98%; (b) R2CO2H, HOBt, EDC, N,N-diisopropylamine, dichloromethane, rt, 12 h, 35–50%; (c) 10%
Pd/C, H2, MeOH, rt, 2 h, 40–50%.
O
O
O
O
O
O
H
N
H
N
N
NH2
N
NHR3
a
b
H
N
H
N
H
N
BnO
BnO
O
BnO
O
10
13
14
O
O
H
N
NHR3
c
H
N
HO
O
15
Scheme 3. Reagents and conditions: (a) carbonyl diimidazole, N,N-diisopropylethylamine, dichloromethane, rt, 4 h, 88%; (b) R3NH2, toluene, reflux, 18 h, 35–50%; (c) 10% Pd/
C, H2, MeOH, rt, 2 h, 40–50%.

S. K. Lee et al. / Bioorg. Med. Chem. Lett. 21 (2011) 133–136
135
Table 1
0
PDF inhibition and in vitro antibacterial activities for P2 side chain
O
O
H
N
O
[AA]
H
N
O
HO
Compound
AA
IC50 (nM)
MIC (lg/ml)
P. aeruginosa PDF
S. pneumoniae
H. influenzae
M. catarrhalis
S. aureus
1
29
330
183
603
169
0.2
3.2
1.6
6.3
6.3
0.2
0.8
1.6
3.2
0.4
0.1
1.6
0.1
0.1
0.4
50.0
12.5
12.5
100
9a
9b
9c
9d
Alanine
Valine
t-Leucine
Proline
12.5
Table 2
0
PDF inhibition and in vitro antibacterial activities for P3 amides
O
O
H
N
R2
H
N
HO
O
Compound
R2
IC50 (nM)
MIC (lg/ml)
P. aeruginosa PDF
S. pneumoniae
H. influenzae
M. catarrhalis
S. aureus
1
9b
29
183
60
51
117
22
43
73
52
8
0.2
1.6
0.8
3.2
0.2
0.2
0.4
0.2
0.4
0.1
0.4
0.2
1.6
0.2
0.2
0.1
0.2
0.2
0.1
0.1
0.2
0.4
0.1
0.1
1.6
0.4
0.1
0.8
1.6
0.1
0.1
0.1
0.1
50.0
12.5
3.2
3.2
1.6
0.8
1.6
0.8
1.6
0.4
6.4
O-t-Butyl
i-Propyl
Ph
Pyridin-2-yl
Ph(3-MeO)
Ph(3-F)
Pyridin-3-yl
Pyridin-4-yl
Quinolin-2-yl
i-Quinolin-1-yl
12a
12b
12c
12d
12e
12f
12g
12h
12i
5
Table 3
0
PDF inhibition and in vitro antibacterial activities for P3 ureas
O
O
H
N
NHR3
H
N
HO
O
Compound
NHR3
IC50 (nM)
MIC (lg/ml)
P. aeruginosa PDF
S. pneumoniae
H. influenzae
M. catarrhalis
S. aureus
1
9b
29
183
16
10
49
41
41
43
0.2
1.6
0.4
1.6
0.4
0.1
0.2
1.6
0.2
1.6
0.1
0.2
0.4
0.2
0.1
0.1
0.1
0.1
0.8
0.1
0.1
0.1
0.1
0.1
50.0
12.5
1.6
1.6
1.6
0.8
O-t-Butyl
15a
15b
15c
15d
15e
15f
NH-i-Propyl
NH-c-Pentyl
NH-Ph
NH-Ph(2-MeO)
NH-Ph(2-F)
NH-Pyridin-2-yl
0.4
0.8
0
Introduction of amide derivatives at P3 site (Table 2) led to
compounds having more potent activity than the carbamate com-
Urea derivatives (Table 3) also displayed potent PDF inhibition
and antibacterial activity against tested strains. Both alkyl and aro-
0
0
pound (9b) (Table 1). Variation in the P3 amide derivatives did not
matic ureas were well tolerated at the P3 position. Compound 15d
0
show much difference in PDF inhibition and antibacterial activity.
Substitution at the phenyl ring (12d, 12e) slightly improved the en-
zyme inhibition and antibacterial activity. Nitrogen atom’s position
in the pyridine ring appeared to have little effect on antibacterial
activity. Introduction of quinoline (12h) and isoquinoline (12i)
showed increased enzyme inhibition, but antibacterial activity
was similar to that of pyridine derivatives.
having the same urea P3 moiety in compound 1 displayed signifi-
cantly increased antibacterial activity against S. aureus than com-
pound 1, which showed that chiral alkyl chain and reverse
hydroxamic acid might be important factor to improve antibacte-
rial activity against S. aureus.
In order to obtain an insight on the structural differences be-
tween 1 and 15d in their binding modes, we conducted a modeling

136
S. K. Lee et al. / Bioorg. Med. Chem. Lett. 21 (2011) 133–136
(Gly110). These factors may increase antibacterial activity of com-
pound 15 against S. aureus.
A series of non-peptide, reverse hydroxamide inhibitors was de-
signed based on the known peptide inhibitor 1. An SAR study of
these non-peptide inhibitors led to identification of potent PDF
inhibitors. Modeling study shows that compound 1 and 15d have
different binding modes on active site of S. aureus PDF.
Acknowledgements
This work was supported by a grant from the National Research
Foundation of Korea (NRF) funded by the Korea Government
(MEST) (No. 20100001707), and a grant from Korea Health and
Welfare (A092006). This work was also supported by 2010 BK21
project for Medicine, Dentistry and Pharmacy.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2010.11.056.
References and notes
Figure 2. Docking model of compound 1 (yellow) and compound 15d (green) were
superimposed with active site of X-ray crystal structure of S. aureus PDF (RCSB
protein data bank ID: 1Q1Y). The Zn2+ atom is colored in red. The accessible surface
of the binding site is shown in purple.
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study based upon the X-ray crystal structure of S. aureus PDF.11 The
compound 1 and 15d fit into the active site of S. aureus PDF and the
resulting 3D structures of 1 and 15d are superimposed on the ac-
tive site (Fig. 2). Superimposition of these structures yields a close
0
0
0
overlap between the P1 side chains of 1 and 15d, but P2 and P3
0
side chains of 1 and 15d show the different binding modes. P2 side
chain of compound 15d is located more deeply in the binding
0
pocket than that of compound 1. Additionally P3 site of compound
11. Yoon, H. J.; Kim, H. L.; Lee, S. K.; Kim, H. W.; Kim, H. W.; Lee, J. Y.; Mikami, B.;
Suh, S. W. Proteins 2004, 57, 639.
15d is not overlapped with compound 1 and oxygen atom of urea
group in compound 15d is hydrogen bonding with backbone atom