Synthesis and evaluation of 1-(1H-indol-3-yl)ethanamine derivatives as new antibacterial agents

Article abstract of DOI:10.1016/j.bmc.2011.03.060

A collection of 3-substituted indole derivatives was prepared using nucleophilic addition of indoles to nitrones. The compounds were then tested for their antibacterial activity against almost thirty bacterial strains representative of common human pathog

Full text of DOI:10.1016/j.bmc.2011.03.060

Bioorganic & Medicinal Chemistry 19 (2011) 3204–3215
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry
journal homepage: www.elsevier.com/locate/bmc
Synthesis and evaluation of 1-(1H-indol-3-yl)ethanamine derivatives
as new antibacterial agents
Olga N. Burchak a, , Emmanuelle Le Pihive b, Laure Maigre b, Xavier Guinchard a, Pascale Bouhours c,
⇑
Claude Jolivalt c, Dominique Schneider b, Max Maurin b,d, Carmela Giglione e, Thierry Meinnel e,
Jean-Marc Paris c, Jean-Noël Denis a,
⇑
a Département de Chimie Moléculaire (SERCO), UMR-5250, CNRS, Université Joseph Fourier, BP-53, 38041 Grenoble Cedex 9, France
b Laboratoire Adaptation et Pathogénie des Micro-organismes, UMR-5163, CNRS, Université Joseph Fourier, Grenoble 1, Institut Jean Roget, Campus Santé, Domaine de la Merci,
BP 170, F-38042 Grenoble Cedex 9, France
c Chimie ParisTech (Ecole Nationale Supérieure de Chimie de Paris), Laboratoire Charles Friedel, UMR-7223, CNRS, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05, France
d CHU de Grenoble, Université Joseph Fourier, BP217, 38043 Grenoble Cedex 9, France
e CNRS, ISV, UPR2355, Bâtiment 23A, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette Cedex, France
a r t i c l e i n f o
a b s t r a c t
Article history:
A collection of 3-substituted indole derivatives was prepared using nucleophilic addition of indoles to
nitrones. The compounds were then tested for their antibacterial activity against almost thirty bacterial
strains representative of common human pathogens. Two types of indolic molecules inhibit the growth of
Staphylococcus aureus, including MRSA and VISA strains, with MIC values ranging from 8 to 16 mg/L.
Ó 2011 Elsevier Ltd. All rights reserved.
Received 12 November 2010
Revised 20 March 2011
Accepted 28 March 2011
Available online 2 April 2011
Keywords:
Indolic derivatives
Substituted hydroxylamines
Antibacterial activity
1. Introduction
concern many gram-negative species such as Escherichia coli, Pseu-
domonas aeruginosa, and Acinetobacter baumanii.5 The discovery of
Antibiotics changed the history of mankind in the early forties.
Frequent and often deadly diseases were successfully cured and for
half a century, this revolution was considered as definitely ac-
quired, occulting the extraordinary adaptability of the bacterial
world.1 Unfortunately, over the last 15 years, bacterial resistances
have evolved much faster than innovation. The increased preva-
lence and worldwide dissemination of multidrug-resistant bacteria
has resulted in a major decrease in therapeutic options, especially
in the hospital setting.2 Among the gram-positive bacteria, major
antibiotic-resistant pathogens belong to the genera Staphylococcus,
Enterococcus and Streptococcus. As for Staphylococcus sp., the
widespread and long-term use of beta-lactam and glycopeptide
antibiotics has led to the emergence of meticillin-resistant Staphy-
lococcus aureus (MRSA) and vancomycin-intermediate Staphylococ-
cus aureus (VISA) strains.3 Resistance has also emerged to
beta-lactams in Streptococcus pneumoniae and Enterococcus sp.,
and to glycopeptides in Enterococcus sp.4 Multidrug-resistance also
antibacterial agents that operate via novel modes of action and are
thus not prone to currently existing resistance mechanisms, is now
urgent.
The sources of antibacterial compounds are either natural prod-
ucts or synthetic molecules. Though most of the antibiotics on
the market today originate from natural products or their
semisynthetic derivatives,6 research for new natural antibiotics is
restricted due to their structural complexity, instability and limited
availability as compared to synthetic chemicals. On the other hand,
despite the ability of chemists to prepare libraries containing thou-
sands of synthetic compounds, major discoveries relevant to infec-
tious disease treatment remains rare and, arguably, serendipitous.7
This could be explained by a weak structural diversity and poor
physicochemical properties of available commercial compound li-
braries. Consequently, the creation of diverse collections of unique,
highly potent bioactive small molecules could dramatically accel-
erate the rate of biochemical discoveries of new antibiotics.8
One approach to this problem is the creation of compound col-
lections based on ‘privileged scaffolds’.7a Due to their versatile
binding properties, these frameworks (or substructures) are able
to provide potent and selective ligands for a range of different bio-
logical targets. Our choice of indole scaffold9 for a search of novel
⇑
Corresponding authors. Tel.: +33 476 635 863; fax: +33 476 635 983 (O.N.B.);
tel.: +33 476 514 426; fax: +33 476 635 983 (J.-N.D.).
E-mail addresses: olga.burchak@ujf-grenoble.fr (O.N. Burchak), jean-noel.denis@
ujf-grenoble.fr (J.-N. Denis).
0968-0896/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmc.2011.03.060

O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
3205
antibiotics accounts for several reasons. Firstly, the indole nucleus
OH
R
is a widespread substructure found in molecules which exhibit a
wide spectrum of pharmacological activities,7a,10 including a sig-
nificant antimicrobial one.11 Furthermore, it has been shown that
even nonsubstituted indole nucleus possesses a weak antibacterial
activity.12 Secondly, a versatile and efficient chemical approach to-
wards 3-substituted indoles by the nucleophilic addition of indoles
to nitrones has been developed by our research group (Fig. 1).13
This method was successfully employed14 to the total synthesis
of marine sponge bis(indole) alkaloids of the hamacanthin, spong-
otine, and topsentin classes, exhibiting significant antibiotic
activity.11c
In this Letter, we report the synthesis of a collection of differ-
ently substituted indolic derivatives and the results on their anti-
bacterial activity against almost thirty bacterial strains. Some
information about mechanism of action, as well as the cytotoxicity
data of synthesized compounds, is also reported.
N
Bn
O
R
Bn
4
3
5
6
N
a
X
X
+
N
55-98%
N
H
H
1a-c
2a-i
3aa-ci
b 44-78%
O
N
OH
NH
R
R
Ph
c
X
X
32-77%
N
H
N
H
5aa-ci
4aa-ci
only for R = CH2NHBoc
78-99%
d
OH
NH
X = H, 5-F, 5-Cl,
5-Br, 5-I, 6-F,
H2N
2. Results and discussion
2.1. Chemistry
6-Cl, 6-Br, 4-Br
X
R = Me, i-Bu, CH2NHBoc
2HCl
N
H
6ca-ci
The synthesis of the indole library is outlined in Scheme 1. Cou-
pling reaction13 in acidic conditions between three nitrones 1a–c15
and nine commercially available indoles 2a–i efficiently provided
the indolic N-hydroxylamines 3aa–ci (Table 1). Then the latter
compounds have been oxidized to aldonitrones 4aa–ci by manga-
nese dioxide in toluene.16 A hydroxyaminolysis of indolic nitrones
4aa–ci was performed yielding N-hydroxylamines 5aa–ci, that
have been subjected to Boc-cleavage reaction. A series of amino-
N-hydroxylamines 6ca–ci was obtained as stable solids. Finally, a
collection of 66 indole derivatives was created, and all synthesized
products possess N-(1-(1H-indol-3-yl)ethanamine substructure
(Table 1). Moreover, using simple and efficient chemical transfor-
mations we have obtained four different sublibraries of indolic
molecules: secondary N-hydroxylamines 3aa–ci, aldonitrones
4aa–ci, primary N-hydroxylamines 5aa–ci and primary amines
6ca–ci. The diversity of functional groups of library members en-
hances the possibility to discover biologically active molecules.
Scheme 1. Synthesis of 3-substituted indoles. Reagents and conditions: (a) HCl,
MeOH, 0 °C; (b) MnO2, toluene, 100 °C; (c) NH2OHÁHCl, MeOH, rt; (d) HCl, MeOH,
0 °C.
strains allowed us to test their inhibitory activity against bacterial
efflux pumps. These results will be presented in a separate
publication.
Disubstituted N-hydroxylamines 3aa–ci provided six indolic
molecules showing a significant antibacterial activity (Table 2).
The N-hydroxylamines 3cc–ce and 3cg–ch are bacteriostatic
against all tested Staphylococcus sp. strains with MIC values rang-
ing from 8 to 16 mg/L. A weak antibacterial activity was also ob-
served against Streptococcus sp. for compounds 3cc–ce, with MIC
values of 64–128 mg/L for S. pneumoniae and 32–64 lg/ml for S.
pyogenes CIP 10422. Furthermore, compounds 3bb, 3cc and 3ce
were weakly active against H. influenzae with MIC values of
64 lg/ml. Structural diversity of the sublibrary members allowed
us to draw some SAR observations. Growth of the side alkyl chain
size of N-hydroxylamines 3aa–ci from methyl to isobutyl and then
to CH2-NH-Boc increases the antibacterial activity. These results
demonstrate that a bulky group at this position of disubstituted
N-hydroxylamines is required for antibacterial activity. It can be
hypothesized that CH2-NH-Boc functional group can interact with
bacterial target by means of hydrogen bonds of carbamate func-
tion. Furthermore, substitution at the C(5) or C(6) position of in-
dole core by a halogen such as chlorine, bromine or iodine, is
essential to improve antibacterial activity.
The monosubstituted N-hydroxylamines 5aa–ci of the second
sublibrary, obtained by benzyl cleavage reaction of disubstituted
N-hydroxylamines 3aa–ci, display a weak antibacterial activity
against Staphylococcus strains with MIC values of 64–128 mg/L
(Table 3). Two opposite observations were made for this group of
indolic derivatives. (1) In the case of N-hydroxylamines 5aa–be
with simple aliphatic side chain (R = Me or i-Bu), the benzyl
cleavage lead to an improvement of the antibacterial activity. It
is especially true for the compounds 5ab–ae and 5bb–be substi-
tuted by a halogen at position C(5) of the indole core. (2) In
contrast, in the case of monosubstituted N-hydroxylamines 5ca–
ci with carbamate side chain (R = CH2NHBoc), the benzyl cleavage
results in reduction of the antibacterial activity. This last observa-
tion demonstrates that benzyl and CH2-NH-Boc functional groups
may be simultaneously required for antibacterial activity of
sublibrary 3ca–ci compounds.
2.2. Biological activity
The indolic compounds were tested for their antimicrobial
activity against a panel of 28 reference bacterial strains belonging
to 17 different species representative of common human patho-
gens. The minimum inhibitory concentrations (MICs) of the tested
compounds allowing complete inhibition of visual bacterial
growth show that compounds from one of four sublibraries,
namely the aldonitrones 4aa–ci, are completely inactive (MIC
>128 mg/L) towards gram-positive and gram-negative bacteria. In
contrast, several primary and secondary N-hydroxylamine com-
pounds belonging to the three other groups display a significant
antibacterial activity against Staphylococcus sp. and a weak activity
against S. pneumoniae. This indicates that the N-hydroxylamine
function group plays an important role for antibacterial activity
of N-(1-(1H-indole-3-yl)ethyl)hydroxyamines. It should be
mentioned that inactivity of aldonitrones 4aa–ci against bacterial
NR1R2
O
Bn
NR3R4
N
X
+
3
N
H
X
NHBoc
N
H
Figure 1. The chemical approach towards 3-substituted indoles.

3206
O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
Table 1
Synthesis of 3-substituted indoles
Indole
R
X
Yielda (%)
Indole
R
X
Yielda (%)
Indole
R
X
Yielda (%)
3aa
3ab
3ac
3ad
3ae
3ba
3bb
3bc
3bd
3be
3ca
3cb
3cc
3cd
3ce
3cf
Me
Me
Me
Me
Me
i-Bu
i-Bu
i-Bu
H
98
85
85
68
70
93
79
79
56
55
90
98
87
84
83
85
82
87
80
53
50
51
4ad
4ae
4ba
4bb
4bc
4bd
4be
4ca
4cb
4cc
4cd
4ce
4cf
4cg
4ch
4ci
5aa
5ab
5ac
5ad
5ae
5ba
Me
Me
i-Bu
i-Bu
i-Bu
i-Bu
i-Bu
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
Me
5-Br
5-I
H
5-F
5-Cl
5-Br
5-I
45
51
59
44
50
52
50
78
66
66
64
68
72
71
72
52
66
60
55
62
58
64
5bb
5bc
5bd
5be
5ca
5cb
5cc
5cd
5ce
5cf
5cg
5ch
5ci
6ca
6cb
6cc
6cd
6ce
6cf
i-Bu
i-Bu
i-Bu
i-Bu
5-F
46
41
36
32
65
58
62
56
75
40
77
57
68
98
94
78
98
99
89
95
89
99
5-F
5-Cl
5-Br
5-I
5-Cl
5-Br
5-I
H
5-F
5-Cl
5-Br
5-I
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NH2
CH2NH2
CH2NH2
CH2NH2
CH2NH2
CH2NH2
CH2NH2
CH2NH2
CH2NH2
H
5-F
5-Cl
5-Br
5-I
H
i-Bu
i-Bu
5-F
5-Cl
5-Br
5-I
6-F
6-Cl
6-Br
4-Br
H
5-F
5-Cl
5-Br
5-I
6-F
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
CH2NHBoc
Me
H
6-Cl
6-Br
4-Br
H
5-F
5-Cl
5-Br
5-I
6-F
6-Cl
6-Br
4-Br
H
5-F
5-Cl
5-Br
5-I
3cg
3ch
3ci
4aa
4ab
4ac
Me
Me
Me
Me
6-F
6cg
6ch
6ci
6-Cl
6-Br
4-Br
Me
Me
5-F
5-Cl
i-Bu
H
a
Isolated and purified yield. All compounds gave correct IR, 1H and 13C NMR and LC-MS analyses.
Table 2
Antibiotic activity of disubsituted N-hydroxylamines 3aa–ci against Staphylococcus sp. and Streptococcus pneumoniaea
Indole
MIC (mg/L)
MRSAc VISA ATCC
Indole
MIC (mg/L)
S.
S.
S.
S. aureus
MRSA VISA ATCC
106414
S.
S.
aureusb
106414
epidermidisd
pneumoniaee
epidermidis
pneumoniae
Cip
0.5
0.125
32
0.25
0.5–1
Gen
0.125-
0.25
—
>128
>128
16
8–16
8–16
>128
16
8–16
>128
0.25
>64
0.125
—
3aa
3ab
3ac
3ad
3ae
3ba
3bb
3bc
3bd
3be
128
—
—
64
—
Cfx
3ca
3cb
3cc
3cd
3ce
3cf
3cg
3ch
3ci
—
—
—
0.125
>128
>128
64
128
64
>128
>128
>128
>128
>128
>128
>128
>128
32
64–128
>128
>128
>128
>128
>128
>128
>128
—
>128
>128
>128
>128
—
>128
>128
>128
>128
16
64–128
>128
>128
>128
>128
>128
>128
>128
—
>128
>128
16
>128
>128
16
8
8
>128
16
16
>128
>128
16
16
8
>128
16
16
16
8–16
>128
16
16
>128
128
128
128
>128
>128
>128
>128
>128
>128
>128
>128
>128
>128
>128
a
b
c
Cip, ciprofloxacin; Gen, gentamicin: Cfx, cefotaxime.
MIC values of the following S. aureus strains: ATCC 25923, ATCC 29213, ATCC 9144, ATCC 6538, CIP 65.6 and CIP 103428.
MIC values of meticillin-resistant S. aureus CIP 65.25 and ATCC 33592.
MIC values of the following S. epidermidis strains: ATCC 12228, CIP 81.55 and CIP 103627.
MIC values of Streptococcus pneumoniae ATCC 49619 and ATCC 6303.
d
e
Finally, Boc cleavage reaction, leading to the free amino-N-
Table 3
hydroxylamines 6ca–ci sublibrary, induces an outstanding
increase of antibacterial activity (Table 4), compared to sublibrary
5ca–ci. Indeed, a significant activity was recorded for all the ami-
no-N-hydroxylamines hydrochlorides 6ca–ci against Staphylococ-
cus sp., including MRSA and VISA strains. Moreover, a weak
activity was also highlighted against Streptococcus sp., with MIC
values ranging from 64 to 128 mg/L for S. pneumoniae, Streptococ-
cus agalactiae, S. pyogenes, S. mitis, E. faecium and E. faecalis strains.
Compounds 6cc, 6ce and 6cg were also weakly active against H.
influenzae, with MIC values of 64–128 mg/L. Lastly, the amino-N-
hydroxylamines was the only sublibrary exhibiting a weak activity
against other Gram negative bacilli. We recorded MIC values rang-
ing from 16 to 128 mg/L against E. coli, K. pneumoniae, E. cloacae, S.
marcescens, P. aeruginosa and A. baumanii strains. For this subli-
brary, the important role of the halogen atom was also demon-
strated. The fluorine, chlorine or bromine atoms at the C(5) or
C(6) positions of the indole core increased the antibiotic activity
of indolic derivatives 6cb–ch against Staphylococcus sp., with MIC
values ranging from 8 to 32 mg/L.
Antibiotic activity of monosubstituted N-hydroxyl-amines 5aa–ci against Staphylo-
coccus sp.a
Indole
MIC (mg/L)
S. aureusb S. epidermidisc
Indole
MIC (mg/L)
S. aureus S. epidermidis
Cip
0.5
128
64
32
64
64
64
32–64
16
32
0.25
64
64
16
64
32
32
32
32
16
16
Gen
5ca
5cb
5cc
5cd
5ce
5cf
5cg
5ch
5ci
0.125–0.25
>128
>128
64
32-64
32
>128
128
64
0.125
>128
>128
64
64
64
>128
>128
64
5aa
5ab
5ac
5ad
5ae
5ba
5bb
5bc
5bd
5be
128
128
32
a
Cip, ciprofloxacin; Gen, gentamicin.
MIC values of the following S. aureus strains: ATCC 25923, ATCC 29213, ATCC
b
9144, ATCC 6538, CIP 65.6 and CIP 103428.
c
MIC values of the following S. epidermidis strains: ATCC 12228, CIP 81.55 and
CIP 103627.

O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
3207
One relevant way to guide the synthesis work towards an in-
crease of the potency of the synthesized molecules as antimicrobial
compounds is to elucidate their mode of action. Based on the struc-
ture similarity between our N-hydroxylamines and indolic aceto-
hydroxamic acids,11a,b peptide deformylase (PDF) was postulated
to be a possible target inside the bacterial cell. The ability of several
indolic derivatives including 5cd and 6cd, both displaying a 5-Br
substitution, to inhibit the activity of E. coli PDF (EcPDF) was tested
in vitro. Compound 6cd was chosen because it exhibits the lowest
MIC value against E. coli among all the compounds tested in this
study (Table 4), whereas the monosubstituted N-hydroxylamine
5cd had no antibacterial activity (Table 3). In the presence of
that is, six molecules from the first sublibrary of secondary
N-hydroxylamines (3ba, 3cc, 3cd, 3ce, 3cg, and 3ch), nine mole-
cules from the third group of primary N-hydroxylamines (5ac,
5ae–be, 5cd, and 5ce), and all nine molecules from the last subli-
brary of primary amines (6ca–ci). The indolic compounds were
tested at 10 and 1
cell types: KB (oral carcinoma), HCT116 (colon cancer cell line) and
MRC5 (human noncancerous cells in rapid proliferation). At 10 M,
lM concentrations on three selected eukaryotic
l
only three indoles (3cc, 3ce, 3cg) out of the 24 tested compounds
displayed a cytotoxic effect with a cell growth inhibition ranging
from 72% to 98%. In contrast, none of these compounds had detect-
able cytotoxicity, at 1 lM. These data show that the members of
1
l
M concentration the tested compounds displayed only modest
PDF inhibition capacity (25%). Complete inhibition of EcPDF activ-
ity was observed at 500 M of compound 6cd, whereas at the same
our library have a moderate cytotoxic effect on human cells at con-
centrations where they are active as antimicrobial compounds,
which is a positive for their future development as antibiotics.
l
concentration inhibition by compound 5cd reached only 54%.
These data, indicating that 6cd is more potent than 5cd, are in
keeping with the in vivo data showing that 5cd antimicrobial activ-
ity against E. coli (MIC >128 mg/L) is weaker than that observed
with 6cd (MIC 16–32 mg/L). This evidences the role of the substi-
tution at position 3 of indole unit in PDF inhibition, a feature
already reported in SAR analysis of PDF.11a,b Hence, it should be
stressed that the N-hydroxylamine compound 6cd only showed a
weak affinity for EcPDF compared to other efficient PDF inhibitors
reported in the literature such as actinonin. Indeed, by comparison,
another 5-Br indole derivative substituted with an acetohydroxa-
mic acid at position 3 (AB47) was reported to inhibit PDF with
3. Conclusions
In an attempt to find novel type of antibacterial agents, we have
synthesized and fully characterized the collection of 3-substituted
indole derivatives. The evaluation of the antibacterial activity of
these compounds, using a large panel of human pathogens, al-
lowed us to distinguish two types of indolic N-hydroxylamines
3ca–ci and 6ca–ci that inhibit predominantly the growth of Staph-
ylococcus strains, including MRSA and VISA strains. (Fig. 2). The SAR
studies demonstrated that the presence of a halogen at positions
C(5) or C(6) of the indole core is essential for the antibacterial
activity of indolic compounds. The presence of ethanamine substi-
tuent (R = CH2NH2 or R = CH2NHBoc) at alkyl side chain is also
an IC50 of 0.035
is higher than 1
l
M11a whereas IC50 of compounds 5cd and 6cd
M. However, AB47 is only a modest antimicrobial
l
compound angainst E. coli as the associated MIC value is identical
to that of 6cd (16–32 mg/L). These data do not allow excluding that
the target is PDF and might suggest that the permeability of E. coli
to 6cd is improved. Increasing the passive penetration of 6cd in the
bacterium is likely to compensate for the lower potency of the
compound. In this context, it should be reminded that 5-Br indole
binds weakly but specifically to PDF and that N-hydroxylamine
derivatives display similar inhibition properties as 6cd.
OH
OH
NH
BocHN
H2N
N
Bn
X
X
2HCl
N
H
N
H
3ca-ci
6ca-ci
As a preliminary evaluation of their potential side effects in hu-
mans, in vitro cytotoxicity assays were performed for all indolic
compounds possessing antibacterial activity (MIC <32–64 mg/L),
Figure 2. The chemical structures of the most active N-hydroxylamines 3ca–ci and
6ca–ci.
Table 4
Antibiotic activity of amino-N-hydroxylamines 6ca–ci against gram-positive and gram-negative strainsa
Indole
MIC (mg/L)
S.
MRSAc VISA ATCC
106414
S.
S.
Streptococcusf Enterococcusg Gram-negative
bacillih
E. coli ATCC
25922
H. influenzae ATCC
49766
aureusb
epidermidisd pneumoniaee
Cip
Gen
0.5
0.125
0.25
32
>64
0.25
0.125
0.5–1
—
0.25–2
—
1
—
0.016–2
0.5–32
0.064
1
0.5
—
0.125–
0.25
—
32–64
8–16
16
16
16–32
16
Cfx
6ca
6cb
6cc
6cd
6ce
6cf
6cg
6ch
6ci
—
—
32
8
16
16
16
16
—
32
8
16
8–16
16–32
16
16
16
0.125
>128
64
64–128
64
64
64
64
64
0.016–0.063
>128
32–128
128
64
128
64–128
64–128
128
0.5–2
>128
64–128
>128
128
128
128
128
>128
>128
—
>128
32–128
128
64–128
64–128
64–128
64–128
64-128
128->128
—
>128
32
64
16–32
32
64
32
32
128
0.032
>128
>128
128
—
64
16
16
16
32
16
64
>128
128
—
16
16–32
32
16–32 16
16
32
16
32
32
128
128
—
a
b
c
Cip, ciprofloxacin; Gen, gentamicin: Cfx, cefotaxime.
MIC values of the following S. aureus strains: ATCC 25923, ATCC 29213, ATCC 9144, ATCC 6538, CIP 65.6 and CIP 103428.
MIC values of meticillin-resistant S. aureus CIP 65.25 and ATCC 33592.
MIC values of the following S. epidermidis strains: ATCC 12228, CIP 81.55 and CIP 103627.
MIC values of Streptococcus pneumoniae ATCC 49619 and ATCC 6303.
MIC values of Streptococcus agalactiae ATCC 12400, Streptococcus pyogenes CIP 104226 and S. mitis CIP 103335.
MIC values of Enterococcus faecium CIP 54.32 and Enterococcus faecalis ATCC 29212.
d
e
f
g
h
MIC values of K. pneumoniae ATCC 35657, E. cloacae ATCC 13047, S. marcescens CIP 103551, P. aeruginosa CIP 5933 and A. baumanii ATCC 19606.

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O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
essential for the antibiotic activity of N-(1-(1H-indol-3-yl)ethyl)-
hydroxylamines.
119.7, 121.5, 122.7, 126.6, 126.7, 127.8 (2 C), 129.3 (2 C), 136.2,
138.5 (2 C). MS (ES+): m/z (%) = 289 (9) [M+Na]+, 267 (1) [M+H]+,
144 (100) [M+HÀN(OH)Bn]+.
Our results represent a valuable starting point for the prepara-
tion a new series of 1-(1H-indol-3-yl)ethanamine derivatives with
the aim of improving their antibacterial activity. Our attempts to
identify possible intracellular targets of our compounds revealed
one putative target is PDF. However, our data show that com-
pounds such as 6cd exhibits only weak affinity for PDF; at this
stage, we cannot exclude therefore the existence of other intracel-
lular targets. Thus, in depth investigation of the mode of action of
our compounds including bacterial uptake is required. This micro-
biological approach could be associated to rationale design of fur-
ther members of this indolic class of compounds in order to
provide potent antibacterial agents.
4.1.1.2. N-Benzyl-N-(1-(5-fluoro-1H-indol-3-yl)ethyl)hydroxy-
lami-ne 3ab. Compound 3ab (240 mg, 85%) was obtained from
nitrone 1a (149 mg, 1.0 mmol) and 5-fluoroindole 2b (135 mg,
1.0 mmol) as a white solid. IR (neat): 695, 740, 920, 1170, 1455,
1485, 1580, 2900, 2970, 3415 cmÀ1 1H NMR (300 MHz, CDCl3–
.
CD3OD): d = 1.61 (d, J = 6.7 Hz, 3H), 3.60 (d, J = 13.5 Hz, 1H), 3.81
(d, J = 13.5 Hz, 1H), 4.18 (q, J = 6.7 Hz, 1H), 6.89 (dt, J1 = 9.3 Hz,
J2 = 2.5 Hz, 1H), 7.18–7.32 (m, 7H), 7.44 (dd, J1 = 10.2 Hz,
J2 = 2.3 Hz, 1H). 13C NMR (75 MHz, CDCl3–CD3OD): d = 18.0, 59.4,
60.5, 104.1 (d, J = 23.7 Hz), 109.2 (d, J = 26.5 Hz), 111.4 (d,
J = 9.7 Hz), 124.3, 126.2, 127.4 (2 C), 128.8 (2 C), 132.7, 138.4 (2
C), 157.1 (d, J = 232.7 Hz). 19F NMR (282 MHz, CDCl3–CD3OD):
d = À126.2 (dt, J1 = 9.5 Hz, J2 = 4.5 Hz, 1F). MS (ES+): m/z (%) = 307
(15) [M+Na]+, 285 (10) [M+H]+, 162 (100) [M+HÀN(OH)Bn]+.
4. Experimental part
4.1. Chemistry
4.1.1.3. N-Benzyl-N-(1-(5-chloro-1H-indol-3-yl)ethyl)hydroxy-
lami-ne 3ac. Compound 3ac (255 mg, 85%) was obtained from
nitrone 1a (149 mg, 1.0 mmol) and 5-chloroindole 2c (152 mg,
1.0 mmol) as a white solid. IR (neat): 695, 740, 805, 905, 1100,
Purchased reagents were used without purification. Reactions
were monitored by thin layer chromatography (TLC) using com-
mercial aluminum-backed silica gel plates (Merck G 60 F254). TLC
spots were viewed under ultraviolet light and by heating the plate
after treatment with either a 0.5% solution of ninhydrine in 3% eth-
anolic acetic acid or a 2% solution of potassium permanganate in
7% aqueous sodium carbonate; N-hydroxylamines were detected
with a 1% triphenyl tetrazolium chloride (TTC) in ethanol (red col-
or). Product purification by gravity column chromatography was
performed using Macherey–Nagel Silica Gel 60 (70–230 mesh).
Infrared (IR) spectra were recorded on a Nicolet Magna-550 Fourier
transform infrared spectrometer (FTIR) equipped with an ATR
(Attenuated Total Reflection) device and the data are reported in
reciprocal centimeters (cmÀ1). 1H NMR and 13C NMR spectra were
run on Bruker Advance300 spectrometer. Chemical shifts for 1H
spectra are values downfield from tetramethylsilane in CDCl3 (d
0.00), or CD3OD (d 3.31) and are reported as follows: chemical shift
(ppm), multiplicity, coupling constants (Hz), and integration. Mass
spectra (MS) were recorded on a ThermoFinnigan PolarisQ ion-trap
spectrometer using DCI (ammonia/methane 63/37) or on a Bruker
Esquire 3000 plus (ESI) in order to improve the bacterial activity of
these compounds.
1230, 1375, 1455, 2875, 3415 cmÀ1 1H NMR (300 MHz, CDCl3–
.
CD3OD): d = 1.61 (d, J = 6.7 Hz, 3H), 3.61 (d, J = 13.5 Hz, 1H), 3.80
(d, J = 13.5 Hz, 1H), 4.19 (q, J = 6.7 Hz, 1H), 7.09 (dd, J1 = 8.6 Hz,
J2 = 2.0 Hz, 1H), 7.18–7.46 (m, 7H), 7.76 (d, J = 2.0 Hz, 1H). 13C
NMR (75 MHz, CDCl3–CD3OD): d = 18.1, 59.0, 60.6, 111.9, 118.9,
121.2, 124.0, 124.1 (2 C), 126.4, 127.5 (2 C), 128.9 (2 C), 134.6,
138.3 (2 C). MS (ES+): m/z (%) = 323 (9) [M+Na]+, 301 (12)
[M+H]+, 178 (100) [M+HÀN(OH)Bn]+.
4.1.1.4. N-Benzyl-N-(1-(5-bromo-1H-indol-3-yl)ethyl)hydroxy-
lami-ne 3ad. Compound 3ad (235 mg, 68%) was obtained from
nitrone 1a (149 mg, 1.0 mmol) and 5-bromoindole 2d (196 mg,
1.0 mmol) as a white solid. IR (neat): 695, 740, 802, 885, 1045,
1100, 1375, 1455, 2965, 3415 cmÀ1 1H NMR (300 MHz, CDCl3–
.
CD3OD): d = 1.60 (d, J = 6.7 Hz, 3H), 3.60 (d, J = 13.5 Hz, 1H), 3.80
(d, J = 13.5 Hz, 1H), 4.19 (q, J = 6.7 Hz, 1H), 7.17–7.34 (m, 8H),
7.93 (d, J = 1.3 Hz, 1H). 13C NMR (75 MHz, CDCl3–CD3OD):
d = 18.0, 59.4, 60.5, 111.5, 112.3, 122.0, 123.6, 123.9, 126.2, 127.4
(2 C), 128.8 (2 C), 134.8, 138.3 (2 C). MS (ES+): m/z (%) = 367 (14)
[M+Na]+, 245 (8) [M+H]+, 222 (100) [M+HÀN(OH)Bn]+.
4.1.1. General procedure for the synthesis of indolic N-hydroxyl-
amines 3aa–ci
4.1.1.5.
N-Benzyl-N-(1-(5-iodo-1H-indol-3-yl)ethyl)hydroxyl-
A cold solution of hydrochloric acid was prepared by reaction of
143 lL (157 mg, 2.0 mmol) of freshly distilled acetyl chloride with
amine 3ae. Compound 3ae (274 mg, 70%) was obtained from nit-
rone 1a (149 mg, 1.0 mmol) and 5-iodoindole 2e (243 mg,
1.0 mmol) as a white solid. IR (neat): 700, 750, 795, 880, 1040,
5 mL of dry methanol. This solution was stirred at 0 °C during
15 min and was added to a mixture of both nitrone (1.0 mmol)
and indole (1.0 mmol) in 5 mL of dry methanol. The reaction mix-
ture was stirred at 0 °C during 2 h to completion. A saturated aque-
ous solution of NaHCO3 was then added. The mixture was
extracted with DCM (3 Â 10 mL), and the collected organic layers
were washed with brine, dried over Na2SO4, filtered, and concen-
trated under vacuum. Column chromatography using EtOAc–
pentane (1/99—40/60) yielded pure products.
1115, 1230, 1370, 1435, 1455, 2970, 3310 cmÀ1
.
1H NMR
(300 MHz, CDCl3–CD3OD): d = 1.60 (d, J = 6.7 Hz, 3H), 3.60 (d,
J = 13.4 Hz, 1H), 3.80 (d, J = 13.4 Hz, 1H), 4.19 (q, J = 6.7 Hz, 1H),
7.16–7.28 (m, 7H), 7.38 (dd, J1 = 8.6 Hz, J2 = 1.4 Hz, 1H), 8.14 (d,
J = 1.3 Hz, 1H). 13C NMR (75 MHz, CDCl3–CD3OD): d = 18.1, 58.8,
60.5, 81.6, 112.9, 123.3, 126.3, 127.4 (2 C), 128.4, 128.8 (2 C),
129.2, 135.2, 138.3 (2 C). MS (ES+): m/z (%) = 415 (10) [M+Na]+,
393 (10) [M+H]+, 267 (100).
4.1.1.1. N-Benzyl-N-(1-(1H-indol-3-yl)ethyl)hydroxylamine 3aa.
Compound 3aa (260 mg, 98%) was obtained from nitrone 1a
(149 mg, 1.0 mmol) and indole 2a (117 mg, 1.0 mmol) as a white
solid. IR (neat): 695, 740, 750, 920, 1010, 1095, 1120, 1345, 1370,
4.1.1.6. N-Benzyl-N-(1-(1H-indol-3-yl)-3-methylbutyl)hydroxyl-
amine 3ba. Compound 3ba (286 mg, 93%) was obtained from nit-
rone 1b (191 mg, 1.0 mmol) and indole 2a (117 mg, 1.0 mmol) as a
white solid. IR (neat): 700, 740, 810, 1010, 1095, 1230, 1340, 1455,
1420, 1460, 1495, 2900, 2930, 2965, 3045, 3410 cmÀ1 1H NMR
.
1495, 2865, 2955, 3060, 3410 cmÀ1 1H NMR (300 MHz, CDCl3):
.
(300 MHz, CDCl3–CD3OD): d = 1.60 (d, J = 6.7 Hz, 3H), 3.65 (d,
J = 13.3 Hz, 1H), 3.81 (d, J = 13.3 Hz, 1H), 4.25 (q, J = 6.7 Hz, 1H),
7.08–7.28 (m, 8H), 7.33–7.36 (m, 1H), 7.75–7.78 (m, 1H). 13C
NMR (75 MHz, CDCl3–CD3OD): d = 18.5, 59.2, 61.0, 111.1, 118.9,
d = 0.84 (d, J = 6.6 Hz, 3H), 0.88 (d, J = 6.6 Hz, 3H), 1.47–1.56 (m,
1H), 1.88–2.08 (m, 2H), 3.61 (d, J = 13.4 Hz, 1H), 3.71 (d,
J = 13.4 Hz, 1H), 4.18 (dd, J1 = 9.3 Hz, J2 = 5.6 Hz, 1H), 5.29 (br s,
1H), 7.10–7.25 (m, 8H), 7.30–7.32 (m, 1H), 7.71 (d, J = 7.7 Hz,

O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
3209
1H), 8.12 (br s, 1H). 13C NMR (75 MHz, CDCl3): d = 22.1, 23.5, 25.3,
42.3, 61.6, 61.9, 111.1, 119.5, 120.0, 121.9, 123.5, 126.9, 127.7,
128.1 (2 C), 129.3 (2 C), 136.2, 138.6 (2 C). MS (ES+): m/z
(%) = 240 (100) [M+NaÀBn]+, 186 (71) [M+HÀN(OH)Bn]+.
4.1.1.11. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(1H-indol-3-
yl)-ethylcarbamate 3ca. Compound 3ca (343 mg, 90%) was ob-
tained from nitrone 1c (264 mg, 1.0 mmol) and indole 2a
(117 mg, 1.0 mmol) as a white solid.12a
4.1.1.7. N-Benzyl-N-(1-(5-fluoro-1H-indol-3-yl)-3-methylbutyl)-
hydroxylamine 3bb. Compound 3bb (258 mg, 79%) was obtained
from nitrone 1b (191 mg, 1.0 mmol) and 5-fluoroindole 2b
(135 mg, 1.0 mmol) as a white solid. IR (neat): 695, 740, 790,
4.1.1.12. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(5-fluoro-1H-
indol-3-yl)ethylcarbamate 3cb. Compound 3cb (390 mg, 98%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 5-fluoroin-
dole 2b (135 mg, 1.0 mmol) as a white solid. IR (neat): 695, 745,
845, 935, 1165, 1290, 1455, 1490, 1540, 1655, 2890, 2975, 3300,
930, 1055, 1175, 1350, 1365, 1455, 1485, 1575, 2950, 3355 cmÀ1
.
1H NMR (300 MHz, CDCl3–CD3OD): d = 0.85 (d, J = 6.7 Hz, 3H),
0.89 (d, J = 6.6 Hz, 3H), 1.42–1.56 (m, 1H), 1.88–2.05 (m, 2H),
3.60 (d, J = 13.4 Hz, 1H), 3.73 (d, J = 13.4 Hz, 1H), 4.09 (dd,
J1 = 9.5 Hz, J2 = 5.5 Hz, 1H), 6.91 (dt, J1 = 9.1 Hz, J2 = 2.4 Hz, 1H),
7.17–7.31 (m, 7H), 7.37 (dd, J1 = 10.2 Hz, J2 = 2.4 Hz, 1H). 13C
NMR (75 MHz, CDCl3–CD3OD): d = 21.7, 23.2, 25.1, 41.9, 61.4,
62.1, 104.4 (d, J = 23.7 Hz), 109.6 (d, J = 26.5 Hz), 111.6 (d,
J = 9.7 Hz), 125.4, 126.7, 127.8 (2 C), 129.1 (2 C), 132.8, 138.5 (2
C), 157.5 (d, J = 233.0 Hz). 19F NMR (282 MHz, CDCl3–CD3OD):
d = À121.6 (dt, J1 = 9.8 Hz, J2 = 4.6 Hz, 1F). MS (ES+): m/z (%) = 349
(11) [M+Na]+, 327 (2) [M+H]+, 258 (14), 204 (100), 148 (48), 91
(13).
3410 cmÀ1 1H NMR (300 MHz, CD3OD): d = 1.43 (s, 9H), 3.49–
.
3.81 (m, 4H), 4.13 (t, J = 5.4 Hz, 1H), 6.90 (dt, J1 = 9.1 Hz,
J2 = 2.4 Hz, 1H), 7.20–7.40 (m, 8H). 13C NMR (75 MHz, CD3OD):
d = 28.8 (3C), 44.2, 60.9, 62.4, 78.2, 103.2 (d, J = 24.8 Hz), 110.6
(d, J = 26.4 Hz), 113.0 (d, J = 9.4 Hz), 124.3, 127.3, 127.8, 129.0 (2
C), 130.2 (2 C), 132.9, 136.7, 140.3, 156.7, 159.3 (d, J = 236.1 Hz).
19F NMR (282 MHz, CD3OD): d = À124.2 (dt, J1 = 9.8 Hz,
J2 = 4.8 Hz, 1F). MS (ES+): m/z (%) = 422 (21) [M+Na]+, 400 (97)
[M+H]+, 277 (17), 221 (100), 177 (20).
4.1.1.13. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(5-chloro-1H-
indol-3-yl)ethylcarbamate 3cc. Compound 3cc (360 mg, 87%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 5-chloroin-
dole 2c (152 mg, 1.0 mmol) as a white solid. IR (neat): 695, 735,
4.1.1.8. N-Benzyl-N-(1-(5-chloro-1H-indol-3-yl)-3-methylbutyl)-
hydroxylamine 3bc. Compound 3bc (270 mg, 79%) was obtained
from nitrone 1b (191 mg, 1.0 mmol) and 5-chloroindole 2c
(157 mg, 1.0 mmol) as a white solid. IR (neat): 695, 740, 795,
790, 895, 910, 1165, 1295, 1520, 1655, 2970, 3315 cmÀ1 1H NMR
.
(300 MHz, CDCl3–CD3OD): d = 1.48 (s, 9H), 3.58–3.63 (m, 2H),
3.60 (d, J = 13.7 Hz, 1H), 3.81 (d, J = 13.7 Hz, 1H), 4.07 (t,
J = 5.4 Hz, 1H), 5.37 (t, J = 6.2 Hz, 1H), 7.11 (dd, J1 = 8.6 Hz,
J2 = 2.0 Hz, 1H), 7.20–7.37 (m, 8H), 7.68 (br s, 1H). 13C NMR
(75 MHz, CDCl3–CD3OD): d = 29.8 (3C), 45.3, 59.0, 63.7, 81.3,
113.9 (2 C), 120.7, 123.5 (2 C), 126.4 (2 C), 126.8, 128.4, 129.5 (2
C), 130.3, 136.4, 139.7, 158.0. MS (ES+): m/z (%) = 438 (22)
[M+Na]+, 416 (100) [M+H]+, 293 (18), 237 (89), 193 (16).
890, 1055, 1110, 1435, 1465, 2960, 3295 cmÀ1
.
1H NMR
(300 MHz, CDCl3–CD3OD): d = 0.85 (d, J = 6.7 Hz, 3H), 0.90 (d,
J = 6.6 Hz, 3H), 1.42–1.57 (m, 1H), 1.85–2.05 (m, 2H), 3.60 (d,
J = 13.3 Hz, 1H), 3.72 (d, J = 13.3 Hz, 1H), 4.11 (dd, J1 = 9.4 Hz,
J2 = 5.4 Hz, 1H), 7.11 (dd, J1 = 8.6 Hz, J2 = 1.9 Hz, 1H), 7.21–7.34
(m, 7H), 7.68 (d, J = 1.8 Hz, 1H). 13C NMR (75 MHz, CDCl3–CD3OD):
d = 21.8, 23.2, 25.1, 42.0, 61.4, 61.8, 112.1, 119.1, 121.6, 124.6,
125.1, 126.7, 127.8 (2 C), 129.1 (2 C), 134.6, 138.4 (2 C). MS
(ES+): m/z (%) = 365 (11) [M+Na]+, 343 (3) [M+H]+, 220 (100), 164
(43).
4.1.1.14. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(5-bromo-1H-
indol-3-yl)ethylcarbamate 3cd. Compound 3cd (385 mg, 84%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 5-bromoin-
dole 2d (196 mg, 1.0 mmol) as a white solid.14a
4.1.1.9. N-Benzyl-N-(1-(5-bromo-1H-indol-3-yl)-3-methylbutyl)-
hydroxylamine 3bd. Compound 3bd (217 mg, 56%) was obtained
from nitrone 1b (191 mg, 1.0 mmol) and 5-bromoindole 2d
(196 mg, 1.0 mmol) as a white solid. IR (neat): 700, 745, 795, 935,
4.1.1.15.
tert-Butyl 2-(benzyl(hydroxy)amino)-2-(5-iodo-1H-
indol-3-yl)ethylcarbamate 3ce. Compound 3ce (420 mg, 83%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 5-iodoin-
dole 2e (243 mg, 1.0 mmol) as a white solid. IR (neat): 695, 740,
790, 880, 910, 1165, 1295, 1365, 1390, 1455, 1525, 1660, 2960,
1050, 1110, 1435, 1455, 1595, 2865, 2960, 3300 cmÀ1 1H NMR
.
(300 MHz, CDCl3–CD3OD): d = 0.85 (d, J = 6.6 Hz, 3H), 0.90 (d,
J = 6.6 Hz, 3H), 1.43–1.57 (m, 1H), 1.85–2.05 (m, 2H), 3.60 (d,
J = 13.4 Hz, 1H), 3.72 (d, J = 13.4 Hz, 1H), 4.10 (dd, J1 = 9.5 Hz,
J2 = 5.5 Hz, 1H), 7.21–7.28 (m, 8H), 7.84 (d, J = 0.7 Hz, 1H). 13C
NMR (75 MHz, CDCl3–CD3OD): d = 21.7, 23.2, 25.0, 42.0, 61.3,
61.8, 112.1, 112.6, 122.1, 124.0, 124.9, 126.7, 127.8 (2 C), 129.1 (2
C), 134.8, 138.4 (2 C). MS (ES+): m/z (%) = 409 (10) [M+Na]+, 387
(3) [M+H]+, 360 (12), 266 (100), 208 (34).
3315 cmÀ1 1H NMR (300 MHz, CDCl3–CD3OD): d = 1.48 (s, 9H),
.
3.57–3.61 (m, 2H), 3.59 (d, J = 14.0 Hz, 1H), 3.83 (d, J = 14.0 Hz,
1H), 4.07 (t, J = 5.8 Hz, 1H), 5.47 (br s, 1H), 7.18–7.30 (m, 7H),
7.41 (dd, J1 = 8.5 Hz, J2 = 1.6 Hz, 1H), 8.03 (s, 1H). 13C NMR
(75 MHz, CDCl3–CD3OD): d = 29.9 (3C), 44.3, 59.1, 63.6, 84.2, 97.8,
115.1 (2 C), 123.7, 124.5, 126.4, 126.8, 128.2, 129.6 (2 C), 130.4,
131.5, 132.4, 134.9, 138.2, 157.5. MS (ES+): m/z (%) = 530 (33)
[M+Na]+, 508 (100) [M+H]+, 329 (63).
4.1.1.10. N-Benzyl-N-(1-(5-iodo-1H-indol-3-yl)-3-methylbutyl)-
hyd-roxylamine 3be. Compound 3be (240 mg, 55%) was ob-
tained from nitrone 1b (191 mg, 1.0 mmol) and 5-iodoindole 2e
(243 mg, 1.0 mmol) as a white solid. IR (neat): 700, 685, 745,
4.1.1.16. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(6-fluoro-1H-
indol-3-yl)ethylcarbamate 3cf. Compound 3cf (340 mg, 85%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 6-fluoroin-
dole 2f (135 mg, 1.0 mmol) as a white solid. IR (neat): 695, 735,
800, 830, 910, 1095, 1140, 1165, 1290, 1520, 1625, 1655, 2875,
795, 855, 935, 1055, 1110, 1365, 1435, 1455, 2960, 3295 cmÀ1
.
1H NMR (300 MHz, CDCl3–CD3OD): d = 0.85 (d, J = 6.5 Hz, 3H),
0.90 (d, J = 6.6 Hz, 3H), 1.43–1.55 (m, 1H), 1.84–2.06 (m, 2H),
3.57 (d, J = 13.4 Hz, 1H), 3.74 (d, J = 13.4 Hz, 1H), 4.08 (dd,
J1 = 9.5 Hz, J2 = 5.3 Hz, 1H), 7.19–7.28 (m, 7H), 7.38–7.41 (m, 1H),
8.04 (d, J = 1.1 Hz, 1H). 13C NMR (75 MHz, CDCl3–CD3OD):
d = 21.4, 22.9, 24.8, 42.0, 61.1, 62.3, 81.8, 113.0, 124.1, 126.4,
127.5 (2 C), 128.3, 128.9 (2 C), 129.2, 135.0, 138.4 (2 C). MS
(ES+): m/z (%) = 457 (6) [M+Na]+, 435 (1) [M+H]+, 312 (100), 256
(17).
2975, 3365, 3410 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.50 (s,
.
9H), 3.54–3.63 (m, 2H), 3.62 (d, J = 14.0 Hz, 1H), 3.83 (d,
J = 14.0 Hz, 1H), 4.08 (t, J = 5.7 Hz, 1H), 4.92 (t, J = 6.8 Hz, 1H),
6.50 (br s, 1H), 6.88 (dt, J1 = 9.4 Hz, J2 = 2.3 Hz, 1H), 7.02 (dd,
J1 = 9.6 Hz, J2 = 2.0 Hz, 1H), 7.18–7.27 (m, 6H), 7.56 (dd,
J1 = 8.7 Hz, J2 = 5.3 Hz, 1H), 8.42 (br s, 1H). 13C NMR (75 MHz,
CDCl3): d = 28.7 (3C), 44.0, 60.9, 64.0, 80.1, 97.7 (d, J = 26.2 Hz),
108.7 (d, J = 24.4 Hz), 120.7 (d, J = 10.4 Hz), 123.9, 124.0, 127.1,

3210
O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
128.3 (2 C), 128.8 (2 C), 132.3, 136.3, 138.9, 158.7, 160.3 (d,
J = 238.1 Hz). 19F NMR (282 MHz, CDCl3): d = À125.0 (dt,
J1 = 9.6 Hz, J2 = 4.7 Hz, 1F). MS (ES+): m/z (%) = 422 (58) [M+Na]+,
400 (94) [M+H]+, 277 (20), 221 (100), 173 (12).
930, 1115, 1175, 1285, 1445, 1490, 1580, 1630, 2870, 2905,
3185 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.91 (d, J = 6.8 Hz,
.
3H), 5.38 (q, J = 6.8 Hz, 1H), 6.78 (dt, J1 = 9.0 Hz, J2 = 2.3 Hz, 1H),
7.03–7.07 (m, 2H), 7.19 (dd, J1 = 9.6 Hz, J2 = 2.3 Hz, 1H), 7.33–
7.35 (m, 3H), 7.59 (s, 1H), 8.20–8.23 (m, 2H), 9.63 (br s, 1H).
13C NMR (75 MHz, CDCl3): d = 18.9, 68.9, 103.2 (d, J = 23.8 Hz),
110.5 (d, J = 26.2 Hz), 112.4 (d, J = 4.7 Hz), 112.5 (d, J = 9.8 Hz),
126.0 (d, J = 9.8 Hz), 126.1, 128.5 (2 C), 128.9 (2 C), 130.1,
130.6, 133.0, 133.3, 157.9 (d, J = 235.2 Hz). 19F NMR (282 MHz,
CDCl3): d = À123.4 (dt, J1 = 9.4 Hz, J2 = 4.4 Hz, 1F). MS (ES+): m/z
(%) = 305 (100) [M+Na]+, 283 [M+H]+, 216 (34), 162 (45).
4.1.1.17. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(6-chloro-1H-
indol-3-yl)ethylcarbamate 3cg. Compound 3cg (340 mg, 82%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 6-chloroin-
dole 2g (152 mg, 1.0 mmol) as a white solid. IR (neat): 695, 735,
800, 905, 1105, 1160, 1290, 1365, 1455, 1520, 1655, 2850, 2975,
3360, 3405 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.50 (s, 9H),
.
3.54–3.63 (m, 2H), 3.62 (d, J = 14.0 Hz, 1H), 3.80 (d, J = 14.0 Hz,
1H), 4.07 (t, J = 5.6 Hz, 1H), 4.92 (t, J = 6.2 Hz, 1H), 6.52 (br s, 1H),
7.08 (dd, J1 = 8.5 Hz, J2 = 1.7 Hz, 1H), 7.18–7.26 (m, 6H), 7.33 (d,
J = 1.4 Hz, 1H), 7.55 (d, J = 8.6 Hz, 1H), 8.45 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 28.5 (3C), 43.7, 60.6, 64.7, 79.9, 111.2 (2 C),
120.4 (2 C), 120.5, 124.2, 125.7, 126.8, 128.1 (2 C), 128.6, 136.3,
138.7, 157.7. MS (ES+): m/z (%) = 438 (17) [M+Na]+, 416 (97)
[M+H]+, 293 (17), 237 (100), 193 (9).
4.1.2.3. (Z)-N-Benzylidene-1-(5-chloro-1H-indol-3-yl)ethan-
amine oxide 4ac. Compound 4ac (230 mg, 51%) was obtained
from N-hydroxylamine 3ac (451 mg, 1.50 mmol) and MnO2
(653 mg, 7.50 mmol) as a beige foam. IR (neat): 690, 750, 795,
890, 1030, 1110, 1230, 1290, 1370, 1450, 1520, 2880, 3130 cmÀ1
.
1H NMR (300 MHz, CDCl3): d = 1.90 (d, J = 6.8 Hz, 3H), 5.37 (q,
J = 6.8 Hz, 1H), 6.95–7.07 (m, 3H), 7.33–7.36 (m, 3H), 7.51 (d,
J = 1.6 Hz, 1H), 7.60 (s, 1H), 8.20–8.23 (m, 2H), 9.77 (br s, 1H). 13C
NMR (75 MHz, CDCl3): d = 19.0, 68.7, 111.9, 112.9, 117.7, 122.4,
125.5, 125.9, 126.8, 128.5 (2 C), 128.9 (2 C), 130.1, 130.7, 133.4,
134.8. MS (ES+): m/z (%) = 321 (100) [M+Na]+, 299 (17) [M+H]+,
216 (13), 178 (54).
4.1.1.18. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(6-bromo-1H-
indol-3-yl)ethylcarbamate 3ch. Compound 3ch (400 mg, 87%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 6-bromoin-
dole 2h (196 mg, 1.0 mmol) as a white solid.14a
4.1.1.19. tert-Butyl 2-(benzyl(hydroxy)amino)-2-(4-bromo-1H-
indol-3-yl)ethylcarbamate 3ci. Compound 3ci (370 mg, 80%)
was obtained from nitrone 1c (264 mg, 1.0 mmol) and 4-bromoin-
dole 2i (196 mg, 1.0 mmol) as a white solid. IR (neat): 695, 730,
910, 1120, 1165, 1290, 1330, 1455, 1560, 1655, 2830, 2980,
4.1.2.4. (Z)-N-Benzylidene-1-(5-bromo-1H-indol-3-yl)ethan-
amine oxide 4ad. Compound 4ad (140 mg, 45%) was obtained
from N-hydroxylamine 3ad (311 mg, 0.90 mmol) and MnO2
(392 mg, 4.50 mmol) as a beige foam. IR (neat): 690, 750, 795,
1030, 1110, 1230, 1285, 1445, 2870, 3150 cmÀ1
.
1H NMR
3290, 3375 cmÀ1
.
1H NMR (300 MHz, CD3OD): d = 1.43 (s, 9H),
(300 MHz, CDCl3): d = 1.93 (d, J = 6.8 Hz, 3H), 5.40 (q, J = 6.8 Hz,
1H), 6.98 (d, J = 8.6 Hz, 1H), 7.06–7.14 (m, 2H), 7.36–7.39 (m,
3H), 7.61 (s, 1H), 7.68 (d, J = 1.7 Hz, 1H), 8.22–8.25 (m, 2H),
9.45 (br s, 1H). 13C NMR (75 MHz, CDCl3): d = 19.1, 68.7, 112.1,
113.2, 113.3, 120.8, 125.1, 125.7, 127.5, 128.5 (2 C), 128.9 (2
C), 130.2, 130.7, 133.2, 135.1. MS (ES+): m/z (%) = 365 (100)
[M+Na]+, 343 (38) [M]+, 222 (98).
3.51–3.69 (m, 2H), 3.69 (d, J = 14.3 Hz, 1H), 3.88 (d, J = 14.3 Hz,
1H), 5.29 (t, J = 6.0 Hz, 1H), 7.00 (t, J = 7.8 Hz, 1H), 7.19–7.31 (m,
6H), 7.42 (d, J = 8.1 Hz, 1H), 7.60 (s, 1H). 13C NMR (75 MHz,
CD3OD): d = 28.9 (3C), 42.7, 62.2, 64.1, 80.2, 112.1, 114.3, 123.0,
125.1, 125.7, 126.6, 126.9, 127.3, 129.0 (2 C), 130.0, 132.8, 135.8,
138.9, 156.4. MS (ES+): m/z (%) = 482 (26) [M+Na]+, 460 (100)
[M+H]+, 281 (37).
4.1.2.5. (Z)-N-Benzylidene-1-(5-iodo-1H-indol-3-yl)ethanamine
oxide 4ae. Compound 4ae (180 mg, 51%) was obtained from N-
hydroxylamine 3ae (353 mg, 0.90 mmol) and MnO2 (392 mg,
4.50 mmol) as a beige foam. IR (neat): 690, 750, 795, 880, 1030,
4.1.2. General procedure for the synthesis of indolic nitrones
4aa–ci
A stirred solution of indolic N-hydroxylamine 3aa–ci in toluene
was warmed to 100 °C. Five equiv. of manganese dioxide were then
added. The resulting heterogeneous mixture was then stirred at
100 °C during 5 min. It was then cooled and filtered on celite. Re-
sulted solution was concentrated under vacuum. The crude extract
was purified by column chromatography on silica gel (treated by
2.5% of trietylamine) using EtOAc–pentane (5/95—90/10) yielded
pure products.
1110, 1230, 1285, 1320, 1370, 1445, 2840, 3120 cmÀ1 1H NMR
.
(300 MHz, CDCl3): d = 1.91 (d, J = 6.8 Hz, 3H), 5.38 (q, J = 6.8 Hz,
1H), 6.85 (d, J = 8.5 Hz, 1H), 6.98 (d, J = 2.4 Hz, 1H), 7.26 (dd,
J1 = 8.6 Hz, J2 = 1.5 Hz, 1H), 7.36–7.38 (m, 3H), 7.60 (s, 1H), 7.88
(d, J = 1.0 Hz, 1H), 8.21–8.24 (m, 2H), 9.58 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 19.1, 68.6, 83.6, 111.6, 113.8, 125.4, 127.0,
128.3, 128.5 (2 C), 128.9 (2 C), 130.1, 130.4, 130.7, 133.3, 135.5.
MS (ES+): m/z (%) = 413 (86) [M+Na]+, 391 (25) [M+H]+, 324 (21),
267 (100).
4.1.2.1. (Z)-N-Benzylidene-1-(1H-indol-3-yl)ethanamine oxide
4aa. Compound 4aa (250 mg, 53%) was obtained from N-hydrox-
ylamine 3aa (479 mg, 1.80 mmol) and MnO2 (783 mg, 9.00 mmol)
as a beige foam. IR (neat): 685, 730, 750, 825, 1040, 1120, 1135,
4.1.2.6. (Z)-N-Benzylidene-1-(1H-indol-3-yl)-3-methylbutane-1-
amine oxide 4ba. Compound 4ba (325 mg, 59%) was obtained
from N-hydroxylamine 3ba (554 mg, 1.80 mmol) and MnO2
(783 mg, 9.00 mmol) as a orange foam. IR (neat): 690, 740, 925,
1010, 1105, 1220, 1295, 1340, 1450, 1580, 2865, 2955, 3055,
1290, 1435, 1455, 1580, 3175 cmÀ1 1H NMR (300 MHz, CDCl3):
.
d = 1.96 (d, J = 6.4 Hz, 3H), 5.46 (q, J = 6.4 Hz, 1H), 7.03–7.15 (m,
3H), 7.26–7.35 (m, 4H), 7.52 (s, 1H), 7.59 (d, J = 7.8 Hz, 1H), 8.17–
8.21 (m, 2H), 9.28 (br s, 1H). 13C NMR (75 MHz, CDCl3): d = 19.2,
69.1, 111.8, 112.7, 118.5, 120.0, 122.3, 124.3, 125.9, 128.4 (2 C),
128.8 (2 C), 130.3, 130.5, 132.6, 136.5. MS (ES+): m/z (%) = 287
(21) [M+Na]+, 265 (3) [M+H]+, 144 (100).
.
3210, 3405 cmÀ1 1H NMR (300 MHz, CDCl3): d = 0.95 (d,
J = 6.6 Hz, 3H), 0.99 (d, J = 6.6 Hz, 3H), 1.61–1.75 (m, 1H), 1.96–
2.06 (m, 1H), 2.45–2.55 (m, 1H), 5.40 (t, J = 7.5 Hz, 1H), 7.04–7.09
(m, 3H), 7.19–7.23 (m, 1H), 7.33–7.35 (m, 3H), 7.62 (s, 1H), 7.63–
7.67 (m, 1H), 8.21–8.24 (m, 2H), 9.23 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 22.4, 22.6, 25.2, 41.6, 71.9, 111.7, 111.8,
118.2, 119.8, 122.0, 124.6, 126.1, 128.4 (2 C), 128.7 (2 C), 130.2,
130.5, 133.2, 136.3. MS (ES+): m/z (%) = 329 (81) [M+Na]+, 307
(100) [M+H]+.
4.1.2.2. (Z)-N-Benzylidene-1-(5-fluoro-1H-indol-3-yl)ethan-
amine oxide 4ab. Compound 4ab (210 mg, 50%) was obtained
from N-hydroxylamine 3ab (426 mg, 1.50 mmol) and MnO2
(653 mg, 7.50 mmol) as a beige foam. IR (neat): 690, 755, 800,

O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
3211
4.1.2.7. (Z)-N-Benzylidene-1-(5-fluoro-1H-indol-3-yl)-3-methyl-
butane-1-amine oxide 4bb. Compound 4bb (200 mg, 44%) was
obtained from N-hydroxylamine 3bb (456 mg, 1.40 mmol) and
MnO2 (609 mg, 7.00 mmol) as a beige foam. IR (neat): 690, 750,
78%) was obtained from N-hydroxylamine 3ca (724 mg,
1.90 mmol) and MnO2 (827 mg, 9.50 mmol) as a beige foam.14a
4.1.2.12. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(5-
fluoro-1H-indol-3-yl)ethanamine oxide 4cb. Compound 4cb
(210 mg, 66%) was obtained from N-hydroxylamine 3cb (320 mg,
0.80 mmol) and MnO2 (348 mg, 4.00 mmol) as a beige foam. IR
(neat): 670, 695, 785, 940, 1130, 1150, 1175, 1240, 1370, 1455,
795, 940, 1120, 1175, 1455, 1490, 1580, 2955, 3185 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 0.97 (d, J = 6.6 Hz, 3H), 1.01 (d,
J = 6.6 Hz, 3H), 1.62–1.73 (m, 1H), 1.93–2.04 (m, 1H), 2.44–2.54
(m, 1H), 5.31 (dd, J1 = 8.5 Hz, J2 = 6.4 Hz, 1H), 6.73 (dt, J1 = 9.1 Hz,
J2 = 2.4 Hz, 1H), 6.94 (dd, J1 = 8.8 Hz, J2 = 4.5 Hz, 1H), 7.10 (d,
J = 2.6 Hz, 1H), 7.25 (dd, J1 = 9.3 Hz, J2 = 2.4 Hz, 1H), 7.36–7.40 (m,
3H), 7.68 (s, 1H), 8.26–8.29 (m, 2H), 9.32 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 22.3, 22.7, 25.1, 41.2, 71.7, 102.9 (d,
J = 23.8 Hz), 110.3 (d, J = 26.3 Hz), 111.7 (d, J = 4.8 Hz), 112.4 (d,
J = 9.8 Hz), 126.2 (d, J = 9.8 Hz), 126.5, 128.5 (2 C), 128.8 (2 C),
130.3, 130.5, 132.8, 133.6, 157.9 (d, J = 234.8 Hz). 19F NMR
(282 MHz, CDCl3): d = À123.9 (dt, J1 = 9.5 Hz, J2 = 4.5 Hz, 1F). MS
(ES+): m/z (%) = 347 (100) [M+Na]+, 325 (10) [M+H]+, 258 (28),
204 (68), 148 (57).
1505, 1685, 2970, 3060, 3295, 3465 cmÀ1 1H NMR (300 MHz,
.
CDCl3): d = 1.44 (s, 9H), 3.78-3.87 (m, 1H), 3.98–4.07 (m, 1H),
5.22–5.29 (m, 1H), 5.52–5.57 (m, 1H), 6.88 (dt, J1 = 9.1 Hz,
J2 = 2.5 Hz, 1H), 7.18 (dd, J1 = 9.0 Hz, J2 = 4.4 Hz, 1H), 7.34–7.42
(m, 5H), 8.22–8.25 (m, 2H), 8.86 (br s, 1H). 13C NMR (75 MHz,
CDCl3–CD3OD): d = 27.9 (3C), 42.2, 71.4, 79.6, 103.0 (d,
J = 23.1 Hz), 110.2 (d, J = 26.3 Hz), 112.1 (d, J = 9.6 Hz), 125.7,
128.2 (2 C), 128.9 (2 C), 129.6, 130.8, 132.4, 136.2, 156.7, 157.7
(d, J = 234.7 Hz). 19F NMR (282 MHz, CDCl3): d = À123.3 (dt,
J1 = 9.3 Hz, J2 = 4.3 Hz, 1F). MS (ES+): m/z (%) = 420 (47) [M+Na]+,
398 (28) [M+H]+, 277 (15), 221 (100), 177 (15).
4.1.2.8. (Z)-N-Benzylidene-1-(5-chloro-1H-indol-3-yl)-3-methyl-
butane-1-amine oxide 4bc. Compound 4bc (240 mg, 50%) was
obtained from N-hydroxylamine 3bc (480 mg, 1.40 mmol) and
MnO2 (609 mg, 7.00 mmol) as a beige foam. IR (neat): 690, 750,
4.1.2.13. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(5-
chloro-1H-indol-3-yl)ethanamine oxide 4cc. Compound 4cc
(190 mg, 66%) was obtained from N-hydroxylamine 3cc (290 mg,
0.70 mmol) and MnO2 (305 mg, 3.50 mmol) as a beige foam. IR
(neat): 690, 750, 795, 895, 1130, 1160, 1250, 1365, 1450, 1505,
795, 890, 1110, 1130, 1215, 1450, 2870, 2955, 3170 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 0.96 (d, J = 6.6 Hz, 3H), 1.00 (d,
J = 6.6 Hz, 3H), 1.59–1.75 (m, 1H), 1.90–1.99 (m, 1H), 2.43–2.52
(m, 1H), 5.33 (dd, J1 = 8.6 Hz, J2 = 6.3 Hz, 1H), 6.86–6.94 (m, 2H),
7.02 (d, J = 2.6 Hz, 1H), 7.37–7.40 (m, 3H), 7.56 (d, J = 1.7 Hz, 1H),
7.70 (s, 1H), 8.26–8.30 (m, 2H), 9.52 (br s, 1H). 13C NMR (75 MHz,
CDCl3): d = 22.2, 22.7, 25.1, 41.2, 71.5, 111.1, 112.8, 117.4, 122.1,
125.4, 126.3, 127.0, 128.6 (2 C), 128.9 (2 C), 130.2, 130.6, 133.8,
134.6. MS (ES+): m/z (%) = 363 (78) [M+Na]+, 341 (29) [M+H]+, 220
(100), 164 (72).
1695, 2980, 3265 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.41 (s,
.
9H), 3.71–3.76 (m, 1H), 3.95–4.03 (m, 1H), 5.39–5.55 (m, 2H),
6.90–6.98 (m, 2H), 7.02–7.10 (m, 1H), 7.30–7.39 (m, 3H), 7.59–
7.62 (m, 2H), 8.20–8.24 (m, 2H), 9.70 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 28.2 (3C), 42.7, 71.5, 79.8, 108.9, 112.7,
117.8, 122.4, 125.6, 125.7, 126.9, 128.5 (2 C), 128.9 (2 C), 129.9,
130.8, 134.4, 135.3, 156.2. MS (ES+): m/z (%) = 436 (40) [M+Na]+,
414 (34) [M+H]+, 293 (12), 237 (100), 193 (12).
4.1.2.9. (Z)-N-Benzylidene-1-(5-bromo-1H-indol-3-yl)-3-methyl-
butane-1-amine oxide 4bd. Compound 4bd (130 mg, 52%) was
obtained from N-hydroxylamine 3bd (252 mg, 0.65 mmol) and
MnO2 (283 mg, 3.25 mmol) as a beige foam. IR (neat): 690, 750,
4.1.2.14. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(5-
bromo-1H-indol-3-yl)ethanamine oxide 4cd. Compound 4cd
(365 mg, 64%) was obtained from N-hydroxylamine 3cd (575 mg,
1.25 mmol) and MnO2 (544 mg, 6.25 mmol) as a beige foam.14a
795, 885, 1110, 1130, 1215, 1450, 2870, 2955, 3165 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 0.96 (d, J = 6.6 Hz, 3H), 1.00 (d,
J = 6.6 Hz, 3H), 1.59–1.72 (m, 1H), 1.89–1.98 (m, 1H), 2.42–2.52
(m, 1H), 5.32 (dd, J1 = 8.5 Hz, J2 = 6.2 Hz, 1H), 6.80 (d, J = 8.7 Hz,
1H), 6.98–7.05 (m, 2H), 7.38–7.40 (m, 3H), 7.70 (d, J = 1.5 Hz, 1H),
7.71 (s, 1H), 8.27–8.30 (m, 2H), 9.59 (br s, 1H). 13C NMR (75 MHz,
CDCl3): d = 22.2, 22.8, 25.1, 41.2, 71.4, 110.9, 113.0, 113.3, 120.4,
124.6, 126.1, 127.6, 128.6 (2 C), 128.9 (2 C), 130.2, 130.6, 133.9,
134.8. MS (ES+): m/z (%) = 407 (84) [M+Na]+, 385 (21) [M+H]+, 266
(100), 208 (39).
4.1.2.15. (Z)-N-benzylidene-2-(tert-butoxycarbonylamino)-1-(5-
iodo-1H-indol-3-yl)ethanamine oxide 4ce. Compound 4ce
(240 mg, 68%) was obtained from N-hydroxylamine 3ce (355 mg,
0.70 mmol) and MnO2 (305 mg, 3.50 mmol) as a beige foam. IR
(neat): 690, 750, 795, 880, 1160, 1250, 1365, 1450, 1505, 1695,
2930, 2970, 3275 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.42 (s,
.
9H), 3.71–3.81 (m, 1H), 3.94–4.05 (m, 1H), 5.29–5.40 (m, 1H),
5.48–5.55 (m, 1H), 6.87 (d, J = 9.5 Hz, 1H), 7.10 (d, J = 2.3 Hz, 1H),
7.28 (dd, J1 = 8.6 Hz, J2 = 1.4 Hz, 1H), 7.36–7.41 (m, 3H), 7.61 (s,
1H), 7.97 (s, 1H), 8.21–8.25 (m, 2H), 9.50 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 28.3 (3C), 42.8, 71.3, 80.0, 83.7, 108.7, 113.6,
125.1, 127.1, 128.4, 128.6 (2 C), 128.9 (2 C), 130.0, 130.6, 130.8,
135.1, 135.3, 156.2. MS (ES+): m/z (%) = 528 (100) [M+Na]+, 506
(40) [M+H]+, 439 (6), 329 (86).
4.1.2.10. (Z)-N-Benzylidene-1-(5-iodo-1H-indol-3-yl)-3-methyl-
butane-1-amine oxide 4be. Compound 4be (150 mg, 50%) was
obtained from N-hydroxylamine 3be (304 mg, 0.70 mmol) and
MnO2 (305 mg, 3.50 mmol) as a beige foam. IR (neat): 690, 750,
795, 880, 1110, 1135, 1320, 1450, 2870, 2955, 3195 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 0.97 (d, J = 6.6 Hz, 3H), 1.01 (d,
J = 6.6 Hz, 3H), 1.60–1.73 (m, 1H), 1.89–1.98 (m, 1H), 2.43–2.52
(m, 1H), 5.32 (dd, J1 = 8.6 Hz, J2 = 6.1 Hz, 1H), 6.71 (d, J = 8.5 Hz,
1H), 7.01 (d, J = 2.5 Hz, 1H), 7.20 (dd, J1 = 8.6 Hz, J2 = 1.6 Hz, 1H),
7.38–7.41 (m, 3H), 7.70 (s, 1H), 7.90 (d, J = 1.5 Hz, 1H), 8.27–8.31
(m, 2H), 9.41 (br s, 1H). 13C NMR (75 MHz, CDCl3): d = 22.3, 22.8,
25.1, 41.3, 71.3, 83.5, 110.8, 113.8, 125.7, 126.6, 128.5, 128.6 (2
C), 128.9 (2 C), 130.2, 130.3, 130.6, 133.8, 135.2. MS (ES+): m/z
(%) = 455 (58) [M+Na]+, 433 (13) [M+H]+, 312 (100).
4.1.2.16. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(6-
fluoro-1H-indol-3-yl)ethanamine oxide 4cf. Compound 4cf
(200 mg, 72%) was obtained from N-hydroxylamine 3cf (280 mg,
0.70 mmol) and MnO2 (305 mg, 3.50 mmol) as a beige foam. IR
(neat): 675, 685, 835, 950, 1135, 1270, 1320, 1455, 1530, 1685,
2910, 2985, 3160, 3370 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.44
.
(s, 9H), 3.80–3.88 (m, 1H), 3.98–4.07 (m, 1H), 5.22–5.29 (m, 1H),
5.56–5.60 (m, 1H), 6.87 (dt, J1 = 9.4 Hz, J2 = 2.3 Hz, 1H), 6.95 (dd,
J1 = 9.4 Hz, J2 = 2.1 Hz, 1H), 7.28 (dd, J = 2.3 Hz, 1H), 7.39–7.42 (m,
3H), 7.57 (s, 1H), 7.62–7.67 (m, 1H), 8.21–8.25 (m, 2H), 8.80 (br
s, 1H). 13C NMR (75 MHz, CDCl3–CD3OD): d = 27.6 (3C), 42.0,
71.4, 79.3, 97.3 (d, J = 23.8 Hz), 108.0 (d, J = 25.0 Hz), 108.7, 118.7
4.1.2.11.
(Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-
(1H-indol-3-yl)ethanamine oxide 4ca. Compound 4ca (560 mg,

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O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
(d, J = 8.7 Hz), 122.3, 124.2 (d, J = 3.4 Hz), 128.1 (2 C), 128.9 (2 C),
129.5, 130.6, 135.9 (d, J = 12.6 Hz), 136.4, 156.6, 159.5 (d,
J = 237.2 Hz). 19F NMR (282 MHz, CDCl3): d = À120.4 (m, 1F). MS
(ES+): m/z (%) = 420 (100) [M+Na]+, 398 (12) [M+H]+, 331 (8), 277
(6), 221 (36), 177 (5).
1580, 2850, 2920, 3250, 3415 cmÀ1 1H NMR (300 MHz, CDCl3):
.
d = 1.40 (d, J = 6.6 Hz, 3H), 4.25 (q, J = 6.6 Hz, 1H), 6.78 (td,
J1 = 9.1 Hz, J2 = 2.2 Hz, 1H), 6.93 (s, 1H), 7.03–7.20 (m, 4H), 8.52
(br s, 1H). 13C NMR (75 MHz, CDCl3): d = 17.8, 53.9, 103.9 (d,
J = 23.8 Hz), 110.5 (d, J = 26.3 Hz), 112.0 (d, J = 9.7 Hz), 115.4 (d,
J = 4.8 Hz), 126.5 (d, J = 9.8 Hz), 132.7, 157.8 (d, J = 234.7 Hz). 19F
NMR (282 MHz, CDCl3): d = À124.0 (dt, J1 = 9.5 Hz, J2 = 4.4 Hz, 1F).
MS (ES+): m/z (%) = 217 (5) [M+Na]+, 162 [M+HÀNH2OH]+.
4.1.2.17. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(6-
chloro-1H-indol-3-yl)ethanamine oxide 4cg. Compound 4cg
(205 mg, 71%) was obtained from N-hydroxylamine 3cg (290 mg,
0.70 mmol) and MnO2 (305 mg, 3.50 mmol) as a beige foam. IR
(neat): 690, 750, 800, 905, 1130, 1160, 1250, 1365, 1450, 1505,
4.1.3.3. N-(1-(5-Chloro-1H-indol-3-yl)ethyl)hydroxylamine 5ac.
Compound 5ac (75 mg, 55%) was obtained from nitrone 4ac
(194 mg, 0.65 mmol) and NH2OH.HCl (136 mg, 1.95 mmol) as a
beige foam. IR (neat): 670, 795, 890, 1105, 1225, 1340, 1370,
1685, 2970, 3275 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.41 (s,
.
9H), 3.67–3.80 (m, 1H), 3.94–4.06 (m, 1H), 5.43–5.58 (m, 2H),
6.93–7.07 (m, 3H), 7.33–7.38 (m, 3H), 7.48–7.53 (m, 1H), 7.61 (s,
1H), 8.20–8.24 (m, 2H), 9.65 (br s, 1H). 13C NMR (75 MHz, CDCl3):
d = 28.2 (3C), 42.6, 71.7, 79.8, 109.3, 111.6, 119.2, 120.5, 124.4,
124.9, 127.9, 128.5 (2 C), 128.9 (2 C), 129.9, 130.8, 135.4, 136.4,
156.3. MS (ES+): m/z (%) = 436 (81) [M+Na]+, 414 (33) [M+H]+,
293 (16), 237 (100), 193 (14).
1420, 1460, 3260, 3420 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.38
.
(d, J = 6.6 Hz, 3H), 4.24 (q, J = 6.6 Hz, 1H), 6.58 (br s, 2H), 6.89 (s,
1H), 6.97–7.07 (m, 2H), 7.52 (s, 1H), 8.50 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 18.0, 53.8, 112.4, 115.4, 118.5, 122.4, 123.8,
125.3, 127.3, 134.5. MS (ES+): m/z (%) = 233 (6) [M+Na]+, 178
[M+HÀNH2OH]+.
4.1.2.18. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(6-
bromo-1H-indol-3-yl)ethanamine oxide 4ch. Compound 4ch
(430 mg, 72%) was obtained from N-hydroxylamine 3ch (598 mg,
1.30 mmol) and MnO2 (566 mg, 6.50 mmol) as a beige foam.14a
4.1.3.4. N-(1-(5-Bromo-1H-indol-3-yl)ethyl)hydroxylamine 5ad.
Compound 5ad (110 mg, 62%) was obtained from nitrone 4ad
(240 mg, 0.70 mmol) and NH2OH.HCl (146 mg, 2.10 mmol) as a
beige solid. IR (neat): 795, 865, 885, 1085, 1225, 1245, 1330,
1375, 1435, 1455, 2805, 3120, 3405 cmÀ1 1H NMR (300 MHz,
.
4.1.2.19. (Z)-N-Benzylidene-2-(tert-butoxycarbonylamino)-1-(4-
bromo-1H-indol-3-yl)ethanamine oxide 4ci. Compound 4ci
(155 mg, 52%) was obtained from N-hydroxylamine 3ci (299 mg,
0.65 mmol) and MnO2 (283 mg, 3.25 mmol) as a beige foam. IR
(neat): 690, 750, 780, 1125, 1165, 1270, 1365, 1430, 1500, 1525,
CD3OD): d = 1.50 (d, J = 6.6 Hz, 3H), 4.35 (q, J = 6.6 Hz, 1H), 7.15–
7.26 (m, 3H), 7.83 (dd, J1 = 1.9 Hz, J2 = 0.5 Hz, 1H). 13C NMR
(75 MHz, CDCl3): d = 19.2, 55.3, 113.0, 113.9, 116.8, 122.5, 125.0,
125.2, 129.6, 136.7. MS (ES+): m/z (%) = 277 (7) [M+Na]+, 224
[M+HÀNH2OH]+.
1690, 2865, 2975, 3440 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.40
.
(s, 9H), 3.64–3.84 (m, 1H), 3.89–4.10 (m, 1H), 5.27–5.52 (m, 1H),
6.38–6.55 (m, 1H), 6.65–6.84 (m, 1H), 6.91–7.20 (m, 2H), 7.27–
7.53 (m, 4H), 7.85 (s, 1H), 8.17–8.36 (m, 2H), 10.08 (br s, 1H). 13C
NMR (75 MHz, CDCl3): d = 28.3 (3C), 43.3, 69.6, 79.7, 109.0, 111.1,
112.5, 122.7, 123.8, 124.5, 127.0, 128.5 (2 C), 129.1 (2 C), 130.2,
130.7, 136.2, 137.3, 156.0. MS (ES+): m/z (%) = 482 (100) [M+Na]+,
458 (63) [M+H]+, 339 (15), 283 (61), 239 (17).
4.1.3.5. N-(1-(5-Iodo-1H-indol-3-yl)ethyl)hydroxylamine 5ae.
Compound 5ae (70 mg, 58%) was obtained from nitrone 4ae
(156 mg, 0.40 mmol) and NH2OH.HCl (83 mg, 1.20 mmol) as a
beige foam. IR (neat): 755, 795, 875, 980, 1100, 1225, 1320,
1370, 1450, 3250, 3415 cmÀ1 1H NMR (300 MHz, CDCl3–CD3OD):
.
d = 1.44 (d, J = 6.6 Hz, 3H), 4.30 (q, J = 6.6 Hz, 1H), 7.03–7.07 (m,
2H), 7.27–7.32 (m, 1H), 7.94 (s, 1H). 13C NMR (75 MHz, CDCl3):
d = 18.5, 54.1, 82.7, 113.6, 115.1, 123.4, 127.8, 129.0, 130.1, 135.6.
MS (ES+): m/z (%) = 325 (8) [M+Na]+, 270 [M+HÀNH2OH]+.
4.1.3. General procedure for the synthesis of indolic
N-hydroxylamines 5aa–ci
To a stirred solution of indolic nitrone 4aa–ci in methanol three
equiv. of hydroxylamine hydrochloride were added. The resulting
mixture was stirred during 1 h at room temperature and then solu-
tion was concentrated under vacuum. A saturated aqueous solu-
tion of NaHCO3 was added. The mixture was then extracted with
Et2O (3x10 mL), and the collected organic layers were washed with
brine, dried over Na2SO4, filtered, and concentrated under vacuum.
Column chromatography using EtOAc–pentane (10/90—99/1)
yielded pure products.
4.1.3.6. N-(1-(1H-Indol-3-yl)-3-methylbutyl)hydroxylamine 5ba.
Compound 5ba (125 mg, 64%) was obtained from nitrone 4ba
(275 mg, 0.90 mmol) and NH2OH.HCl (188 mg, 2.70 mmol) as a or-
ange foam. IR (neat): 740, 1010, 1045, 1095, 1230, 1340, 1455,
2865, 2955, 3410 cmÀ1 1H NMR (300 MHz, CDCl3): d = 0.85 (d,
.
J = 6.6 Hz, 3H), 0.89 (d, J = 6.6 Hz, 3H), 1.43–1.56 (m, 1H), 1.73–
1.89 (m, 2H), 4.35 (dd, J1 = 8.9 Hz, J2 = 5.8 Hz, 1H), 6.91 (d,
J = 1.9 Hz, 1H), 7.06–7.28 (m, 3H), 7.67 (d, J = 7.7 Hz, 1H), 8.23 (br
s, 1H). 13C NMR (75 MHz, CDCl3): d = 22.1, 23.5, 25.2, 41.6, 57.6,
111.3, 115.1, 119.1, 119.5, 122.0, 122.9, 126.6, 136.2. MS (ES+):
m/z (%) = 241 (15) [M+Na]+, 186 (100) [M+HÀNH2OH]+.
4.1.3.1. N-(1-(1H-Indol-3-yl)ethyl)hydroxylamine 5aa. Com-
pound 5aa (105 mg, 66%) was obtained from nitrone 4aa
(238 mg, 0.90 mmol) and NH2OH.HCl (188 mg, 2.70 mmol) as a
brown foam. IR (neat): 740, 850, 915, 980, 1010, 1095, 1230,
4.1.3.7. N-(1-(5-Fluoro-1H-indol-3-yl)-3-methylbutyl)hydroxyl-
amine 5bb. Compound 5bb (60 mg, 46%) was obtained from nit-
rone 4bb (178 mg, 0.55 mmol) and NH2OH.HCl (115 mg,
1.65 mmol) as a yellow foam. IR (neat): 795, 935, 1095, 1175,
1340, 1365, 1455, 1550, 1620, 2865, 2975, 3055, 3405 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 1.48 (d, J = 6.6 Hz, 3H), 4.40 (q,
J = 6.6 Hz, 1H), 6.83 (d, J = 1.6 Hz, 1H), 7.04–7.21 (m, 3H), 7.63 (d,
J = 7.8 Hz, 1H), 8.18 (br s, 1H). 13C NMR (75 MHz, CDCl3): d = 18.5,
54.0, 111.3, 116.1, 118.9, 119.5, 122.0, 122.2, 126.2, 136.1. MS
(ES+): m/z (%) = 199 (6) [M+Na]+, 144 (100) [M+HÀNH2OH]+.
1365, 1455, 1485, 1580, 1630, 2890, 2955, 3270, 3420 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 0.78 (d, J = 6.8 Hz, 3H), 0.81 (d,
J = 6.8 Hz, 3H), 1.35–1.48 (m, 1H), 1.60–1.76 (m, 2H), 4.17 (dd,
J1 = 8.7 Hz, J2 = 6.0 Hz, 1H), 5.30 (br s, 2H), 6.82 (td, J1 = 9.1 Hz,
J2 = 2.5 Hz, 1H), 6.97 (s, 1H), 7.12 (dd, J1 = 8.8 Hz, J2 = 4.4 Hz, 1H),
7.25 (dd, J1 = 9.8 Hz, J2 = 2.4 Hz, 1H), 8.24 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 22.2, 23.4, 25.2, 41.4, 57.6, 104.2 (d,
J = 23.7 Hz), 110.5 (d, J = 26.4 Hz), 111.9 (d, J = 9.7 Hz), 115.7,
4.1.3.2. N-(1-(5-Fluoro-1H-indol-3-yl)ethyl)hydroxylamine 5ab.
Compound 5ab (75 mg, 60%) was obtained from nitrone 4ab
(183 mg, 0.65 mmol) and NH2OH.HCl (136 mg, 1.95 mmol) as a
brown foam. IR (neat): 795, 850, 935, 1175, 1225, 1455, 1485,

O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
3213
124.6, 127.0 (d, J = 9.8 Hz), 132.8, 157.7 (d, J = 234.6 Hz). MS (ES+):
m/z (%) = 259 (11) [M+Na]+, 204 (100) [M+HÀNH2OH]+.
1H NMR (300 MHz, CDCl3): d = 1.44 (s, 9H), 3.40–3.45 (m, 1H),
3.56–3.70 (m, 1H), 4.29 (t, J = 5.3 Hz, 1H), 5.03 (br s, 1H), 7.05–
7.10 (m, 2H), 7.20 (d, J = 9.0 Hz, 1H), 7.59 (s, 1H), 8.84 (br s, 1H).
13C NMR (75 MHz, CDCl3): d = 28.3 (3C), 42.5, 58.7, 79.9, 112.4,
118.7, 122.5, 124.1, 125.3, 127.3, 134.5 (2 C), 157.1. MS (ES+):
m/z (%) = 348 (14) [M+Na]+, 326 (16) [M+H]+, 237 (100), 193 (12).
4.1.3.8. N-(1-(5-Chloro-1H-indol-3-yl)-3-methylbutyl)hydroxyl-
amine 5bc. Compound 5bc (65 mg, 41%) was obtained from nit-
rone 4bc (215 mg, 0.63 mmol) and NH2OH.HCl (131 mg,
1.89 mmol) as a yellow foam. IR (neat): 800, 885, 1040, 1070,
1100, 1220, 1330, 1460, 2870, 2915, 2955, 3120, 3265 cmÀ1 1H
.
4.1.3.14. tert-Butyl 2-(5-bromo-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5cd. Compound 5cd (145 mg, 56%) was ob-
tained from nitrone 4cd (320 mg, 0.70 mmol) and NH2OH.HCl
(146 mg, 2.10 mmol) as a beige foam.14a
NMR (300 MHz, CDCl3–CD3OD): d = 0.78 (d, J = 6.6 Hz, 3H), 0.82
(d, J = 6.6 Hz, 3H), 1.36–1.49 (m, 1H), 1.68–1.74 (m, 2H), 4.20 (dd,
J1 = 8.4 Hz, J2 = 6.2 Hz, 1H), 6.99–7.07 (m, 2H), 7.16–7.25 (m, 1H),
7.57 (d, J = 1.9 Hz, 1H). 13C NMR (75 MHz, CDCl3–CD3OD):
d = 21.8, 23.2, 25.0, 41.2, 57.3, 112.3, 113.9, 118.2, 121.8, 124.4,
124.7, 127.6, 134.6. MS (ES+): m/z (%) = 275 (10) [M+Na]+, 220
(100) [M+HÀNH2OH]+.
4.1.3.15. tert-Butyl 2-(5-iodo-1H-indol-3-yl)-2-(hydroxyamino)-
ethylcarbamate 5ce. Compound 5ce (125 mg, 75%) was obtained
from nitrone 4ce (202 mg, 0.40 mmol) and NH2OH.HCl (83 mg,
1.20 mmol) as a beige foam. IR (neat): 750, 795, 1160, 1250,
4.1.3.9. N-(1-(5-Bromo-1H-indol-3-yl)-3-methylbutyl)hydroxyl-
amine 5bd. Compound 5bd (75 mg, 36%) was obtained from nit-
rone 4bd (270 mg, 0.70 mmol) and NH2OH.HCl (146 mg,
2.10 mmol) as a yellow foam. IR (neat): 755, 795, 880, 1100,
1365, 1455, 1510, 1685, 2925, 2975, 3280, 3410 cmÀ1 1H NMR
.
(300 MHz, CDCl3): d = 1.44 (s, 9H), 3.40–3.49 (m, 1H), 3.50–3.61
(m, 1H), 4.26 (t, J = 5.2 Hz, 1H), 5.08 (br s, 1H), 6.95 (s, 1H), 7.04
(d, J = 8.5 Hz, 1H), 7.35 (dd, J1 = 8.5 Hz, J2 = 1.4 Hz, 1H), 7.94 (s,
1H), 8.96 (br s, 1H). 13C NMR (75 MHz, CDCl3): d = 28.3 (3C), 42.5,
58.5, 79.9, 83.0, 112.1, 113.4, 123.5, 127.9, 128.8, 130.3, 135.1,
157.0. MS (ES+): m/z (%) = 440 (18) [M+Na]+, 418 (56) [M+H]+,
376 (100).
1365, 1455, 2865, 2955, 3265, 3420 cmÀ1 1H NMR (300 MHz,
.
CDCl3–CD3OD): d = 0.79 (d, J = 6.7 Hz, 3H), 0.82 (d, J = 6.7 Hz, 3H),
1.39–1.48 (m, 1H), 1.67–1.73 (m, 2H), 4.19 (dd, J1 = 8.7 Hz,
J2 = 6.0 Hz, 1H), 7.03 (s, 1H), 7.13–7.14 (m, 2H), 7.74–7.75 (m,
1H). 13C NMR (75 MHz, CDCl3–CD3OD): d = 21.9, 23.2, 25.0, 41.3,
57.3, 112.3, 112.7, 114.2, 121.3, 124.2, 124.4, 128.3, 134.9. MS
(ES+): m/z (%) = 319 (12) [M+Na]+, 266 (100) [M+HÀNH2OH]+.
4.1.3.16. tert-Butyl 2-(6-fluoro-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5cf. Compound 5cf (50 mg, 40%) was ob-
tained from nitrone 4cf (159 mg, 0.40 mmol) and NH2OH.HCl
(83 mg, 1.20 mmol) as a beige foam. IR (neat): 800, 950, 1140,
4.1.3.10. N-(1-(5-Iodo-1H-indol-3-yl)-3-methylbutyl)hydroxyl-
amine 5be. Compound 5be (65 mg, 32%) was obtained from nit-
rone 4be (260 mg, 0.60 mmol) and NH2OH.HCl (125 mg,
1.80 mmol) as a yellow foam. IR (neat): 755, 795, 875, 1100,
1160, 1250, 1365, 1455, 1500, 1685, 2920, 2975, 3290, 3415 cm
À1
.
1H NMR (300 MHz, CDCl3): d = 1.43 (s, 9H), 3.45–3.51 (m, 1H),
1365, 1455, 2865, 2955, 3260, 3415 cmÀ1 1H NMR (300 MHz,
.
3.60–3.65 (m, 1H), 4.34 (t, J = 5.3 Hz, 1H), 5.02 (br s, 1H), 6.83
(dt, J1 = 9.6 Hz, J2 = 2.3 Hz, 1H), 6.97 (dd, J1 = 9.6 Hz, J2 = 2.3 Hz,
1H), 7.03 (s, H), 7.49 (dd, J1 = 8.7 Hz, J2 = 5.3 Hz, 1H), 8.74 (br s,
1H). 13C NMR (75 MHz, CDCl3): d = 28.4 (3C), 42.4, 58.6, 79.9,
97.6 (d, J = 26.2 Hz), 108.4 (d, J = 24.5 Hz), 122.8, 122.9, 128.8 (d,
J = 12.2 Hz), 136.0, 136.1, 158.4, 160.0 (d, J = 238.5 Hz). 19F NMR
(282 MHz, CDCl3): d = À120.7 (m, 1F). MS (ES+): m/z (%) = 332
(43) [M+Na]+, 310 (6) [M+H]+, 239 (100), 221 (75).
CDCl3): d = 0.87 (d, J = 6.8 Hz, 3H), 0.89 (d, J = 6.8 Hz, 3H), 1.43-
1.57 (m, 1H), 1.66–1.82 (m, 2H), 4.25 (dd, J1 = 8.7 Hz, J2 = 5.9 Hz,
1H), 6.96 (d, J = 1.9 Hz, 1H), 7.01 (d, J = 8.5 Hz, 1H), 7.40 (dd,
J1 = 8.5 Hz, J2 = 1.5 Hz, 1H), 8.04 (d, J = 1.3 Hz, 1H), 8.33 (s, 1H).
13C NMR (75 MHz, CDCl3): d = 22.3, 23.3, 25.2, 41.5, 57.4, 83.2,
113.3, 115.2, 123.5, 128.2, 129.3, 130.4, 135.4. MS (ES+): m/z
(%) = 367 (10) [M+Na]+, 312 (100) [M+HÀNH2OH]+.
4.1.3.17. tert-Butyl 2-(6-chloro-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5cg. Compound 5cg (100 mg, 77%) was ob-
tained from nitrone 4cg (165 mg, 0.40 mmol) and NH2OH.HCl
(83 mg, 1.20 mmol) as a beige foam. IR (neat): 800, 905, 1160,
4.1.3.11. tert-Butyl 2-(1H-indol-3-yl)-2-(hydroxyamino)ethylc-
arba-mate 5ca. Compound 5ca (265 mg, 65%) was obtained from
nitrone 4ca (531 mg, 1.40 mmol) and NH2OH.HCl (292 mg,
4.20 mmol) as a beige foam.14a
1250, 1365, 1455, 1510, 1685, 2925, 2975, 3280, 3415 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 1.43 (s, 9H), 3.40–3.62 (m, 2H), 4.30
(t, J = 5.4 Hz, 1H), 5.06 (br s, 1H), 6.98–7.03 (m, 2H), 7.24–7.26
(m, 1H), 7.45 (d, J = 9.0 Hz, 1H), 8.87 (br s, 1H). 13C NMR
(75 MHz, CDCl3): d = 28.3 (3C), 42.4, 58.5, 79.9, 111.3, 119.8,
120.3, 123.3, 124.8, 128.0, 136.4 (2 C), 157.1. MS (ES+): m/z
(%) = 348 (18) [M+Na]+, 326 (14) [M+H]+, 301 (12), 237 (100),
193 (11).
4.1.3.12. tert-Butyl 2-(5-fluoro-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5cb. Compound 5cb (80 mg, 58%) was ob-
tained from nitrone 4cb (179 mg, 0.45 mmol) and NH2OH.HCl
(94 mg, 1.35 mmol) as a beige foam. IR (neat): 795, 850, 935,
1160, 1250, 1365, 1455, 1490, 1510, 1685, 2925, 2975, 3300,
3415 cmÀ1 1H NMR (300 MHz, CDCl3): d = 1.42 (s, 9H), 3.43–3.50
.
(m, 1H), 3.55–3.68 (m, 1H), 4.28 (t, J = 5.3 Hz, 1H), 5.04 (br s, 1H),
6.88 (dt, J1 = 9.0 Hz, J2 = 2.4 Hz, 1H), 7.07 (s, H), 7.19 (dd,
J1 = 8.8 Hz, J2 = 4.4 Hz, 1H), 7.21–7.30 (m, 1H), 8.79 (br s, 1H). 13C
NMR (75 MHz, CDCl3): d = 28.3 (3C), 42.4, 58.7, 79.9, 104.1 (d,
J = 23.2 Hz), 110.6 (d, J = 26.5 Hz), 112.0 (d, J = 9.2 Hz), 124.4,
126.6 (d, J = 10.2 Hz), 132.6 (2 C), 157.2, 157.8 (d, J = 236.7 Hz).
19F NMR (282 MHz, CDCl3): d = À124.1 (m, 1F). MS (ES+): m/z
(%) = 332 (49) [M+Na]+, 310 (7) [M+H]+, 239 (44), 221 (100).
4.1.3.18. tert-Butyl 2-(6-bromo-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5ch. Compound 5ch (170 mg, 57%) was ob-
tained from nitrone 4ch (366 mg, 0.80 mmol) and NH2OH.HCl
(167 mg, 2.40 mmol) as a beige foam.14a
4.1.3.19. tert-Butyl 2-(4-bromo-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5ci. Compound 5ci (75 mg, 68%) was ob-
tained from nitrone 4ci (137 mg, 0.30 mmol) and NH2OH.HCl
(63 mg, 0.90 mmol) as a beige foam. IR (neat): 735, 775, 1160,
4.1.3.13. tert-Butyl 2-(5-chloro-1H-indol-3-yl)-2-(hydroxyami-
no)-ethylcarbamate 5cc. Compound 5cc (80 mg, 62%) was ob-
tained from nitrone 4cc (165 mg, 0.40 mmol) and NH2OH.HCl
(83 mg, 1.20 mmol) as a beige foam. IR (neat): 795, 860, 895,
1250, 1335, 1365, 1510, 1685, 2925, 2975, 3275, 3415 cmÀ1 1H
.
NMR (300 MHz, CDCl3): d = 1.43 (s, 9H), 3.57–3.75 (m, 2H), 5.06–
5.16 (m, 2H), 6.93 (t, J = 7.8 Hz, 1H), 7.18–7.25 (m, 3H), 9.18
1160, 1250, 1365, 1455, 1515, 1685, 2925, 2975, 3290, 3410 cmÀ1
.

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O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
(br s, 1H). 13C NMR (75 MHz, CDCl3): d = 28.3 (3C), 42.2, 57.2, 79.8,
110.9, 112.9, 113.3, 122.8, 124.2, 124.4, 124.5, 137.5, 157.4. MS
(ES+): m/z (%) = 384 (28) [M+Na]+, 372 (14) [M+H]+, 360 (11), 328
(100), 293 (23).
114.8, 114.9, 122.1, 126.9, 129.2, 129.6, 136.9. MS (ES+): m/z
(%) = 270 (100).
4.1.4.5. 2-(5-Iodo-1H-indol-3-yl)-2-(hydroxyamino)ethanamine
dihydrochloride 6ce. Compound 6ce (100 mg, 99%) was obtained
from N-hydroxylamine 5cfe (104 mg, 0.25 mmol) as a light brown
solid. IR (neat): 795, 880, 1000, 1110, 1230, 1450, 2690, 2865,
4.1.4. General procedure for the synthesis of indolic
N-hydroxylamines 6ca–ci
3100 cmÀ1 1H NMR (300 MHz, CD3OD): d = 3.79 (dd, J1 = 13.2 Hz,
.
A cold solution of hydrochloric acid was prepared by reaction of
ten equiv. (compare to N-hydroxylamine quantity) of freshly dis-
tilled acetyl chloride with 3 mL of dry methanol. This solution
was stirred at 0 °C during 15 min and was then added to a solution
of indolic N-hydroxylamine 5ca–ci in 1 mL of dry methanol. The
resulting mixture was stirred during 2 h at 0 °C. Methanol was then
slowly evaporated under vacuum (t<20 °C). The indolic 1,2-dia-
mine salts 6ca–ci was obtained as light brown solids.
J2 = 8.7 Hz, 1H), 3.97 (dd, J1 = 13.2 Hz, J2 = 5.5 Hz, 1H), 5.26
(dd, J1 = 8.7 Hz, J2 = 5.5 Hz, 1H), 7.33 (d, J = 8.6 Hz, 1H), 7.51 (dd,
J1 = 8.6 Hz, J2 = 1.5 Hz, 1H), 7.78 (s, 1H), 8.19 (d, J = 1.5 Hz, 1H).
13C NMR (75 MHz, CDCl3): d = 40.1, 56.6, 84.7, 102.8, 115.3,
128.4, 129.2, 130.0, 132.4, 137.2. MS (ES+): m/z (%) = 318 (100)
[M+H]+.
4.1.4.6. 2-(6-Fluoro-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6cf. Compound 6cf (25 mg, 89%) was
obtained from N-hydroxylamine 5cf (31 mg, 0.1 mmol) as a light
brown solid. IR (neat): 815, 850, 950, 980, 1100, 1135, 1230,
4.1.4.1. 2-(1H-Indol-3-yl)-2-(hydroxyamino)ethanamine dihy-
dro-chloride 6ca. Compound 6ca (155 mg, 98%) was obtained
from N-hydroxylamine 5ca (175 mg, 0.60 mmol) as a light brown
solid. IR (neat): 740, 1000, 1105, 1235, 1340, 1460, 1595, 2975,
1450, 1500, 2670, 2900, 3290 cmÀ1 1H NMR (300 MHz, CD3OD):
.
d = 3.79 (dd, J1 = 13.1 Hz, J2 = 8.8 Hz, 1H), 3.97 (dd, J1 = 13.1 Hz,
J2 = 5.5 Hz, 1H), 5.28 (dd, J1 = 8.8 Hz, J2 = 5.5 Hz, 1H), 6.99 (dt,
J1 = 9.0 Hz, J2 = 2.3 Hz, 1H), 7.20 (dd, J1 = 9.0 Hz, J2 = 2.3 Hz, 1H),
7.77 (s, 1H), 7.79 (dd, J1 = 9.0 Hz, J2 = 5.1 Hz, 1H). 13C NMR
(75 MHz, CD3OD): d = 40.1, 56.9, 99.1 (d, J = 25.5 Hz), 103.7,
110.2 (d, J = 24.7 Hz), 120.5 (d, J = 10.8 Hz), 124.0, 128.8 (d,
J = 8.7 Hz), 138.3, 161.8 (d, J = 236.7 Hz). 19F NMR (282 MHz,
CDCl3): d = À122.1 (dt, J1 = 9.6 Hz, J2 = 5.1 Hz, 1F). MS (ES+): m/z
(%) = 210 (100) [M+H]+.
3050, 3185, 3385 cmÀ1 1H NMR (300 MHz, CD3OD): d = 3.81 (dd,
.
J1 = 13.1 Hz, J2 = 8.9 Hz, 1H), 3.98 (dd, J1 = 13.1 Hz, J2 = 5.6 Hz, 1H),
5.28 (dd, J1 = 8.9 Hz, J2 = 5.6 Hz, 1H), 7.17–7.28 (m, 2H), 7.50 (dt,
J1 = 8.0 Hz, J2 = 1.2 Hz, 1H), 7.77 (s, 1H), 7.81 (d, J = 8.0 Hz). 13C
NMR (75 MHz, CD3OD): d = 40.2, 57.1, 103.3, 113.2, 119.2, 121.7,
124.0, 127.4, 128.1, 138.2. MS (ES+): m/z (%) = 214 (19) [M+Na]+,
192 (5) [M+H]+, 159 (100).
4.1.4.2. 2-(5-Fluoro-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6cb. Compound 6cb (50 mg, 94%) was
obtained from N-hydroxylamine 5cb (62 mg, 0.2 mmol) as a light
brown solid. IR (neat): 800, 935, 1155, 1185, 1455, 1490, 1585,
4.1.4.7. 2-(6-Chloro-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6cg. Compound 6cg (80 mg, 95%) was
obtained from N-hydroxylamine 5cg (91 mg, 0.28 mmol) as a
light brown solid. IR (neat): 810, 980, 1060, 1400, 1485, 2705,
2690, 2865 cmÀ1 1H NMR (300 MHz, CD3OD): d = 3.31 (dd,
.
2970, 3410 cmÀ1 1H NMR (300 MHz, CD3OD): d = 3.80 (dd,
.
J1 = 13.2 Hz, J2 = 9.0 Hz, 1H), 3.80 (dd, J1 = 13.2 Hz, J2 = 5.6 Hz,
1H), 5.26 (dd, J1 = 9.0 Hz, J2 = 5.6 Hz, 1H), 7.02 (dt, J1 = 9.0 Hz,
J2 = 2.4 Hz, 1H), 7.47 (dd, J1 = 9.0 Hz, J2 = 4.5 Hz, 1H), 7.52 (dd,
J1 = 9.6 Hz, J2 = 2.4 Hz, 1H), 7.83 (s, 1H). 13C NMR (75 MHz,
CDCl3): d = 40.0, 56.9, 103.6 (d, J = 9.2 Hz), 104.4 (d, J = 23.7 Hz),
112.3 (d, J = 26.7 Hz), 114.2 (d, J = 9.8 Hz), 127.9 (d, J = 10.7 Hz),
130.0, 134.7, 159.8 (d, J = 238.7 Hz). 19F NMR (282 MHz, CD3OD):
d = À124.9 (dt, J1 = 9.4 Hz, J2 = 4.5 Hz, 1F). MS (ES+): m/z (%) = 194
(100) [M+H]+.
J1 = 13.2 Hz, J2 = 8.8 Hz, 1H), 3.98 (dd, J1 = 13.2 Hz, J2 = 5.6 Hz,
1H), 5.30 (dd, J1 = 8.8 Hz, J2 = 5.6 Hz, 1H), 7.18 (dd, J1 = 8.5 Hz,
J2 = 1.8 Hz, 1H), 7.52 (d, J = 1.8 Hz, 1H), 7.80 (d, J = 8.5 Hz, 1H),
7.81 (s, 1H). 13C NMR (75 MHz, CDCl3): d = 40.1, 56.7, 103.8,
113.0, 120.7, 122.2, 126.1, 129.2, 129.9, 138.5. MS (ES+): m/z
(%) = 226 (100) [M+H]+.
4.1.4.8. 2-(6-Bromo-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6ch. Compound 6ch (120 mg, 89%)
was obtained from N-hydroxylamine 5ch (148 mg, 0.4 mmol)
as a light brown solid. IR (neat): 800, 895, 985, 1050, 1110,
4.1.4.3. 2-(5-Chloro-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6cc. Compound 6cc (40 mg, 78%) was
obtained from N-hydroxylamine 5cc (55 mg, 0.17 mmol) as a
light brown solid. IR (neat): 800, 895, 1000, 1110, 1405, 1455,
1300, 1335, 1405, 1445, 1495, 2695, 2895, 3105 cmÀ1 1H NMR
.
(300 MHz, CD3OD): d = 3.79 (dd, J1 = 13.2 Hz, J2 = 8.9 Hz, 1H),
3.96 (dd, J1 = 13.2 Hz, J2 = 5.5 Hz, 1H), 5.26 (dd, J1 = 8.9 Hz,
J2 = 5.5 Hz, 1H), 7.31 (dd, J1 = 8.6 Hz, J2 = 1.8 Hz, 1H), 7.68–7.78
(m, 3H). 13C NMR (75 MHz, CDCl3): d = 40.1, 56.7, 103.8, 116.1,
117.3, 121.0, 124.8, 126.4, 129.1, 139.0. MS (ES+): m/z (%) = 270
(100) [M+H]+.
2690, 2920 cmÀ1 1H NMR (300 MHz, CD3OD): d = 3.80 (dd,
.
J1 = 13.1 Hz, J2 = 8.9 Hz, 1H), 3.96 (dd, J1 = 13.1 Hz, J2 = 5.6 Hz,
1H), 5.25 (dd, J1 = 8.9 Hz, J2 = 5.6 Hz, 1H), 7.22 (dd, J1 = 8.7 Hz,
J2 = 1.9 Hz, 1H), 7.48 (d, J = 8.7 Hz, 1H), 7.83 (s, 1H), 7.84 (d,
J = 1.9 Hz, 1H). 13C NMR (75 MHz, CDCl3): d = 40.1, 56.7, 103.3,
114.6, 119.0, 124.2, 127.5, 128.6, 129.9, 136.8. MS (ES+): m/z
(%) = 226 (100) [M+H]+.
4.1.4.9. 2-(4-Bromo-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6ci. Compound 6ci (55 mg, 99%) was
obtained from N-hydroxylamine 5ci (59 mg, 0.16 mmol) as a
light brown solid. IR (neat): 730, 770, 810, 915, 990, 1165,
4.1.4.4. 2-(5-Bromo-1H-indol-3-yl)-2-(hydroxyamino)ethan-
amine dihydrochloride 6cd. Compound 6cd (135 mg, 98%)
was obtained from N-hydroxylamine 5cd (148 mg, 0.4 mmol) as
a light brown solid. IR (neat): 795, 885, 995, 1110, 1155, 1230,
1195, 1425, 1485, 2675, 2890, 2965 cmÀ1 1H NMR (300 MHz,
.
CD3OD): d = 3.85 (dd, J1 = 13.4 Hz, J2 = 8.2 Hz, 1H), 4.00 (dd,
J1 = 13.4 Hz, J2 = 6.0 Hz, 1H), 6.16 (dd, J1 = 8.2 Hz, J2 = 6.0 Hz,
1H), 7.14 (t, J = 8.0 Hz, 1H), 7.37 (dd, J1 = 8.0 Hz, J2 = 0.8 Hz, 1H),
7.52 (dd, J1 = 8.0 Hz, J2 = 0.8 Hz, 1H), 7.94 (d, J = 2.5 Hz, 1H). 13C
NMR (75 MHz, CDCl3): d = 40.4, 56.4, 104.0, 113.1, 113.9, 124.9,
125.3, 126.3, 129.8, 139.7. MS (ES+): m/z (%) = 270 (100)
[M+H]+.
1455, 2675, 2870 cmÀ1 1H NMR (300 MHz, CD3OD): d = 3.79
.
(dd, J1 = 13.1 Hz, J2 = 8.8 Hz, 1H), 3.95 (dd, J1 = 13.1 Hz,
J2 = 5.5 Hz, 1H), 5.25 (dd, J1 = 8.8 Hz, J2 = 5.5 Hz, 1H), 7.33–7.36
(m, 1H), 7.42–7.45 (m, 1H), 7.81 (d, J = 2.0 Hz, 1H), 7.98 (d,
J = 1.8 Hz, 1H). 13C NMR (75 MHz, CDCl3): d = 40.1, 56.7, 103.2,

O. N. Burchak et al. / Bioorg. Med. Chem. 19 (2011) 3204–3215
3215
4.2. Microbiology
and the final assay buffer contained 10% of this solvent. For the
determination of inhibition potency of EcPDF, to prevent the effects
associated with slow binding,11a each inhibitor was incubated with
the enzyme for 10 min at 25 °C before kinetic analysis, which was
initiated by adding the peptide substrate.
Stock solutions of the indolic compounds were prepared in
dimethylsulfoxide (DMSO, Sigma-Aldrich, France) at a concentra-
tion of 25.6 mg/mL. These stock solutions were further 1:20 diluted
in sterile 10% DMSO solution. Working solutions of the indolic
compounds contained less than 5% DMSO which was verified to
be nontoxic for all bacterial strains tested. The antibacterial activ-
ity of indolic compounds was evaluated against 28 gram-positive
or gram-negative reference strains belonging to 17 different
species, obtained from the American Type Culture Collection
(Mannasas VA, USA) or from the Institut Pasteur Collection (Paris,
France): six methicillin-susceptible S. aureus strains (ATCC 25923,
ATCC 29213, ATCC 9144, ATCC 6538, CIP 65.6 and CIP 103428),
two methicillin-resistant S. aureus (MRSA) strains (CIP 65.25 and
ATCC 33592), one vancomycin-intermediate S. aureus (VISA) strain
(ATCC 106414), three S. epidermidis strains (ATCC 12228, CIP 81.55
and CIP 103627), two S. pneumoniae strains (ATCC 49619, ATCC
6303), and one strain each for the species S. agalactiae (ATCC
12400), S. pyogenes (CIP 104226), S. mitis (CIP 103335), Enterococ-
cus faecium (CIP 54.32), E. faecalis (ATCC 29212), Listeria innocua
(CIP 80.11), Bacillus subtilis (CIP 5262), E. coli (ATCC 25922), Klebsi-
ella pneumoniae (ATCC 35657), Enterobacter cloacae (ATCC 13047),
Serratia marcescens (CIP 103551), P. aeruginosa (CIP 5933), A. bau-
manii (ATCC 19606) and Haemophilus influenzae (ATCC 49766).
The minimal inhibitory concentrations (MICs) of the indolic
compounds against previously mentioned bacterial strains were
Acknowledgments
This work was supported by the grant ANR-08-EBIO-012 from
the Agence Nationale de la Recherche (ANR, France). The authors
wish to thank Karim Hamiche (UPR 2355 CNRS, Gif-sur-Yvette)
for the tests of PDF inhibition and Dr. Thierry Cresteil (UPR 2301
CRNS, Gif-sur-Yvette) for the tests of cytotoxicity.
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plate were filled with a 106 cfu/ml bacterial inoculum (180
lL
per well) and serial dilutions of the indolic compound to be tested
(20 L per well), at ten-fold the desired final concentration, rang-
ing from 2 to 128 g/ml. The bacterial growth medium was Muel-
l
l
ler–Hinton broth (AES Chemunex, France), supplemented with 5%
sheep blood (BioMérieux, France) for the fastidious species S. pneu-
moniae, S. mitis, and H. influenzae. One well that did not receive any
antibiotic served as a growth control. Experiments were made at
least twice for each indolic compound to confirm results. MICs
were read after 18 h incubation of the plates at 37 °C. They corre-
sponded to the minimal indolic compound concentration allowing
complete inhibition of visible growth. MIC values were also deter-
mined for the three antibiotics ciprofloxacin, gentamicin and cefo-
taxime, taken as controls. Deformylase activity was determined in
HEPES buffer at pH 7.5 and at 37 °C by a PDF–formate dehydroge-
nase coupled assay.17 Deformylation rate of Formyl-Met-Ala-Ser
(1 mM) in the presence of EcPDF (20 nM; purified in the presence
of NiCl2) was assayed by coupling with formate dehydrogenase
(Sigma) and was directly proportional to the rate of production
of NADH. Formation of NADH was monitored using UV spectros-
copy at 340 nm. All inhibitors were diluted in dimethylsulfoxide,
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