The synthesis and 16S A-site rRNA recognition of carbohydrate-free aminoglycosides

Article abstract of DOI:10.1016/j.bmcl.2005.08.027

The first carbohydrate-free aminoglycoside analogs bearing the 2-deoxystreptamine moiety were synthesized from asymmetrically protected 2-deoxystrepamine and subsequently demonstrated to have significant binding to the 16S A-site rRNA target and moderate

Full text of DOI:10.1016/j.bmcl.2005.08.027

Bioorganic & Medicinal Chemistry Letters 15 (2005) 4919–4922
The synthesis and 16S A-site rRNA recognition of
carbohydrate-free aminoglycosides
Xiaojing Wang, Michael T. Migawa,* Kristin A. Sannes-Lowery and Eric E. Swayze
Ibis Therapeutics, A Division of Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA
Received 5 April 2005; revised 8 August 2005; accepted 9 August 2005
Available online 13 September 2005
Abstract—The first carbohydrate-free aminoglycoside analogs bearing the 2-deoxystreptamine moiety were synthesized from asym-
metrically protected 2-deoxystrepamine and subsequently demonstrated to have significant binding to the 16S A-site rRNA target
and moderate functional activity.
Ó 2005 Elsevier Ltd. All rights reserved.
Although aminoglycosides were discovered over 60
years ago, they are still among the most potent antibiot-
ics in the clinic.1 However, aminoglycosides have poor
oral bioavailability and pharmacokinetics, and their
oto- and nephro-toxicity remain obstacles that limit
their use to ꢀlast resortꢁ or to combination therapies.2,3
In addition, bacterial resistance has been increasing, a
serious problem that requires the development of better
aminoglycosides with structural motifs that block the
many aminoglycoside modifying enzymes.1,4 Therefore,
research to discover modified aminoglycosides has been
an ongoing focus of several research groups.5–10
noglycoside analogs and their initial evaluation in an
FTICR mass spectrometer binding assay.
Our initial synthetic strategy focused on the protected
2-deoxystreptamine (2-DOS) analog 1. We found this
previously reported compound easy to prepare, scalable,
and suitably enantiopure.11 First, we sought to avoid
basic conditions to avoid any acetyl group migration.
To this end, the Pummerer rearrangement18,19 was
adopted successfully to functionalize position 4 of the
2-DOS analog 1 with a methylthiomethylene group.
Subsequent chlorination by sulfuryl chloride and reac-
tion with thiolquinoline gave intermediate 3a in an
85% yield. On the other hand, p-methoxybenzyl imi-
date20,21 and compound 1 were treated with campho-
sulfonic acid under anhydrous conditions to yield
compound 3b in a good yield. Deacetylation of 3a,b
went smoothly to give the key diol intermediates 4a,b,
individually. Reduction of 4a,b by transfer hydrogena-
tion using hydrazine and Raney Ni gave the diamine
5a,b in good to excellent yields (see Scheme 1).
One approach11–13 is to replace one or more carbohy-
drate rings with an open alkylamino chain. In one exam-
ple, a crystal structure14 of an analog bound to the 16S
A-site rRNA was offered together with good antibacte-
rial activity as evidence of the potential for success of
this strategy.13 Our own work, focusing on replacing
the A-ring with a suitable aromatic moiety, has been
previously demonstrated as another strategy for produc-
ing analogs lacking the easily modified carbohydrate
rings.15–17 Such A-ring replacements have been demon-
strated to have good binding to the 16S A-site rRNA
along with antibacterial effects. Moreover, computer
modeling suggests that this strategy would not be mutu-
ally exclusive with the carbohydrate ring replacement
strategy. Therefore, we sought to combine both of these
strategies and prepare aminoglycoside analogs lacking
one sugar ring. Herein, we report the synthesis of ami-
Previous carbohydrate ring replacement strategies have
relied on a successful alcohol allylation followed by a
subsequent oxidative cleavage to introduce an aldehyde
moiety.11–13 However, the presence of a thiol group
prone to oxidation prompted us to look for an alterna-
t
tive route. Alkylation of compounds 4a,b with butyl-a-
bromoacetate proved to be feasible, while iodoacetonit-
rile and bromoacetaldehyde diethyl acetal failed to give
the desired products. After alkylation, carboxylic acids
6a and 7a were obtained exclusively, probably due to
hydrolysis facilitated by the neighboring hydroxy group.
Although the yield for 6a and 7a was relatively low
*
Corresponding author. Tel.: +1 7606032713; fax: +1 7606034653;
e-mail: mmigawa@isisph.com
0960-894X/$ - see front matter Ó 2005 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2005.08.027

4920
X. Wang et al. / Bioorg. Med. Chem. Lett. 15 (2005) 4919–4922
N3
N3
N3
H2N
c
e
d
HO
AcO
RO
RO
HO
RO
HO
N3
a
N3
N3
NH2
AcO
OAc
OAc
3a,b
OH
OH
1
4a,b
5a,b
b
S
N
N3
MeS
O
AcO
a: R =
b: R =
F3C
N3
OAc
2
O
Scheme 1. Reagents and conditions: (a) DMSO, AcOH, Ac2O, rt, 2.5 d (80%); (b) (i) SO2Cl2, DCM, rt, 30 min, (ii) NaH, 7-trifluoromethyl-4-
quinolinethiol, CH3CN, rt, 2.5 h (85%); (c) pMeOBnOC(NH)CCl3, CSA, DCM, rt, 2 d; (d) LiOH, THF, iPrOH, H2O, rt, 2 h (72% 1–4b);
(e) NH4OH, MeOH, rt, 16 h (91% for 4a); (f) NH2NH2, Raney Ni, 1 h (82% for 5a, 92% for 5b).
N3
N3
N3
N3
RO
HO
RO
N3
a
RO
RO
N3
b,c
N3
N3
+
O
O
O
4a,b
+
O
O
OH
O
CO2H
HO
8a,b
CO2H
OH
6a,b
7a,b
9a,b
N3
H2N
N3
H2N
RO
HO
RO
HO
e, f or g
d
N3
NH2
RO
RO
N3
NH2
+
+
O
O
O
O
OH
OH
BocHN
N
N
H2N
N
N
H
NHBoc
NH2
H
H
H
10a,b
11a,b
12a,b
13a,b
Scheme 2. R = a,b same as in Scheme 1. Reagents and conditions: (a) NaH, BrCH2CO2tBu, THF (45% for 6a and 7a, 85% for 6b and 7b); (b)
EDACÆHCl, DMAP, THF, rt, 4 h; (c) DIBAL, toluene, À78 °C, 1.5 h (86% for 8a, 78% for 9a, 85% for 8b and 9b); (d) BocNH2(CH2)3NH2, AcOH,
NaCNBH3, MeOH, rt, 4 h (quantitative); (e) NH2NH2, Raney Ni, EtOH rt, 2 h; (f) TFA, (iPr)3SiH, rt, 5 min (for 12a and 13a); (g) 2,6-lutidine,
TMSOTf, Et3N, DCM, MeOH, rt, 16 h (for 12b and 13b).
N3
N3
RO
HO
+
RO
N3
O
N3
a
O
O
OH
6a + 7a
O
N
NMe2
Me2N
N
H
H
14
15
S
N
b
b
R =
F3C
H2N
H2N
RO
HO
RO
NH2
O
NH2
O
O
OH
O
N
H
NMe2
Me2N
N
H
16
17
Scheme 3. Reagents and conditions: (a) HATU, DIPEA, NH2(CH2)3N(CH3)2, DCM (72% for 14, 81% for 15); (b) NH2NH2, Raney Ni, EtOH, rt,
2 h (75% for 16, 73% for 17).

X. Wang et al. / Bioorg. Med. Chem. Lett. 15 (2005) 4919–4922
4921
(45%) due to partial decomposition, incomplete conver-
sion, and a small amount of di-alkylation, compounds
6a and 7a could easily be obtained, individually, after
column chromatography. Intramolecular lactonization
was achieved quantitatively using 1-(3-dimethylamino-
the translation level. To our delight, the two tightest
binders 12a and 13a from the mass spectrometry assay
did show moderate functional activity.
In conclusion, aminoglycoside analogs lacking a carbo-
hydrate ring have been prepared, demonstrated to have
significant binding to its 16S A-site rRNA target, and
shown to have the ability to inhibit bacterial transla-
tions. This opens up the possibilities of generating
libraries of synthetic compounds mimicking the confor-
mation and function of aminoglycosides lacking the
structural features most recognized by aminoglycoside
modifying enzymes. These compounds offer a new strat-
egy to combat prevalent and persistent bacterial resis-
tance emerging in the clinic.
propyl)-3-ethylcarbodiimide
hydrochloride
(EDA-
CÆHCl); however, attempts to isolate and purify the
lactone were unsuccessful. Alternatively, the lactone
could be reduced by DIBAL, without purification of
the starting material, cleanly and smoothly to give inter-
mediates 8a and 9a, individually. A subsequent reduc-
tive amination, azido reduction, and Boc removal
gave the final compounds 12a and 13a, which were
purified by preparative LC–MS. The p-methoxybenzyl
(PMB) substituted analogs were made in a similar
manner, except intermediates 6b and 7b were not sepa-
rable by silica gel chromatography; however, the final
mixture of compounds 12b and 13b was easily separat-
ed by preparative LC–MS. Regioselective synthesis of
8b or 9b from 4b was attempted using Bu2SnO and
allyl bromide and then oxidative cleavage. Only one
regioisomer 9b was obtained in 18% yield. The regio-
chemistries of compounds 12a,b and 13a,b were ascer-
tained by 1-D NMR (1H, 13C, and DEPT) and 2-D
NMR (COSY, HMQC, and HMBC) (see Scheme 2).
Acknowledgments
We thank Lisa Risen for running antibacterial assays,
and Dr. Richard H. Griffey and Prof. Stephen Hanes-
sian for helpful discussions.
Supplementary data
Supplementary data associated with this article can be
found in the online version at doi:10.1016/
j.bmcl.2005.08.027
The carboxylic acid regioisomers 6a and 7a were also
directly coupled with primary amines to form amides
14 and 15. A subsequent azido reduction using transfer
hydrogenation yielded final compounds 16 and 17. The
regiochemistries of compounds 16 and 17 were con-
firmed by 2-D NMR (see Scheme 3).
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