An efficient and general route to the synthesis of novel aminoglycosides for RNA binding

Article abstract of DOI:10.1055/s-0030-1259305

An alternative and straightforward method to prepare aminoglycoside dimers and heterodimeric conjugates is reported. The novel type of modification may provide a promising way for the development of new ligands effectively targeting to RNA. Georg Thieme V

Full text of DOI:10.1055/s-0030-1259305

LETTER
219
An Efficient and General Route to the Synthesis of Novel Aminoglycosides for
RNA Binding
1
S
A
ynthesis of
N
ove
n
l
A
minoglyco
d
sides rés G. Santana, Ágatha Bastida, Teresa Martínez del Campo, Juan Luis Asensio, Julia Revuelta*
Instituto de Química Orgánica General – CSIC, C/ Juan de la Cierva, 3, 28006 Madrid, Spain
Fax +34(91)5644853; E-mail: julia.revuelta@iqog.csic.es
Received 6 October 2010
Dedicated to Professor Alberto Brandi on the occasion of his 60 birthday
th
3
pathogenic bacteria. The relative toxicity to mammals is
another critical problem of these drugs that largely limits
their intensive clinical use.4
Abstract: An alternative and straightforward method to prepare
aminoglycoside dimers and heterodimeric conjugates is reported.
The novel type of modification may provide a promising way for
the development of new ligands effectively targeting to RNA.
Systematic studies on direct chemical modification of exis-
Key words: aminoglycoside, azide, oligosaccharide synthesis, ting aminoglycoside drugs, with the aim of circumventing
antibiotics, drug design
the resistance mechanisms, without either diminishing
their activity or increasing their toxicity, has opened up a
new era in the history of aminoglycosides.5
Protein synthesis is one of the fundamental processes in
all living cells, and therefore, it is not surprising that the
RNA and protein machinery of the prokaryotic ribosomes
are the target of about half of the antibiotics characterized
Importantly, the results of these efforts suggest that the in-
troduction of new types of interactions between the new
aminoglycosides and RNA are a crucial component in the
development of new types of antibiotics.6
2
thus far. Among the different classes of clinically impor-
In this context, two possible approaches are the dimeriza-
tion of the pharmacophore using the same or different
tant antibiotics that interfere with protein synthesis via
this target (e.g., aminoglycosides, macrolides, and oxazo-
lidinones), aminoglycosides (Figure 1) represent gold-
standard drugs for the treatment of serious Gram-negative
pathogens.
7
8
aminoglycosides and the addition of amino acids, simple
9
10
hydrophilic or hydrophobic moieties, or nucleosides
and oligonucleosides11 to make heterodimeric conjugates
(
Scheme 1).
NH2
first approach: dimeric aminoglycosides
I
O
HO
HO
NH2
II
aminoglycoside
linker
aminoglycoside
H2N
O
O
HO
O
NH2
HO
OH
NH2
second approach: heterodimeric conjugates
aminoglycosides
III
IV
O
OH
O
H2N
OH
neomycin B
aminoglycoside
linker
OH
III
amino acids, nucleosides, ...
OH
I
O
X
OH
NH2
HO
H2N
Scheme 1 General approaches for the introduction of complemen-
tary interactions between aminoglycosides and RNA
O
HO
II
HO
O
O
NH2
H2N
kanamycin A X = OH (1a)
kanamycin B X = NH2
According to different experimental findings, the pseudo-
disaccharide fragment I/II (grey fragment, Figure 1), with
slightly different patterns of OH/NH distribution in unit
Figure 1 Natural aminoglycoside antibiotics
2
I, present in most aminoglycosides, is essential for spe-
cific complex formation with the prokaryotic 16S RNA.12
Despite their secondary importance the amines in sugar
units at the 5- or 6-positions in the 2-DOS ring provide ad-
ditional contacts with the lower and upper stems, respec-
tively, of the RNA receptor as shown by detailed NMR
However, the prolonged clinical and veterinary use of
aminoglycosides has resulted in the rapid spread of anti-
biotic resistance to this family of antibacterial agents in
SYNLETT 2011, No. 2, pp 0219–0222
x
x.
x
x.
2
0
1
1
13
and crystallographic studies carried out in recent years.
Finally, other studies have indicated that the 6-OH in unit
Advanced online publication: 05.01.2011
DOI: 10.1055/s-0030-1259305; Art ID: G30410ST
©
Georg Thieme Verlag Stuttgart · New York

2
20
A. G. Santana et al.
LETTER
III in kanamycin and the 5-OH in unit III of neomycin are sides has been a challenge for which several methods have
not essentials for RNA binding (selected hydroxy groups, been developed. Most of these methods employ, however,
1
4
Figure 1).
undesirable conditions or show limited success. For
example, Wong and co-workers have described a metho-
dology for the conversion of kanamycin A (1a) into tet-
raazidokanamycin (1b) by means of a diazotransfer
reaction with freshly prepared triflyl azide (TfN3).15
However, in this paper for the preparation of triflyl azide
and its application in the diazo transfer to amines triflic
anhydride and sodium azide are used in a biphasic system
of CH Cl –H O, and highly hazardous diazidomethane
can be formed. More recently, Ernst and co-workers have
developed a safe and convenient method for the cop-
per(II)-catalyzed diazo transfer from triflyl azide to pri-
mary amines.16 In this report toluene was identified as a
Bearing in mind these results, these primary positions are
optimal as tethering points between the aminoglycoside
and the linker.
Here, we have developed a general selective synthetic
strategy that allows us to readily synthesize homo- or
heterodimers and heterodimeric conjugates derivates of
aminoglycosides (Scheme 2), by coupling the functional-
ized aminoglycoside unit with different substrates pend-
2
2
2
ing nucleophiles like OH, NH , SH through a substitution
2
reaction.
aminoglycoside,
solvent for the preparation of TfN to avoid the formation
of hazardous byproducts.
3
O
X
nucleosides,
Y
aminoglycoside
n
heterocycles, ...
To test the scope of this version of the diazo transfer reac-
tion in aminoglycosides, protection of neamine (3a) was
investigated (Scheme 3).
Y = OH, NH2, SH
X = leaving group
NH2
O
N3
aminoglycoside,
nucleosides,
O
Y
O
aminoglycoside
HO
HO
i, ii
AcO
AcO
heterocycles, ...
n
H2N
N3
H2N
N3
O
O
Y = OH, NH2, SH
NH2
N3
OH
AcO
OH
AcO
Scheme 2 Proposed general strategy
3
a
3b
Scheme 3 Reagents and conditions: (i) TfN (2.5 equiv for amine),
3
This approach is illustrated in this letter for the synthesis NaHCO , CuSO ·5H O (0.05 equiv), different solvents (see Table 1),
3
4
2
of the kanamycin–kanamycin homodimer 2b (Figure 2).
r.t., 18 h; (ii) Ac O–pyridine (1:2, v/v), DMAP (0.05 equiv), r.t., 16 h.
2
H2N
As a first approximation, we carried out the reaction under
heterogeneous conditions, but the desired compound was
not obtained due to the limited solubility of aminoglyco-
sides in toluene. When the neamine hydrochloride was
NH2
O
HO
HO
HO
NH2
HO O
HO
O
NH2
OH
O
(
subjected to the monophasic conditions (H O–PhMe–
2
16
MeOH) previously described, the aminoglycoside pre-
O
)n
cipitated from the solution, which prevented any reaction
n = 6
with TfN . In order to avoid this, we chose pyridine as co-
3
O
solvent because it dissolves the aminoglycoside, and TfN3
is stable under these conditions.
OH
17
O
HO
H2N
HO
O
OH
NH2
O
HO
The reaction was tested in three different conditions
(Table 1). The triflyl azide solution in toluene was added
to a mixture of neamine (3a), sodium hydrogencarbonate
and copper(II) sulfate in water, followed by a mixture of
methanol and pyridine to obtain a homogeneous turquoise
solution. The TLC indicated the reactions to be complete
within 20 hours.
HO
O
NH2
H2N
2b
Figure 2 Structure of the kanamycin–kanamycin homodimer 2b
As aminoglycoside precursor in this paper, compound 1d
was prepared from kanamycin A (1a) following the four-
step procedure in Scheme 4.
Table 1 Diazo Transfer Reaction Using Different Solvent Ratios
Entry Solvent ratio (H O–PhMe–MeOH–pyridine) Yield of 3b (%)a
Kanamycin A (1a) is first protected as its azido derivative
2
1
b. Azides have several advantages as amino protecting
1
2
3
1:1.7:3:3, homogeneous
1.7:1:3:3, homogeneous
1:4:5:5, homogeneous
75
50
63
groups over carbamates, used in general for the synthesis
of dimeric aminoglycosides. These include less steric
hindrance, greater solubility, and no rotamer formation or
hydrogen or carbon nuclei to complicate NMR spectra.
For these reasons, the preparation of azide-aminoglyco-
7
a
Isolated yields of two steps.
Synlett 2011, No. 2, 219–222 © Thieme Stuttgart · New York

LETTER
Synthesis of Novel Aminoglycosides
221
In order to avoid problems during the purification process, For example, in this letter, to test the scope of this
the crude reaction mixture was subsequently treated with methodology, compound 1d was alkylated with 1,6-di-
acetic anhydride and a catalytic amount of DMAP in py- bromohexane to afford compound 1e in 75% yield.
ridine yielding 3b in moderate to good yields.
Finally, a new monomer unit was alkylated with com-
After the successful conversion of neamine (3a) into 3b, pound 1d, obtaining the protected homodimer kanamy-
the diazotransference of kanamycin A (1a) was under- cin–kanamycin (2a), in 50% yield.
taken. Free kanamycin A (1a) was treated with excess of
The resulting dimer was first reduced under Staudinger
TfN in the presence of CuSO ·5H O in a mixture of H O–
3
4
2
2
conditions to convert the azides into amines. In the last
step this compound was debenzylated by hydrogenolysis
in the presence of trifluoroacetic acid. The reaction mix-
ture was filtered, concentrated, and purified by silica gel
chromatography using NH OH–n-BuOH–EtOH–CH Cl
PhMe–MeOH–pyridine (1:1.7:3:3). After 18 hours and
aqueous workup the tetraazidokanamycin (1b), without
isolation, was acetylated. Finally, O-deacetylation gave
tetraazidekanamycin (1b) with an overall yield 63% from
kanamycin A (1a).
4
2
2
(
5:2:2.5:1), followed by cation-exchange chromatography
This compound was treated with triisopropylsilyl trifluo- to give the pure aminoglycoside dimer kanamycin–
romethanesulfonate and 2,6-lutidine providing the silyl kanamycin 2b (Scheme 5).
ether intermediate, which was subsequently benzylated to
yield 1c. Finally, acidic desilylation afforded compound
OH
OBn
1
d, the key component in this methodology (Scheme 4).
O
BnO
N3
BnO
OBn
N3
O
This monomer 1d that has a specific free hydroxy group
is very useful for the synthesis of dimeric aminoglyco-
sides or heterodimeric conjugates by coupling the func-
tionalized main unit with different linkers (Scheme 2).
BnO
BnO
O
N3
O
N3
1
d
i
OH
OH
O
Br
HO
H2N
HO
OH
NH2
O
HO
HO
O
O
O
O
NH2
H2N
OBn
1a
BnO
OBn
N3
BnO
N3
O
BnO
i
BnO
O
N3
O
N3
OH
1
e
OH
O
HO
N3
HO
OH
N3
ii
O
HO
N3
OH
O
O
N3
N3
O
N3
BnO
BnO
1b
N3 BnO
BnO
O
ii, iii
N3
OBn
O
BnO O
OTIPS
O
OBn
O
BnO
N3
BnO
OBn
N3
O
(
)n
n = 6
BnO
BnO
O
O
O
N3
N3
OBn
1
c
O
BnO
OBn
N3
BnO
N3
O
BnO
iv
BnO
O
O
N3
N3
OH
O
2
a
OBn
BnO
N3
BnO
OBn
N3
iii, iv
2b
O
BnO
BnO
O
O
N3
N3
1
d
Scheme 5 Reagents and conditions: (i)1,6-dibromohexane, NaH,
NaI, DMF, r.t., 16 h, 75%; (ii) 1d, NaH, NaI, DMF, r.t., 48 h, 50%;
Scheme 4 Reagents and conditions: (i) (a) TfN , CuSO ·5H O,
toluene, pyridine–MeOH–H O, r.t., 18 h; (b) Ac O, DMAP, pyridine,
0% (two steps); (c) NaOMe, MeOH, 90%; (ii) TIPSOTf, 2,6-luti-
dine, THF, 10 min, 65%; (iii) BnBr, NaH, TBAI, DMF, r.t., 18 h,
0%; (iv) HF·pyridine, THF, r.t., 1 h, 90%.
3
4
2
(
iii) Me P, NaOH, THF, 55 °C, 24 h; (iv) H , Pd(OH) /C, TFA,
3
2
2
2
2
MeOH–H O, r.t., 72 h, 55% (two steps).
2
7
5
In conclusion, we have developed an efficient and general
route to novel homo- or heterodimers and heterodimeric
conjugates derivates of aminoglycosides. In addition, we
Synlett 2011, No. 2, 219–222 © Thieme Stuttgart · New York

2
22
A. G. Santana et al.
LETTER
have reported a safe and convenient method for the syn-
thesis of azide-aminoglycosides.
Sears, P.; Wright, G. D.; Wong, C.-H. J. Am. Chem. Soc.
000, 5230. (h) Michael, K.; Wang, H.; Tor, Y. Bioorg.
Med. Chem. 1999, 1361. (i) Wang, H.; Tor, Y. Bioorg. Med.
Chem. Lett. 1997, 1951.
2
(
8) Litovchick, A.; Evdokimov, A. G.; Lapidot, A. Biochemistry
Supporting Information for this article is available online at
http://www.thieme-connect.com/ejournals/toc/synlett.
2
000, 2838.
9) Werstuck, G.; Zapp, M. L.; Green, M. R. Chem. Biol. 1996,
29.
(
1
(
10) (a) Wu, S.; Fu, Y.; Yan, R.; Wu, Y.; Lei, X.; Ye, X.-S.
Tetrahedron 2010, 3433. (b) Lee, J.; Kwon, M.; Lee, K. H.;
Jeong, S.; Hyun, S.; ShIn, K. J.; Ju, J. J. Am. Chem. Soc.
2004, 1956. (c) Francois, B.; Szychowski, J.; Adhikari, S.
S.; Pachamuthu, K.; Swayze, E. E.; Griffey, R. H.; Migawa,
M. T.; Westhof, E.; Hanessian, S. Angew. Chem. Int. Ed.
Acknowledgment
This investigation was supported by research grants from the Spa-
nish ‘Plan Nacional’ (MCYT) CTQ2007-67403/BQU, CTQ2010-
1
9073/BQU, from CSIC 200980I152 grant and from CAM, S2009/
ppq-1752. A.G.S. and T.M.C. thanks the CSIC for JAE fellowships.
2
004, 6735. (d) Ding, Y.; Hofstadler, S. A.; Swayze, E. E.;
Risen, L.; Griffey, R. H. Angew. Chem. Int. Ed. 2003, 3409.
e) Ding, Y.; Hofstadler, S. A.; Swayze, E. E.; Griffey, R. H.
References and Notes
(
Org. Lett. 2001, 1621. (f) Wong, C.-H.; Hendrix, M.;
Manning, D. D.; Rosenbohm, C.; Greenberg, W. A. J. Am.
Chem. Soc. 1998, 8319.
(
1) New address: Instituto de Productos Naturales y
Agrobiología, Avd. Astrof. F. Sánchez, 3 38205 San
Cristóbal de La Laguna (Santa Cruz de Tenerife), Spain.
2) Aminoglycoside Antibiotics: From Chemical Biology to
Drug Discovery; Arya, D. P., Ed.; Wiley-Interscience:
Hoboken, 2007.
3) Magnet, S.; Blanchard, J. S. Chem. Rev. 2005, 477.
4) Selimoglu, E. Curr. Pharm. Des. 2007, 119.
5) Houghton, J. L.; Green, K. D.; Chen, W.; Garneau-
Tsodikova, S. ChemBioChem 2010, 880.
(
11) (a) Alguacil, J.; Defaus, S.; Claudio, A.; Trapote, A.;
(
Masides, M.; Robles, J. Eur. J. Org. Chem. 2010, 3102.
(
b) Mei, H.; Xing, L.; Cai, L.; Jin, H.-W.; Zhao, P.; Yang,
Z.-J.; Zhang, L.-H. Bioorg. Med. Chem. Lett. 2008, 5355.
c) Cai, L.; Li, Q.; Ren, B.; Yang, Z.-J.; Zhang, L.-R.; Zhang,
(
(
(
(
L.-H. Tetrahedron 2007, 8135. (d) Chares, I.; Xi, H.; Arya,
D. P. Bioconjugate Chem. 2007, 160. (e) Hyun, S.; Lee,
K. H.; Yu, J. Bioorg. Med. Chem. Lett. 2006, 4757.
(6) (a) Revuelta, J.; Vacas, T.; Corzana, F.; González, C.;
Bastida, A.; Asensio, J. L. Chem. Eur. J. 2010, 2986.
(
2
f) Charles, I.; Xue, L.; Arya, D. P. Bioorg. Med. Chem. Lett.
002, 1259.
(
b) Vourloumis, D.; Winters, G. C.; Simonsen, K. B.;
(
(
12) Fourmy, D.; Recht, M. I.; Puglisi, D. J. Mol. Biol. 1998, 347.
13) (a) Fourmy, D.; Recht, M. I.; Blanchard, S. C.; Puglisi, J. D.
Science 1996, 1367. (b) Carter, A. P.; Clemons, W. M.;
Brodersen, D. E.; Morgan-Warren, R. J.; Wimberly, B. T.;
Ramakrishnan, V. Nature 2000, 340. (c) Vicens, Q.;
Takahashi, M.; Ayida, B. K.; Sándwick, S.; Zhao, Q.; Han,
Q.; Hermann, T. ChemBioChem 2005, 58. (c) Ye, X.-S.;
Zhang, L.-H. Curr. Med. Chem. 2002, 929.
(
7) (a) Chen, G.-H.; Pan, P.; Chen, Y.; Meng, X.-B.; Li, Z.-J.
Tetrahedron 2009, 5922. (b) Bodlenner, A.; Alix, A.;
Weibel, J.-M.; Pale, P.; Ennifar, E.; Paillart, J.-C.; Walter,
P.; Marquet, R.; Dumas, P. Org. Lett. 2007, 4415.
Westhof, E. Chem. Biol. 2002, 747. (d) Francois, B.; Rusell,
R. J. M.; Murray, J. B.; Aboul-ela, F.; Masquida, B.; Vicens,
Q.; Westhof, E. Nucleic Acid Res. 2005, 33, 5677.
(
c) Kondo, J.; Hainrichson, M.; Nudelman, I.; Shallom-
(
e) Kondo, J.; Russell, R. J. M.; Murray, J. B.; Westhof, E.
Biochimie 2006, 1027. (f) Vicens, Q.; Westhof, E. Structure
001, 647.
Shezifi, D.; Barbieri, C. M.; Pilch, D. S.; Westhof, E.;
Baasov, T. ChemBioChem 2007, 1700. (d) Riguet, E.;
Désiré, J.; Boden, O.; Ludwig, V.; Göbel, M.; Bailly, C.;
Décout, J.-I. Bioorg. Med. Chem. Lett. 2005, 4651.
2
(
(
14) Wang, H.; Tor, Y. J. Am. Chem. Soc. 1997, 8734.
15) (a) Alper, P. B.; Hung, S.-C.; Wong, C.-H. Tetrahedron Lett.
(
e) Agnelli, F.; Sucheck, S. J.; Marby, K. A.; Rabuka, D.;
1996, 6029. (b) Nyffeler, P. T.; Liang, G.-H.; Koeller, K.
Yao, S.-L.; Sears, P. S.; Liang, F.-S.; Wong, C.-H. Angew.
Chem. Int. Ed. 2004, 1562. (f) Tok, J. B.-H.; Fenker, J.
Bioorg. Med. Chem. Lett. 2001, 2987. (g) Sucheck, S. J.;
Wong, A. L.; Koeller, K. M.; Boehr, D. D.; Draker, D.-A.;
M.; Wong, C.-H. J. Am. Chem. Soc. 2002, 10773.
16) Titz, A.; Radic, Z.; Schawardt, O.; Ernst, D. Tetrahedron
Lett. 2006, 2383.
17) Yan, R.-B.; Yang, F.; Wu, Y.; Zhang, L.-H.; Yen, X.-S.
Tetrahedron Lett. 2005, 8993.
(
(
Synlett 2011, No. 2, 219–222 © Thieme Stuttgart · New York

Copyright of Synlett is the property of Georg Thieme Verlag Stuttgart and its content may not be copied or
emailed to multiple sites or posted to a listserv without the copyright holder's express written permission.
However, users may print, download, or email articles for individual use.