Synthesis of nucleobase-functionalized β-peptoids and β-peptoid hybrids

Article abstract of DOI:10.1016/j.tetlet.2006.09.057

The solid-phase synthesis of a new class of nucleobase-modified peptide-mimetic oligomers is described. β-Peptoids and β-peptoid hybrids bearing thymine on the side chain are prepared from N-Fmoc-N-[2-(thymin-1-yl)ethyl]-β-alanine.

Full text of DOI:10.1016/j.tetlet.2006.09.057

Tetrahedron Letters 47 (2006) 8069–8071
Synthesis of nucleobase-functionalized b-peptoids and
b-peptoid hybrids
*
´
´
Xavier Mejıas, Lidia Feliu, Marta Planas and Eduard Bardajı
`
Laboratori d’Innovacio´ en Processos i Productes de Sı´ntesi Organica (LIPPSO), Departament de Quımica, Universitat de
´
Girona, Campus de Montilivi, 17071 Girona, Spain
Received 28 July 2006; revised 7 September 2006; accepted 12 September 2006
Available online 2 October 2006
Abstract—The solid-phase synthesis of a new class of nucleobase-modified peptide-mimetic oligomers is described. b-Peptoids and
b-peptoid hybrids bearing thymine on the side chain are prepared from N-Fmoc-N-[2-(thymin-1-yl)ethyl]-b-alanine.
Ó 2006 Elsevier Ltd. All rights reserved.
Over the past 25 years, the highly specific recognition
through the natural pairing of nucleobases has
prompted the design of nucleic acid mimetics as promis-
ing drug candidates in molecular biology and diagnos-
tics.1 Of the many structural motifs examined, peptide
nucleic acids (PNAs) have emerged as the most success-
ful oligonucleotide surrogates.2 PNAs stand out in terms
of their structural simplicity and ability to bind
sequences specifically to ssRNA and DNA. In these
systems, the ribose phosphate backbone is replaced by
a repeating N-(2-aminoethyl)glycine unit to which the
naturally occurring nucleobases are attached via a meth-
ylene carbonyl linkage. Despite their excellent proper-
ties, there are some limitations for the use of PNAs
such as their low solubility and poor cellular uptake.
Many efforts have been made to circumvent these draw-
backs and to optimize the properties of PNAs, which
have led to the synthesis of a wide number of new struc-
tures.3 Recently, peptoid nucleic acids have been de-
scribed, which showed good hybridization with DNA.4
Moreover, nucleobase-modified b-peptides have been
reported as suitable scaffolds for the construction of
well-defined tertiary structures organized by nucleobase
pair recognition.5 Based on the interesting properties
displayed by peptoid nucleic acids and nucleobase-mod-
ified b-peptides, we became interested in studying
compounds which combine both structural features. In
particular, we planned to study the preparation of nucleo-
base-functionalized b-peptoids. The synthesis of these
compounds requires a b-alanine monomer bearing
nucleobases.
Here, we report the synthesis of N-Fmoc-N-[2-(thymin-
1-yl)ethyl]-b-alanine (1) as monomer for the preparation
of nucleobase-functionalized b-peptoids and b-peptoid
hybrids (Fig. 1).
The synthesis of monomer 1 was accomplished as shown
in Scheme 1 using N1-(2-aminoethyl)thymine (2) as the
key compound. There are several reports for the synthe-
sis of 2, most of which based on the direct alkylation of
thymine.6 However, bis-alkylated products are usually
obtained along with the desired mono-alkylated com-
pound. In order to avoid the bis-alkylation, N3-benzoyl-
thymine (3) was prepared following a protocol described
previously by Reese.7 Thymine (1 equiv) was treated
with benzoyl chloride (4 equiv) in pyridine/acetonitrile
(1:2.5) at room temperature for 46 h, yielding N1,N3-
dibenzoylthymine, which was converted into N3-ben-
zoylthymine (3) under basic hydrolysis. Using alkylation
O
NH
N
O
O
N
OH
O
O
Keywords: Nucleoamino acid; b-Peptoid; Solid-phase synthesis.
Corresponding author. Tel.: +34 972 418959; fax: +34 972 418150;
e-mail: eduard.bardaji@udg.es
1
*
Figure 1. Structure of the Fmoc-protected b-alanine monomer 1.
0040-4039/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2006.09.057

8070
X. Mejı´as et al. / Tetrahedron Letters 47 (2006) 8069–8071
O
O
O
N
Bz
Bz
O
i) BzCl, pyridine/CH3CN (1:2.5)
ii) Na2CO3, H2O, dioxane
NH
N
N
N
-Boc-2-bromoethylamine, K2CO3, TBAI
N
H
O
N
H
O
70%
3
4
NHBoc
O
O
NH
NH
N
O
i) Acrylic acid, Na2CO3, H2O
ii) Na2CO3, FmocOSu
TFA/CH2Cl2 (3:1)
97%
N
O
O
N
OH
56%
NH2
O
O
2
1
Scheme 1. Synthesis of the Fmoc-protected b-alanine monomer 1.
reaction conditions described by Taddei,8 thymine 3
(1 equiv) was reacted with N-Boc-2-bromoethylamine
(0.8 equiv) at 70 °C for 4 h in the presence of K2CO3
(1 equiv) and tetrabutylammonium iodide (TBAI)
(0.1 equiv) in DMF to give N3-benzoyl-N1-(N-Boc-2-
aminoethyl)thymine (4) in a 70% yield. The treatment
of 4 with TFA/CH2Cl2 (3:1) at room temperature for
12 h prompted the removal of both benzoyl and Boc
groups, providing N1-(2-aminoethyl)thymine (2) in a
97% yield. The spectroscopic data of 2 were in good
agreement with those reported already.6
The free amino group of thymine derivative 2 (1 equiv)
was alkylated with acrylic acid (1.3 equiv) in H2O in
the presence of Na2CO3 (1 equiv) at 100 °C for 23 h.
The reaction mixture was then cooled to 0 °C and trea-
ted with Na2CO3 (1 equiv) and N-(9-fluorenylmethoxy-
carbonyloxy)succinimide (FmocOSu) (1 equiv). After
stirring at room temperature for 23 h, N-Fmoc-N-[2-
(thymin-1-yl)ethyl]-b-alanine (1) was obtained in a
56% yield. This compound was characterized by NMR
and mass spectrometry.9
T
NH2
5
6
N
H
H
O
6
With the Fmoc-protected b-alanine monomer 1 in hand,
the nucleobase-functionalized b-peptoid 5 and the b-
peptoid hybrids 6 and 7 were prepared (Fig. 2, Scheme
2). Solid-phase synthesis was performed onto an
Fmoc-PAL-PEG-PS10 resin. The couplings of Fmoc-
Gly-OH (3 equiv) or monomer 1 (3 equiv) were medi-
ated by O-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyl-
uronium hexafluorophosphate (HBTU) (3 equiv) and
DIPEA (3 equiv) in DMF for 3–5 h at 25 °C. Upon
completion of couplings, ninhydrin or chloranil tests
were negative.11 Removal of the Fmoc group was
carried out in piperidine/DMF (3:7, 2 + 10 min). The
final treatment of the resin with TFA/H2O (19:1, 2 h)
afforded the expected peptoids which were analyzed by
T
T
O
H
N
N
N
NH2
O
O
T
O
H
7
N
N
H
NH2
O
3
Figure 2. Structure of nucleobase-functionalized b-peptoid 5 and b-
peptoid hybrids 6 and 7 (T stands for nucleobase thymine).
T
i) Piperidine/DMF (3:7)
ii) Fmoc-Gly-OH, HBTU, DIPEA
O
H
iii) Piperidine/DMF (3:7)
iv) Monomer 1, HBTU, DIPEA
N
N
Fmoc
PAL-PEG-PS
Fmoc-PAL-PEG-PS
O
i) Piperidine/DMF (3:7)
T
T
ii) Monomer 1, HBTU, DIPEA
iii) Piperidine/DMF (3:7)
iv) TFA/H2O (19:1)
O
H
N
N
N
H
NH2
O
O
6
Scheme 2. Synthesis of nucleobase-functionalized b-peptoid hybrid 6 (T stands for nucleobase thymine).

X. Mejı´as et al. / Tetrahedron Letters 47 (2006) 8069–8071
8071
HPLC and characterized by ESI-MS.12 Nucleobase-
functionalized b-peptoid 5 was obtained with 90%
HPLC purity, and b-peptoid hybrids 6 and 7 with 91%
and 85% HPLC purities, respectively. These oligomers
showed a low solubility in H2O and in organic solvents
such as CH2Cl2, and were completely soluble in
MeOH/H2O mixtures. The overall synthetic process is
summarized in Scheme 2 for the synthesis of b-peptoid
hybrid 6.
Nielsen, P. E.; Egholm, M.; Berg, R. H.; Buchardt, O.
Science 1991, 254, 1497–1500.
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Bioorg. Med. Chem. Lett. 2006, 16, 2933–2936; (c) Ma, L.-J.;
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In summary, we describe an efficient procedure for the
synthesis of N-Fmoc-N-[2-(thymin-1-yl)ethyl]-b-alanine
and the application of this monomer for the solid-phase
synthesis of b-peptoids and b-peptoid hybrids bearing
thymine on the side chain. These compounds represent
a new class of peptide-mimetic oligomers. Ongoing work
is directed towards the synthesis of b-peptoids and
b-peptoid hybrids bearing other nucleobases and to
perform DNA or ssRNA binding studies with these
new oligomers.
5. (a) Chakraborty, P.; Bruckner, A. M.; Diederichsen, U.
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Eur. J. Org. Chem. 2006, 2410–2416; (b) Chakraborty, P.;
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Acknowledgement
9. Compound 1 was fully characterized: 1H NMR (200 MHz,
DMSO-d6) d = 1.64 (s, 3H), 1.73 (s, 3H), 2.29–2.52 (m,
2H), 3.36–3.74 (m, 6H), 4.15–4.27 (m, 3H), 7.15 (s, 1H),
7.39–7.91 (m, 8H). 13C NMR (50 MHz, CDCl3) d = 12.27,
39.92, 45.96, 46.55, 46.67, 47.02, 67.18, 108.56, 120.53,
125.37, 128.08, 130.42, 141.14, 141.73, 144.20, 151.34,
153.54, 164.70, 171.18. ESI-MS (m/z): 463.6 [M+H]+,
485.7 [M+Na]+.
10. PAL, 5-(4-amino)-methyl-3,5-dimethoxy-phenoxy valeric
acid handle (Peptide Amide Linker); PEG-PS, poly(ethyl-
ene glycol)-polystyrene (graft resin support).
11. (a) Kaiser, E.; Colescott, R. L.; Bossinger, C. D.; Cook, P.
I. Anal. Biochem. 1970, 34, 595–598; (b) Vojkovsky, T.
Pept. Res. 1995, 8, 236–237.
This work was supported by a grant from CIRIT (QFN-
4620).
References and notes
1. (a) Chan, J. H. P.; Lim, S.; Fred Wong, W. S. Clin. Exp.
Pharmacol. Physiol. 2006, 33, 533–540; (b) De Mesmaeker,
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1995, 28, 366–374; (c) Uhlmann, E.; Peyman, A. Chem.
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2. (a) Porcheddu, A.; Giacomelli, G. Curr. Med. Chem. 2005,
12, 2561–2599; (b) Nielsen, P. E. Curr. Opin. Mol. Ther.
2000, 2, 282–287; (c) Nielsen, P. E.; Egholm, M. In Peptide
Nucleic Acids (PNA), Protocols and Applications; Nielsen,
P. E., Egholm, M., Eds.; Horizon Scientific: Norfolk,
1999; (d) Uhlmann, E.; Peyman, A.; Breipohl, G.; Will, D.
W. Angew. Chem., Int. Ed. 1998, 37, 2796–2823; (e)
12. Mass spectrometry analysis of 5, 6, and 7. b-Peptoid 5:
MALDI-MS (m/z): 1357.0 [M+H]+, 1379.0 [M+Na]+,
1395.0 [M+K]+. b-Peptoid hybrid 6: MALDI-MS, (m/z):
521.2 [M+H]+. b-Peptoid hybrid 7: MALDI-MS, (m/z):
881.0 [M+Na]+, 897.0 [M+K]+.