7-Substituted 8-aza-7-deazapurines and 2,8-diaza-7-deaza-purines: Synthesis of nucleosides and oligonucleotides

Article abstract of DOI:10.1081/NCN-200059218

7-Substituted 8-aza-7-deazaadenosines 1a-e were synthesized by Sonogashira cross coupling from the corresponding 7-iodo nucleoside in 36-79% yields. Starting from 7-bromo (or 7-iodo)-8-aza-7-deazaadenine, 2a,b were obtained by acid-catalyzed glycosylation

Full text of DOI:10.1081/NCN-200059218

This article was downloaded by: [University of Colorado at Boulder Libraries]
On: 01 January 2015, At: 08:59
Publisher: Taylor & Francis
Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House,
37-41 Mortimer Street, London W1T 3JH, UK
Nucleosides, Nucleotides and Nucleic Acids
Publication details, including instructions for authors and subscription information:
http://www.tandfonline.com/loi/lncn20
7-SUBSTITUTED 8-AZA-7-DEAZAPURINES AND 2,8-
DIAZA-7-DEAZA-PURINES: SYNTHESIS OF NUCLEOSIDES
AND OLIGONUCLEOTIDES
Wenqing Lin a b , Kuiying Xu a b & Frank Seela a b
a Laboratorium für Organische und Bioorganische Chemie , Institüt für Chemie, Universität
Osnabrück , Osnabrück, Germany
b Center for Nanotechnology (CeNTech) , Münster, Germany
Published online: 15 Nov 2011.
To cite this article: Wenqing Lin , Kuiying Xu & Frank Seela (2005) 7-SUBSTITUTED 8-AZA-7-DEAZAPURINES AND 2,8-DIAZA-7-
DEAZA-PURINES: SYNTHESIS OF NUCLEOSIDES AND OLIGONUCLEOTIDES, Nucleosides, Nucleotides and Nucleic Acids, 24:5-7,
869-873, DOI: 10.1081/NCN-200059218
To link to this article: http://dx.doi.org/10.1081/NCN-200059218
PLEASE SCROLL DOWN FOR ARTICLE
Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained
in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no
representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the
Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and
are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and
should be independently verified with primary sources of information. Taylor and Francis shall not be liable for
any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever
or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of
the Content.
This article may be used for research, teaching, and private study purposes. Any substantial or systematic
reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any
form to anyone is expressly forbidden. Terms & Conditions of access and use can be found at http://
www.tandfonline.com/page/terms-and-conditions

Nucleosides, Nucleotides, and Nucleic Acids, 24 (5–7):869–873, (2005)
Copyright D Taylor & Francis, Inc.
ISSN: 1525-7770 print/ 1532-2335 online
DOI: 10.1081/NCN-200059218
7-SUBSTITUTED 8-AZA-7-DEAZAPURINES AND
2,8-DIAZA-7-DEAZA-PURINES: SYNTHESIS OF
NUCLEOSIDES AND OLIGONUCLEOTIDES
5
Wenqing Lin, Kuiying Xu, and Frank Seela
Laboratorium fu¨ r Organische und
Bioorganische Chemie, Institut fu¨ r Chemie, Universita¨t Osnabru¨ ck, Osnabru¨ ck, Germany and
Center for Nanotechnology (CeNTech), Mu¨ nster, Germany
5
7-Substituted 8-aza-7-deazaadenosines 1a---e were synthesized by Sonogashira cross coupling from
the corresponding 7-iodo nucleoside in 36---79% yields. Starting from 7-bromo (or 7-iodo)-8-aza-7-
deazaadenine, 2a,b were obtained by acid-catalyzed glycosylation followed by deprotection in 53 and
35% yields, repectively. Compounds 2b was applied to cross coupling reaction to give 2c---d in 34---
95% yield. Compounds 2a and 4b were further transformed to the phosphoramidites 5 and 6b in 9
and 49% overall yields, which were incorporated into oligonucleotides.
Keywords 7-Substituted 8-Aza-7-Deazaadenosine, Phosphoramidite, Sonogashira Cross
Coupling, Glycosylation
INTRODUCTION
8-Aza-7-deazapurine (pyrazolo[3,4-d]pyrimidine) nucleosides have attracted
attention due to their biological activities and as constituents of oligonucleotides[1,2]
(Scheme 1).
Earlier, 7-substitutents, such as 7-halogeno and 7-alkynyl, have shown
favourable effects on the stability of duplex DNA.[3] Herein we report on the
synthesis of 7-substituted purine nucleoside analogs 1a--e, 2a--e, 3a,b, and
4a,b, as well as of the phosphoramidites 5 and 6b.
The work was financially supported by the European Community (Grant No.: QLRT-2001-00506,
‘‘Flavitherapeutics’’).
Address correspondence to Frank Seela, Laboratorium fu¨r Organische und Bioorganische Chemie, Institut
fu¨r Chemie, Universit¨at Osnabru¨ck, Barbarastr. 7, Osnabru¨ck 49069, Germany.
869
Order reprints of this article at www.copyright.rightslink.com

870
W. Lin, K. Xu, and F. Seela
NH2
NH2
R
N
R
N
N
N
2a, R = Br
1a, R = propynyl
1b, R = ethynyl
1c, R = 3-phthaloyliminopropynyl
1d, R = 3-trifluoroacetaminopropynyl
1e, R = vinyl
N
2b, R = I
N
H2N
HO
N
O
N
O
2c, R = propynyl
2d, R = ethynyl
2e, R = vinyl
HO
HO
OH
HO
OH
NHBui
X
N
NH2
N
N
X
Bu2NHC
Br
X
N
N
N
N
N
N
N
N
N
N
N
N
N
N
R
N
N
N
R
HCOHN
N
O
O
O
O
DMTO
HO
DMTO
HO
O
P
HO
O
OTBDMS
HO
NCH2CH2CO
NPri2
3a X = H, R = OH
3b X = Br, R = H
3c X = R = H
4a X = H, R = OH
4b X = Br, R = H
4c X = R = H
P
NCH2CH2CO
NPri2
6a, X = H
6b, X = Br
5
SCHEME 1
RESULTS AND DISCUSSION
7-Iodo-8-aza-7-deazaadenosine (7) was prepared according to Cottam et al.,[4]
which was applied to Sonogashira coupling reaction with propynes to give
1a,c,d.[5] Cross-coupling of 7 with trimethylsilylacetylene, followed by desilylation
with K2CO3/MeOH furnished 1b in 36% overall yield. The ethenyl nucleoside 1e
was obtained by coupling of 7 with tri-n-butyl-vinylstanane under the catalysis of a
palladium catalyst and CuI in 74% yield (Scheme 2).
Compound 8a was prepared from 8-aza-7-deaza-2,6-diaminopurine according
to Taylor and Patel.[6] The preparation of 8b was accomplished by iodination of 8-
aza-7-deaza-2,6-diaminopurine with NIS in dichloroethane at refluxing in 65% yield.
Glycosylation of 8a,b with 1-acetyl-2,3,5-tribenzoyl-b-D-ribofuranose under catalysis
of BF3Á Et2O resulted in 9a,b in 70 and 53% yield, respectively. Deprotectin of the
benzoyl groups in the presence of NaOMe/MeOH gave 2a,b. Compound 2b was
further applied to cross coupling reaction to furnish 2c--e in moderate to excellent
yield (Scheme 3).
NH2
I
N
1a, 79%
1b, 36%
1c, 66%
1d, 62%
1e, 74%
CuI, Pd(PPh3)4
Et3N, DMF
N
N
N
alkyne or alkene
O
HO
HO
OH
7
SCHEME 2

W. Lin, K. Xu, and F. Seela
871
NH2
N
X
NH2
X
N
N
N
N
BF3.Et2O
CH3NO2
H2N
BzO
N
H
MeONa
N
2c, 95%
2d, 34%
2e, 67%
CuI, Pd(PPh3)4
Et3N, DMF
2a, 76%
2b, 66%
H2N
BzO
N
8a, X = Br
8b, X = I
MeOH
refluxing
O
+
alkyne or
alkene
OAc
O
BzO
OBz
9a, X = Br, 70%
9b, X = I, 53%
BzO
OBz
SCHEME 3
The syntheses of 4a,b were accomplished from 10a,b via their 1,N6-etheno
derivatives 11a,b. Compounds 10a,b were treated with chloroacetaldehyde in
pH 4ꢀ5 sodium acetate buffer at r.t. overnight to give 11a,b. Treatment of 11a,b
with 0.5 M NaOH at ambient temperature overnight yielded 12a,b, which were
cyclized in the presence of NaNO2 in 80% AcOH to give 3a,b. Removal of the
etheno group of 3a,b by NBS afforded 4a,b in 32 and 18% overall yield,
respectively (Scheme 4).[7]
Treatment of 2a with N,N-di-n-butylformamide dimethyl acetal at r.t. gave a
mixture of 13/14, which was further treated with DMTCl in pyridine to yield 15
in 33% overall yield. Because of the unstability of the imino group in N2, the
formamide was obtained in these two steps. Treatment of 15 with TBDMSCl and
AgNO3 provided 16 (38% yield), along with its 3’-OTBDMS isomer which could be
removed by careful column chromatography. At last, the phosphoramite 5 was
obtained in 75% yield (9% overall yield from 2a) according to the standard
procedure (Scheme 5).
Treatment of 4b with N,N-dimethylformamide dimethyl acetal at r.t. gave 17
in 75% yield. The introduction of the 4,4’-dimethoxytrityl group followed the
standard protocol giving compound 18 in 83% yield. Subsequent phosphitylation
with chloro-(2-cyanoethoxy)-N,N-(diisopropylamino)phosphine gave the phosphor-
amidite 6b in 79% yield (Scheme 6).
Compounds 5 and 6a were employed in solid-phase oligonucleotide synthesis.
Base pairing studies on 4c, incorporated in a 12-mer duplex, showed that this
NH2
N
N
X
X
X
N
N
N
H
N
N
N
3a, 82%
(2 steps)
3b, 83%
NaNO2
4a, 51%
4b, 56%
ClCH2CHO
NaOH
rt
NBS
N
N
N
N
O
N
H2N
NaOAc buffer
pH 4-5
O
O
HO
HO
HO
HO
R
HO
R
HO
R
11a X=H, R=OH, 77%
11b X=Br, R=H, 83%
12a X=H, R=OH
12b X=Br, R=H, 47%
10a X=H, R=OH
10b X=Br, R=H
SCHEME 4

872
W. Lin, K. Xu, and F. Seela
N
Bu2NHC
Br
N
N
Bu2NHC
Br
N
N
N
N
N
N
Bu2NHC
N
N
HCOHN
(MeO)2CHNBu2
MeOH rt
DMTCl
py.
33%
and
2a
O
O
HO
13
HO
(2 steps)
HO
OH
HO
OH
14
N
N
N
N
Bu2NHC
Bu2NHC
Br
Br
Cl
P
N
N
N
N
NCH2CH2CO
(i-Pr)2NEt
75%
N(iPr)2
TBDMSCl
AgNO3
N
N
HCOHN
HCOHN
DMTO
15 HO
SCHEME 5
5
O
O
Py/THF
38%
DMTO
16
HO
OTBDMS
OH
Me2NHC=N
Cl
P
Me2NHC=N
Br
Br
N
N
N
N
NCH2CH2CO
N(iPr)2
Me2NCH(OMe)2
MeOH, rt, 75%
(MeO)2TrCl
Py, 83%
N
N
6b
4b
N
N
N
(i-Pr)2NEt, DCM, 79%
N
O
O
HO
(MeO)2TrO
HO
HO
18
17
SCHEME 6
adenine nucleoside analogue forms a strong base pair with dG [5’-d(TAG GTC
A4cT ACT) Á 3’-d(ATC CAG TGA TGA), Tm = 46°C comparable to 5’-d(TAG
GTC AAT ACT) Á 3’-d(ATC CAG TGA TGA), Tm = 44°C] by forming a face to
face base pair because of the absence of N7. This novel base pair is as stable as that
of the canonical dA-dT pair. However, 4c could not form a stable base pair with
dT, dA, and dC.
In conclusion, 8-aza-7-deazapurine nucleosides 1,2, as well as 2,8-diaza-7-
deazapurine nucleosides 3a,b and 4a,b were prepared in good to excellent yield.
Studies on the biological activities are under way. Compound 2a and 4b were also
transformed to the oligonucleotide building blocks 5 and 6b. Their incorporation
into oligonucleotides is in progress.
REFERENCES
1. Seela, F.; He, Y.; He, J.; Becher, G.; Kro¨schel, R.; Zulauf, M.; Leonard, P. Base-modified oligonucleotides with
increased duplex stability: pyrazolo[3,4-d]pyrimidines replacing purines. In Methods in Molecular Biology;
Herdewijn, P., Ed.; Humana Press Inc.: Totowa, NJ, 2004.
2. He, J.; Seela, F. Org. Biomol. Chem 2003, 1, 1873–1883.

W. Lin, K. Xu, and F. Seela
873
3. Seela, F.; Kro¨schel, R. Nucleic Acids Res. 2003, 31(24), 7150–7158.
4. Cottam, H.B.; Wasson, D.B.; Shih, H.C.; Raychaudhuri, A.; Di Pasquale, G.; Carson, D.A. J. Med. Chem.
1993, 36, 3424–3430.
5. Sonogashira, K.; Tohda, Y.; Hagihara, N. Tetrahedron Lett. 1975, 4467–4470.
6. Taylor, E.C.; Patel, H.H. Tetrahedron 1992, 48, 8089–8100.
7. Seela, F.; Lindner, M.; Gla¸con, V.; Lin, W. J. Org. Chem. 2004, 69, 4695–4700.