A new DNA building block, 4′-selenothymidine: Synthesis and modification to 4′-seleno-AZT as a potential anti-HIV agent

Article abstract of DOI:10.1021/ol1005906

The first synthesis of 4′-selenothymidine (1), a novel DNA building block, and 4′-seleno-AZT (2) was accomplished from 2-deoxy-d-ribose via stereoselective formation of 2-deoxy-4-seleno-d-furanose 17 and a Pummerer-type base condensation as key steps. 4′-

Full text of DOI:10.1021/ol1005906

ORGANIC
LETTERS
2010
Vol. 12, No. 10
2242-2245
A New DNA Building Block,
4′-Selenothymidine: Synthesis and
Modification to 4′-Seleno-AZT as a
Potential Anti-HIV Agent
Varughese Alexander,† Won Jun Choi,† Jeongha Chun,† Hea Ok Kim,† Ji
Hye Jeon,† Dilip K. Tosh,† Hyuk Woo Lee,† Girish Chandra,† Jungwon Choi,‡ and
Lak Shin Jeong*,†
Department of Bioinspired Science and Laboratory of Medicinal Chemistry, College of
Pharmacy, Ewha Womans UniVersity, Seoul 120-750, Korea, and Department of
Chemistry, The UniVersity of Suwon, Kyunggi-do 445-743, Korea
lakjeong@ewha.ac.kr
Received March 11, 2010
ABSTRACT
The first synthesis of 4′-selenothymidine (1), a novel DNA building block, and 4′-seleno-AZT (2) was accomplished from 2-deoxy-D-ribose via
stereoselective formation of 2-deoxy-4-seleno-D-furanose 17 and a Pummerer-type base condensation as key steps. 4′-Selenothymidine (1)
was discovered to adopt the same 2′-endo/3′-exo conformation as thymidine, which is unusual in that 4′-selenouridine has the opposite
conformation to that of uridine.
Thymidine is a DNA building block and serves as a key
element for replication of the cell. Therefore, modified
thymidine or thymidylate derivatives have been extensively
used as biochemical tools to study biochemical behaviors
of enzymes related to cell replication or as antimetabolites
to inhibit normal pathways of cells.1 Several groups reported
the second-generation DNA building block, 4′-thiothymidine,
which is in a bioisosteric relationship with thymidine.2 From
this new template, many biologically active 2′-deoxy-4′-
thionucleosides have been developed.3,4 When compared
with 4′-oxonucleosides, 4′-thionucleosides showed better
glycosidic bond stability against metabolic enzymes or
chemical hydrolysis.3 The X-ray crystallographic analysis
showed that 4′-thiothymidine adopts the same 2′-endo/3′-
exo (South) conformation as thymidine.2 This result indicates
that the sulfur atom of 4′-thiothymidine behaves like the
oxygen atom of thymidine, showing the electronic (gauche)
effect.5
3′-Azido-3′-deoxythymidine (AZT)6 is the representative
of modified thymidine derivatives and has been a drug of
(2) (a) Uenishi, J.; Takahashi, K.; Motoyama, M.; Akashi, H.; Sasaki,
T. Nucleosides Nucleotides 1994, 13, 1347–1361. (b) Tiwari, K. N.;
Montgomery, J. A.; Secrist, J. A., III Nucleosides Nucleotides 1993, 12,
841–846. (c) Rahim, S. G.; Trivedi, N.; Bogunovic-Batchelor, M. V.; Hardy,
G. W.; Mills, G.; Selway, J. W. T.; Snowden, W.; Littler, E.; Coe, P. L.;
Basnak, I.; Whale, R. F.; Walker, R. T. J. Med. Chem. 1996, 39, 789–795.
(d) Secrist, J. A., III; Tiwari, K. N.; Riordan, J. M.; Montgomery, J. A.
J. Med. Chem. 1991, 34, 2361–2366. (e) Dyson, M. R.; Coe, P. L.; Walker,
R. T. J. Med. Chem. 1991, 34, 2782–2786. (f) Uenishi, J.; Takahashi, K.;
Motoyama, M.; Akashi, H. Chem. Lett. 1993, 255–256.
(3) Gunaga, P.; Moon, H. R.; Choi, W. J.; Shin, D. H.; Park, J. G.;
Jeong, L. S. Curr. Med. Chem. 2004, 11, 2585–2637.
† Ewha Womans University.
(4) Van Draanen, N. A.; Freeman, G. A.; Short, S. A.; Harvey, R.;
Jansen, R.; Szczech, G.; Koszalka, G. W. J. Med. Chem. 1996, 39, 538–
542.
‡ The University of Suwon.
(1) Breaker, R. R. Nature 2004, 432, 838–845.
10.1021/ol1005906  2010 American Chemical Society
Published on Web 04/20/2010

choice in treating AIDS and AIDS-related complex (ARC).
AZT is converted into AZT-triphosphate in the cell, which
inhibits HIV-1 RT (reverse transcriptase) competitively and/
or terminates viral DNA chain after being incorporated into
proviral DNA.7 However, the clinical use of AZT is
hampered by severe toxicity such as bone marrow toxicity
and anemia and appearance of AZT-resistant strains.8 A
similar analogue, 3′-azido-2′,3′-dideoxyuridine (AZDU),9
was also discovered as a potent and selective anti-HIV agent.
Although AZDU was less potent than AZT, it showed a
better toxicity profile than AZT due to its different cellular
metabolism.10
selenothymidine (4′-Se-AZT) and to compare its anti-HIV
activity with that of AZT. Herein, we describe the first
synthesis of a new DNA building block, 4′-selenothymidine
and its conformational study, as well as its modification to
4′-Se-AZT.
Scheme 1
.
Retrosynthetic Analysis of the Desired Nucleosides 1
and 2
Scheme 1 illustrates the retrosynthetic analysis of the
desired nucleosides 1 and 2. 4′-Se-AZT (2) can be synthe-
sized from 4′-selenothymidine (1) by opening the 2,3′-
anhydrothymidine derivative with sodium azide. It was
thought that 4′-selenothymidine (1) might be synthesized via
two routes (A and B). The first route was to utilize the
Barton-McCombie deoxygenation13 of the 2′-hydroxyl
derivative 3 which could be easily derived from 4′-seleno-
ribosyl derivative 414 (route A). The second route was to
use the Pummerer-type condensation of selenoxide 5 with
thymine (route B). The selenoxide 5 would be synthesized
from the diol 6 by mesylation followed by ring closure with
Na2Se. The diol 6 might be derived from 7 using a Mitsunobu
reaction as a key step. Thus, it was realized that compound
7 could be easily synthesized from 2-deoxy-D-ribose.
Route A using radical deoxygenation13,15 as a key step
was first tried (Scheme 2). 4′-Selenoribosyl derivative 414
was treated with TIPDSCl2 to give 3′,5′-di-O-protected
derivative 8. Treatment of 8 with phenyl chlorothionoformate
gave the thiocarbonate 9. Radical deoxygenation13,15 of 9
with n-Bu3SnH in the presence of AIBN or Et3B afforded
the ring-cleaved product 10.
Figure 1. Rationale for the design of the target nucleosides.
Recently, we and other groups reported the synthesis of a
novel RNA building block, 4′-selenouridine, and its oligo-
nucleotides.11 From this study, it was revealed that the bulky
selenium atom played a key role in deciding the conformation
of 4′-selenouridine. From this RNA building block, 2′-deoxy-
2′-fluoro-4′-selenoarabinofuranosylcytosine (2′-F-4′-Se-ara-
C) was discovered as a potent anticancer agent.12 Thus, it
was of great interest to synthesize the new DNA building
block, 4′-selenothymidine, as a potential biochemical tool
or as a template for the development of new drugs (Figure
1). It is also interesting to synthesize the 3′-azido-4′-
(5) Altona, C.; Sundaranlingam, M. J. Am. Chem. Soc. 1972, 94, 8205.
(6) Mitsuya, H.; Weinhold, K. J.; Furman, P. A.; St. Clair, M. H.;
Lehrmann, S. N.; Gallo, R. C.; Bolognesi, D.; Barry, D. W.; Broder, S.
Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 7096–7100.
(7) Arts, E. J.; Wainberg, M. A. Antimicrob. Agents Chemother. 1996,
40, 527–540.
(8) Styrt, B. A.; Piazza-Hepp, T. D.; Chikami, G. K. AntiViral Res. 1996,
31, 121–135.
(9) Chu, C. K.; Schinazi, R. F.; Ahn, M. K.; Ullas, G. V.; Gu, Z. P.
J. Med. Chem. 1989, 32, 612–617.
Even under milder conditions, the desired 2′-deoxy deriva-
tive could not be obtained. These observations are in
agreement with those observed during the synthesis of 2′-
(10) Zhu, Z.; Schinazi, R. F.; Chu, C. K.; Williams, G. J.; Colby, C. B.;
Sommadossi, J. P. Mol. Pharmacol. 1990, 38, 929–938.
(11) (a) Jeong, L. S.; Tosh, D. K.; Kim, H. O.; Wang, T.; Hou, X.;
Yun, H. S.; Kwon, Y.; Lee, S. K.; Choi, J.; Zhao, L. X. Org. Lett. 2008,
10, 209–212. (b) Jayakanthan, K.; Johnston, B. D.; Pinto, B. M. Carbohydr.
Res. 2008, 343, 1790–1800. (c) Watts, J. K.; Johnston, B. D.; Jayakanthan,
K.; Wahba, A. S.; Pinto, B. M.; Damha, M. J. J. Am. Chem. Soc. 2008,
130, 8578–8579.
(13) Barton, D. H. R.; McCombie, S. W. J. Chem. Soc., Perkin Trans.
1 1975, 16, 1574–1585.
(14) Tosh, D. K.; Choi, W. J.; Kim, H. O.; Lee, Y.; Pal, S.; Hou, X.;
Choi, J.; Choi, S.; Jeong, L. S. J. Org. Chem. 2008, 73, 4259–4262.
(15) Nozaki, K.; Oshima, K.; Utimoto, K. Tetrahedron Lett. 1988, 29,
(12) Jeong, L. S.; Tosh, D. K.; Choi, W. J.; Lee, S. K.; Kang, Y.-J.;
Choi, S.; Lee, J. H.; Lee, H.; Lee, H. W.; Kim, H. O. J. Med. Chem. 2009,
52, 5303–5306.
6125–6126. (b) Crich, D.; Quintero, L. Chem. ReV. 1989, 89, 1413–1432
.
Org. Lett., Vol. 12, No. 10, 2010
2243

Scheme 2
.
Synthetic Approach to 4′-Selenothymidine via
2′-Deoxygenation
Scheme 3. Synthesis of the Key 4-Selenosugar 17
deoxy-4′-thioribonucleosides.16 In the case of 4′-thionucleo-
sides, the desired 2′-deoxy derivative after deoxygenation
reaction was obtained as a major product, along with the
ring-cleaved derivative. However, we observed the exclusive
formation of 10 under our set of conditions. These observa-
tions led to the postulate that homolytic cleavage of the C-Se
bond occurs rapidly along with the C-O bond, leading to
the ring-cleaved radical intermediate 10 as the exclusive
product. This route was abandoned as it appeared that the
desired 2′-deoxy analogues could not be synthesized under
these conditions. Thus, we opted for an alternative strategy
(route B) which would synthesize the key 4-selenosugar 17
prior to condensing it with thymine, as illustrated in Scheme
3.
Treatment of 2-deoxy-D-ribose with 0.05% HCl in MeOH
followed by benzylation of the remaining hydroxyl groups
afforded the anomeric methoxide 11.17 For the conversion
of 11 into the diol 12, various conventional conditions (acid-
catalyzed hydrolysis and reduction) were attempted, but the
desired diol 12 was obtained in poor yield. As the low yield
resulted from the acid-catalyzed hydrolysis, we decided to
use nonhydrolysis conditions. Oxidation of the anomeric
methoxide 11 with m-CPBA in the presence of BF3·Et2O
yielded the lactone which was reduced with LAH to produce
the diol 1217 in excellent yield. Inversion of stereochemistry
of the secondary hydroxyl group of 13 was achieved by the
Mitsunobu reaction, giving the benzoate 14 after the primary
hydroxyl group of 12 was protected with TBDPS group.
Removal of the benzoyl and TBDPS protecting groups of
14 gave the diol 15, which was converted to the dimesylate
16. Treatment of 16 with selenium and NaBH4 in EtOH at
reflux afforded the key 2-deoxy-4-seleno-D-ribose derivative
17 in very good yield.11 To the best of our knowledge, this
is the first example of a sugar of the 2-deoxy-4-selenoribo-
furanose series.
The 2-deoxy-4-seleno-D-ribose derivative 17 was oxidized
to the 4-selenoxide 18 which was condensed with thymine
in the presence of TMSOTf and Et3N in CH2Cl2 to give the
thymidine analogue 19 (15%) as an inseparable anomeric
mixture (Scheme 4). Treatment of 19 with BCl3 afforded
the 4′-selenothymidine (1) and its R-anomer (1a). Anomeric
configurations of 1 and 1a were assigned on the basis of 1H
NOE experiments. Irradiation on 1′-H of compound 1 gave
no NOE effect on 3′-H, while an NOE effect (1.48%) was
observed in the same experiment on compound 1a. The NOE
effect (1.4%) between 3′-H and H-6 in compound 1 was also
Scheme 4. Synthesis of 4′-Selenothymidine (1) and Its
R-Anomer 1a
(16) Naonori, I.; Daisuke, K.; Noriaki, M.; Akira, M. J. Org. Chem.
2005, 70, 8597–8600.
(17) Takahashi, T.; Hirose, Y.; Iwamoto, H.; Doi, T. J. Org. Chem. 1998,
63, 5742–5743.
2244
Org. Lett., Vol. 12, No. 10, 2010

measured, but no NOE was observed in case of 1a, indicating
that compound 1 is the ꢀ-anomer. Anomeric configuration
of compound 1 was finally confirmed by the X-ray crystal
structure,18 as shown in Figure 2.
Scheme 5. Synthesis of 4′-Seleno-AZT (2)
in CD3OD. An NOE effect (1.44%) between 3′-H and H-6
was observed, but no NOE effect between 1′-H and 3′-H
was measured, indicating that the azido substituent possesses
the desired R-configuration. Anti-HIV activity of 1 and 2
was measured in MT-4 cells infected with the HIV-1 IIIB
strain, but these compounds showed neither anti-HIV activity
nor cytotoxicity up to 100 µM.
In summary, we have accomplished the first synthesis of
4′-selenothymidine (1), which is a novel DNA building block,
and 4′-seleno-AZT (2) as a potential antiviral agent from
2-deoxy-D-ribose. It was also discovered that 4′-selenothy-
midine (1) showed the same 2′-endo/3′-exo (South) confor-
mation as thymidine. The 4′-selenothymidine (1) reported
here is expected to serve as a good template for the
development of new drugs as well as new biochemical tools.
Experiments to identify if 4′-selenothymidine is phospho-
rylated by cellular kinases or incorporated into DNA chain
are underway.
Figure 2. X-ray crystal structure of 1.
X-ray crystallographic analysis indicated that 4′-selenothy-
midine (1) adopts the same 2′-endo/3′-exo (South) conforma-
tion as thymidine (Figure 2). This result is surprising in that
4′-selenouridine adopted opposite conformation to that of
uridine.
As mentioned earlier, as AZT is a potent anti-HIV agent,
4′-selenothymidine (1) was converted to the 4′-seleno-AZT
(2), as illustrated in Scheme 5. Tritylation of 1 gave 5′-trityl
derivative 20 which was converted to the mesylate 21.
Treatment of 21 with NaN3 in the presence of Li2CO3
afforded 3′-azido derivative 23 via the intermediate 22.19
Removal of the trityl group of 23 with formic acid yielded
the 4′-seleno-AZT (2). The configuration of azido group of
2 was confirmed by 1H NOE experiments (400 MHz NMR)
Acknowledgment. This work was supported by a grant
from the WCU project (R31-2008-000-10010-0) and the
NCRC (No. R15-2006-020) of the National Research Foun-
dation (NRF), Korea.
(18) C10H14N2O4Se: Mr ) 305.19, monoclinic, space group P21 (no.
4), a ) 9.2745(7) Å, b ) 5.2059(3) Å, c ) 12.1233(7) Å, V ) 584.97(6)
Å3, T ) 290(2) K, Z ) 2, Fcalc ) 1.733 g cm-3, F(000) ) 308, crystal
dimension 0.40 × 0.30 × 0.20 mm3, µ(MoKR) ) 3.22 mm-1, MoKR
radiation (λ ) 0.71073 Å). Of 5697 reflections collected in the 2θ range
from 3.4 to 27.5° using an ω scan on a Rigaku Rapid R-axis diffractometer,
2410 were unique reflections (Rint ) 0.028). The structure was solved and
refined against F2 using SHELXS97 and SHELXL97, 184 variables, wR2
) 0.055, R1 ) 0.025 (the 2196 reflections having Fo > 2σ(Fo )), GOF )
1.14, and max/min residual electron density 0.35/-0.53 e Å-3. Flack x
parameter ) 0.025(9). Further details of the crystal structure investigation(s)
may be obtained from the Cambridge Crystallographic Data Centre (CCDC),
12 Union Road, Cambridge, CB2 1EZ (U.K.); Tel: (+44)1223-336-408,
Fax: (+44)1223-336-033, e-mail: deposit@ccdc.cam.ac.uk) on quoting the
depository no. CCDC-761848.
Note Added after ASAP Publication. Two references
were added to reference 11 in the version reposted April
29, 2010.
2
2
Supporting Information Available: Complete experi-
mental procedure and 1H and 13C NMR copies of all
compounds described herein. This material is available free
of charge via the Internet at http://pubs.acs.org.
(19) Chen, B.-C.; Quinlan, S. L.; Reid, J. G. Tetrahedron Lett. 1995,
36, 7961–7964.
OL1005906
Org. Lett., Vol. 12, No. 10, 2010
2245