First synthesis of 4′-selenonucleosides showing unusual southern conformation

Article abstract of DOI:10.1021/ol7025558

(Chemical Equation Presented) The first synthesis of 4′- selenonucleosides was achieved using a Pummerer-type condensation as a key step. All stereoelectronic effects shown in 4′-oxonucleosides were overwhelmed by the size of selenium and steric interacti

Full text of DOI:10.1021/ol7025558

ORGANIC
LETTERS
2008
Vol. 10, No. 2
209-212
First Synthesis of 4′-Selenonucleosides
Showing Unusual Southern
Conformation
Lak Shin Jeong,*,† Dilip K. Tosh,† Hea Ok Kim,† Ting Wang,† Xiyan Hou,†
Ho Seop Yun,‡ Youngjoo Kwon,† Sang Kook Lee,† Jungwon Choi,§ and
Long Xuan Zhao†
Laboratory of Medicinal Chemistry, College of Pharmacy, Ewha Womans UniVersity,
Seoul 120-750, Korea, DiVision of Energy Systems Research and Department of
Chemistry, Ajou UniVersity, Suwon 443-749, Korea, and Department of Chemistry,
The UniVersity of Suwon, Kyunggi 445-743, Korea
lakjeong@ewha.ac.kr
Received October 20, 2007
ABSTRACT
The first synthesis of 4
shown in 4 -oxonucleosides were overwhelmed by the size of selenium and steric interactions, driving the conformation to the C2
C3 -exo twist (Southern) conformation.
′
-selenonucleosides was achieved using a Pummerer-type condensation as a key step. All stereoelectronic effects
′
′
-endo/
′
The nucleoside structure has proven to be an effective
template for the development of therapeutically useful agents
with antiviral and antitumor activity. It can also serve as a
precursor to oligonucleotides, which may be useful in
antisense and gene therapy and as biochemical probes.1 For
example, the modification of uridine to 2′-deoxy-2′-fluoro-
â-L-arabinofuranosyl-5-methyluracil (L-FMAU)2 provides a
compound with potent anti-hepatitis B virus (HBV) activity
that can also serve as a building block of antisense oligo-
nucleotides or small interfering RNAs.
Figure 1. Rationale for the design of the target nucleosides.
effects such as resistance and toxicity, and chemical and
enzymatic degradation, has stimulated the search for new
templates and has led to the discovery of 4′-thionucleosides3
and 4′-carbonucleosides,4 which are second-generation nu-
cleosides. The 4′-thionucleoside and the 4′-oxonucleoside are
bioisosterically related and are known to adopt the same
conformation.5
The 4′-oxonucleoside, a first-generation nucleoside (Figure
1), has played a key role in the development of clinical or
biochemical probes. However, the emergence of adverse
† Ewha Womans University.
‡ Ajou University.
§ The University of Suwon.
(1) (a) De Clercq, E. J. Clin. Virol. 2001, 22, 73-89. (b) Obak, T.; Lech-
Maranda, E.; Korycka, A.; Robak, E. Curr. Med. Chem. 1999, 6, 599-
614. (c) Uhlmann, E.; Peyman, A. Chem. ReV. 1990, 90, 543-584.
(2) Ma, T.; Lin, J. S.; Newton, M. G.; Cheng, Y.-C.; Chu, C. K. J. Med.
Chem. 1997, 40, 2750-2754.
(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.
10.1021/ol7025558 CCC: $40.75
© 2008 American Chemical Society
Published on Web 12/19/2007

Notwithstanding the potent biological activity and meta-
bolic stability of 4′-thionucleosides, only a few compounds
have entered clinical development because the compounds
are generally highly cytotoxic. The 4′-carbonucleoside is also
bioisosterically related to the 4′-oxonucleoside and exhibits
excellent chemical and metabolic stability about the glyco-
sidic bond. However, it has been shown to have a conforma-
tion that is very different from that of the 4′-oxonucleoside,
which results in the loss of biological activity.6 Thus, as a
part of our continuing efforts to search for a novel template
for the development of new therapeutic or biochemical
probes, we turned our attention to 4′-selenonucleosides, third-
generation nucleosides which are also bioisosterically related
to the 4′-oxo- or 4′-thionucleosides. Although selenonucleo-
sides7 have been reported as precursors to 2′,3′- and 4′,5′-
unsaturated nucleosides or oligonucleotides containing 2′-
selenonucleosides,8 no examples of 4′-selenonucleosides have
so far been reported in the literature, due to the difficulties
of their synthesis.
deoxy-4′-seleno-NTP) toward RNA and DNA polymerases,
respectively. Thus, in addition to the first synthesis of 4′-
selenonucleosides, it is also of great interest to compare the
conformation of a 4′-selenonucleoside with that of the 4′-
oxonucleoside. We wish to report here the first synthesis
and the unusual conformation of 4′-selenonucleosides. Our
strategy for the synthesis of 4′-selenonucleosides was to
condense the 4-selenoxide with uracil or cytosine, using a
Pummerer-type condensation. The 4-selenoxide was easily
synthesized from D-gulonic-γ-lactone.
Based on this synthetic strategy, we prepared the 4-sele-
nosugar 8 from D-gulonic-γ-lactone, as shown in Scheme 1.
Scheme 1. Syntheis of the Key Selenosugar 8
Uridine assumes the C2′-exo/C3′-endo twist (Northern)
conformation.9 Among the stereoelectronic effects driving
the conformation of uridine are the [O4′-C1′-C2′-O2′] and
[O4′-C4′-C3′-O3′] gauche interactions which cancel one
another.10 The other gauche effect, involving [O2′-C2′-
C1′-N1], tends to drive the N/S equilibrium to the S
conformation, but this effect is weaker with π-deficient
pyrimidines; the dominant driving force leading to the N
conformation in uridine is the anomeric effect, which is much
stronger in pyrimidines than in purines. The same forces
described for uridine, pertain with 4′-thiouridine, but are
weaker in this case. The result is the same; the N conforma-
tion is still preferred. However, in 4′-selenouridine, all
stereoelectronic effects are expected to be overwhelmed by
the size of selenium and steric interactions driving the
conformation to the C2′-endo/C3′-exo twist (Southern)
conformation. This unusual conformation of 4′-selenouridine
could play important roles in developing new therapeutic
agents or biochemical probes for studying antisense oligo-
nucleotide or small interfering RNA (siRNA) interactions
with potential therapeutic targets. This unusual conformation
could also prove very useful for studying the substrate
properties of 4′-selenonucleoside-5′-triphosphate (4′-seleno-
NTP) and 2′-deoxy-4′-selenonucleoside-5′-triphosphate (2′-
2,3;5,6-di-O-Isopropylidene-D-gulonic-γ-lactone (1),11 pre-
pared from D-gulonic-γ-lactone, was converted to the L-
lyxose derivative 4,12 using modifications of the reported
procedures.12 Treatment of 1 with DIBAL-H at -78 °C
afforded the lactol 2 in 82% yield. Selective hydrolysis of 2
with 80% aqueous acetic acid gave 3 in 81% yield. Oxidative
cleavage of diol 3 with sodium metaperiodate followed by
reduction of the resulting aldehyde with sodium borohydride
afforded the L-lyxose derivative 4 in 67% yield. Selective
protection of the primary hydroxyl group of 4 with TBDPSCl
gave the silyl ether 5, which upon treatment with sodium
borohydride provided the diol 6 in excellent yield. Mesylation
of diol 6 with mesyl chloride in the presence of triethyl amine
afforded the dimesylate 7. Treatment of 7 with selenium in
the presence of sodium borohydride in EtOH-THF at 60
°C furnished the 4-seleno sugar 8 in 96% yield.13 The
presence of two doublets of doublets, at δ 2.96 and 3.14
ppm, and disappearance of two methyl peaks of dimesylates,
at δ 3.00 and 3.07 ppm, in the 400 MHz 1H NMR spectrum
of compound 8 in CDCl3 clearly indicated that cyclization
(4) (a) Piperno, A.; Chiacchio, M. A.; Iannazzo, D.; Romeo, R. Curr.
Med. Chem. 2006, 13, 3675-3695. (b) Ferrero, M.; Gotor, V. Chem. ReV.
2000, 100, 4319-4348. (c) Lee, J. A.; Jeong, L. S. AntiViral Chem.
Chemother. 2004, 15, 235-250. (d) Marquez, V. E.; Lim, M.-I. Med. Res.
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Tetrahedron Lett. 1994, 35, 7569-7572. (b) Jeong, L. S.; Nicklaus, M. C.;
George, C.; Marquez, V. E. Tetrahedron Lett. 1994, 35, 7573-7576. (c)
Haeberli, P.; Berger, I.; Pallan, P. S.; Egli, M. Nucleic Acids Res. 2005,
33, 3965-3975.
(6) (a) Marquez, V. E.; Hughes, S. H.; Sei, S.; Agbaria, R. AntiViral
Res. 2006, 71, 268-275. (b) Kalman, A.; Koritzanszky, T.; Beres, J.; Sagi,
G. Nucleosides Nucelotides 1990, 9, 235-243.
(7) Wnuk, S. F. Tetrahedron 1993, 49, 9877-9936.
(8) Jiang, J.; Sheng, J.; Carrasco, N.; Huang, Z. Nucleic Acids Res. 2007,
35, 477-485.
(11) Jeong, L. S.; Lee, H. W.; Jacobson, K. A.; Kim, H. O.; Shin, D.
H.; Lee, J. A.; Gao, Z.-G.; Lu, C.; Duong, H. T.; Gunaga, P.; Lee, S. K.;
Jin, D. Z.; Chun, M. W.; Moon, H. R. J. Med. Chem. 2006, 49, 273-281.
(12) (a) Varela, O.; Zunszain, P. A. J. Org. Chem. 1993, 58, 7860-
7864. (b) Xie, M.; Berges, D. A.; Robins, M. J. J. Org. Chem. 1996, 61,
5178-5179.
(9) Green, E. A.; Rosenstein, R. D.; Abraham, D. J.; Trus, B. L.; Marsh,
R. E. Acta Crystallogr. 1975, B31, 102-107.
(10) Thibaudeau, C.; Chattopadhyaya, J. Stereoelectronic effects in
nucleosides and nucleotides and their structural implications; Uppsala
University Press: Uppsala, 1999.
(13) Liu, H.; Pinto, B. M. J. Org. Chem. 2005, 70, 753-755.
210
Org. Lett., Vol. 10, No. 2, 2008

had occurred, and this was further confirmed by spectral and
analytical data.
With the 4-selenosugar 8 in hand, the next goal was to
synthesize the 4′-selenouridine 13 and 4′-selenocytidine 14
from 8 (Scheme 2). Thus, oxidation of 8 with m-CPBA gave
4′-selenouridine 13 assumes an unusual C2′-endo/C3′-exo
twist (Southern) conformation unlike uridine9 which takes
the C2′-exo/C3′-endo twist (Northern) conformation (Figure
2), indicating that in 4′-selenonucleoside, the anti orientation
Scheme 2. Synthesis of the Final Nucleosides 13 and 14
Figure 2. X-ray crystal structure of 13.
was more favorable than the gauche orientation, presumably
due to the steric effects of selenium. This unusual conforma-
tion may confer resistance to RNA cleaving enzymes such
as RNAse H and nuclease. Furthermore, the O5′-hydroxyl
group in 13 is also in the unusual ap conformation, distinct
from uridine in which this hydroxyl group adopts the +sc
orientation. The unusual ap orientation of the 5′-hydroxyl
group of 4′-selenonucleosides may affect phosphorylation
by the cellular kinases, but it is important to note that the
conformation of compounds in the crystal and the solution
forms can be very different.
Since each N or S conformation identified in the solid
structures of the 4′-oxonucleoside coexist in a dynamic N/S
equilibrium in solution,17 we have also determined the
conformation of 4′-selenouridine in the solution state and
compared it with that of uridine. All protons in 4′-seleno-
uridine except for 4′-H were shifted downfield from those
in uridine (Tables 1 and 2 in the Supporting Information).
The 3J1′-H,2′-H value of 4′-selenouridine was 8.70 Hz, while
the same coupling in uridine was 4.62 Hz, indicating a
different ribose ring puckering. This coupling is generally
small for the C3′-endo ribose ring puckering found in A-form
RNA and larger for the C2′-endo ribose ring puckering
commonly found in B-form DNA.18 In addition to the
comparison of coupling constants, NOE experiments were
also performed in order to confirm the conformation of 4′-
the unstable selenoxide 9 as a diastereomeric mixture, which
was immediately subjected to a Pummerer rearrangement14
in the presence of Ac2O at 100 °C to give the acetate 10.
However, the conventional condensation method which
reacted 10 with silylated uracil in the presence of TMSOTf
failed to give the desired product 11, and it was therefore
decided to attempt a direct Pummerer-type base condensa-
tion15 with the selenoxide 9. This condensation method
afforded the desired uracil derivative 11 (53%) and the
corresponding cytosine derivative 12 (35%) without forma-
tion of their corresponding R-isomers. It is hypothesized that
as in the case of 4′-thionucleosides,15 the condensation
reaction of selenoxide 9 with uracil proceeded via the
R-selenocarbocation intermediate formed by an E2 anti
elimination under the reaction conditions, in which the sole
formation of the â-isomer is attributable to a steric effect11
from 2′,3′-O-isopropylidene group. The presence of two
doublets at δ 6.35 (H-5) and 7.52 (H-6) ppm and a doublet
1
of doublets at δ 5.56 (1′-H) ppm in the 400 MHz H NMR
(16) Crystal structure data for C10H12N2O5Se: Mr ) 319.18, orthorhom-
bic, space group P212121 (no. 19), a ) 4.9520(1) Å, b ) 13.4320(3) Å, c
) 16.9083(5) Å, V ) 1124.65(5) Å3, T ) 293(1) K, Z ) 4, Fcalc ) 1.885
gcm-3, F(000) ) 640, crystal dimension 0.5 × 0.3 × 0.3 mm3, µ(Mo KR)
) 3.355mm-1, Mo KR radiation(λ ) 0.7107 Å). Of 11026 reflections
collected in the 2θ range 3.0 55.0° using an ω scans on a Rigaku Rapid
R-axis diffractometer, 2565 were unique reflections (Rint ) 0.052). The
structure was solved and refined against F2 using SHELXS97 and
SHELXL97, 202 variables, wR2 ) 0.064, R1 ) 0.027 (the 2434 reflections
of 11 in CDCl3 clearly indicated that condensation had
occurred as expected. The anomeric assignment of 11 could
1
not be confirmed by H NMR NOE but was established by
X-ray crystallography (vide infra). Removal of the protecting
groups from 11 with aqueous 50% trifluoroacetic acid
furnished the desired final nucleoside 13, whose structure
was confirmed by X-ray crystallography.16
Compound 12 was similarly converted to the cytosine
derivative 14. X-ray crystallographic analysis showed that
2
having Fo2 > 2σ(Fo )), GOF ) 1.041, and max/min residual electron density
0.59/-0.49 eÅ-3. Flack x parameter ) 0.009(9). Further details of the crystal
structure investigation(s) may be obtained from the Cambridge Crystal-
lographic Data Centre (CCDC, 12 Union Road, Cambridge, CB2 1EZ (UK);
Tel: (+44)1223-336-408, Fax: (+44)1223-336-033, e-mail: deposit@ccdc.
cam.ac.uk) on quoting the depository no. CSD-652601.
(17) (a) Dijkstra, S.; Benevides, J. M.; Thomas, G. J., Jr. J. Mol. Struct.
1991, 242, 283-301. (b) Jagannadh, B.; Reddy, D. V.; Kunwar, A. C.
Biochem. Biophys. Res. Commun. 1991, 179, 386-391.
(14) Veerapen, N.; Taylor, S. A.; Walsby, C. J.; Pinto, B. M. J. Am.
Chem. Soc. 2006, 128, 227-239.
(15) Naka, T.; Minakawa, N.; Abe, H.; Kaga, D.; Matsuda, A. J. Am.
Chem. Soc. 2000, 122, 7233-7243.
Org. Lett., Vol. 10, No. 2, 2008
211

selenouridine. A strong NOE between H-6 and the 2′-H was
detected in 4′-selenouridine, while no NOE effect was
observed in case of uridine, indicating that 4′-selenouridine
exists in the 3′-exo (S) conformation and uridine exists in
the 3′-endo (N) conformation. The base can adopt two
relative orientations, anti and syn, with respect to the sugar
moiety, and these can be described by glycosidic torsion
angle ø (O4′-C1′-N1-C2 in uridine, Se4′-C1′-N1-C2
in 4′-selenouridine). In the anti conformation, the six-
membered uracil ring is pointing away from the sugar, thus
providing a shorter distance between H-6 and the 2′-H in
the 2′-endo or between H-6 and the 3′-H in the 3′-endo sugar
ring than that between H-6 and the 1′-H.19 These data are
all consistent with the observation that replacement of the
ribose ring oxygen by selenium causes a conformational
change from a C3′-endo to a C2′-endo puckered ribose ring
in the solution state, while the same type of uracil link exists
with the ribose sugar ring since the anti-glycosidic torsion
angle is unchanged.
first synthesis of 4′-selenonucleosides. These third-generation
4′-selenonucleosides exhibit an unusual C2′-endo/C3′-exo
twist (Southern) conformation. It was revealed that all
electronic effects found in uridine were overwhelmed by the
steric effects from the bulky selenium, which force 4′-
selenonucleosides to adopt the unusual Sourthern conforma-
tion. This unnatural conformation may provide valuable
information for the study of the conformational preferences
of metabolic enzymes such as kinases and nucleases. We
are sure that the results reported here will open up a new
era in nucleoside, nucleotide, and nucleic acids chemistry.
Acknowledgment. This paper is dedicated to Prof. Chung
K. Chu (University of Georgia) and Dr. Victor E. Marquez
(NCI, NIH) on the occasion of their 65th birthdays. This
work was supported by the National Core Research Center
(NCRC) program (No. R15-2006-020) of the Ministry of
Science and Technology (MOST) and the Korea Science and
Engineering Foundation (KOSEF).
In summary, using a Pummerer-type base condensation
of selenoxide 9 as a key step, we have accomplished the
Supporting Information Available: Complete experi-
mental procedure for all compounds described herein and
1H and 13C NMR copies of 13 and 14. This material is
available free of charge via the Internet at http://pubs.acs.org.
(18) Wuthrich, K. NMR of Proteins and Nucleic Acids; John Wiley &
Sons: New York, 1986; pp 203-223.
(19) Saenger, W. Principles of Nucleic Acid Structure; Springer-
Verlag: New York, 1985; pp 242-320 for nucleic acid structures, pp 21-
23 for sugar pucker.
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