NMR conformational analysis of p-tolyl furanopyrimidine 2′-deoxyribonucleoside and crystal structure of its 3′,5′-di- O-acetyl derivative

Article abstract of DOI:10.1016/j.bmc.2004.11.013

The conformation of a representative molecule of a new, potent class of antiviral-active modified nucleosides is determined. A bicyclic nucleoside, 3-(2′-deoxy-β-d-ribofuranosyl)-6-(4-methylphenyl)-2,3-dihydrofuro[2, 3-d]pyrimidin-2-one, shows C2′-endo and C3′-endo ribose conformations in solution (63:37, 37°C; DMSO-d₆), as determined by ¹H NMR studies. The crystal structure of a 3′,5′-di-O- acetyl-protected derivative (monoclinic, P2₁, a/b/c = 6.666(1)/12.225(1)/24.676(2) A, β = 90.24(1)°, Z = 4) shows exclusively C2′-endo deoxyribose puckering. The base is found in the anti position both in solution and in crystalline form.

Full text of DOI:10.1016/j.bmc.2004.11.013

Bioorganic& Medicinal Chemistry 13 (2005) 1231–1238
NMR conformational analysis of p-tolyl furanopyrimidine
20-deoxyribonucleoside and crystal structure of its
30,50-di-O-acetyl derivative
Noor Esho,a Jean-Paul Desaulniers,b Brian Davies,a Helen M.-P. Chui,b
Meneni Srinivasa Rao,a Christine S. Chow,b Slawomir Szafertc,* and Roman Dembinskia,*
aDepartment of Chemistry and Center for Biomedical Research, Oakland University, 2200 N. Squirrel Rd,
Rochester, MI 48309-4477, USA
bDepartment of Chemistry, Wayne State University, Detroit, MI 48202, USA
cDepartment of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
Received 16 September 2004; revised 8 November 2004; accepted 8 November 2004
Abstract—The conformation of a representative molecule of a new, potent class of antiviral-active modified nucleosides is deter-
mined. A bicyclic nucleoside, 3-(20-deoxy-b-D-ribofuranosyl)-6-(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one, shows
1
C20-endo and C30-endo ribose conformations in solution (63:37, 37ꢀC; DMSO-d6), as determined by H NMR studies. The crystal
0
0
˚
structure of a 3 ,5 -di-O-acetyl-protected derivative (monoclinic, P21, a/b/c = 6.666(1)/12.225(1)/24.676(2) A, b = 90.24(1)ꢀ, Z = 4)
shows exclusively C20-endo deoxyribose puckering. The base is found in the anti position both in solution and in crystalline
form.
ꢁ 2004 Elsevier Ltd. All rights reserved.
1. Introduction
starting from 5-iodouridine (1), synthesis of 5-alkynyl
uridine derivatives (2) via Sonogashira coupling also
leads to the formation of a side product identified
as furanopyrimidine (3, Scheme 1).4c,d,6,7 An increasing
interest in 3 has resulted from its identification as an
extremely potent and selective antiviral agent. In partic-
ular, the C6-substituted bicyclic structure 3 exhibits sig-
nificant therapeutic potential,8,9 which is attributed to
the chemical bypass mechanism of the nucleoside kina-
se.9b,e,10 A variety of nucleoside 3 derivatives with differ-
ent substituents at C6 have been synthesized, and their
antiviral properties have been examined in systematic
structure–activity studies.8,9a,d In particular, the ability
of p-(n-alkyl)phenyl furanopyrimidines to inhibit the
replication of strains of thymidine kinase-competent
(TK+) or -deficient (TK-) varicella-zoster virus (VZV)
surpassed ca. 104 times acyclovir or bromovinyldeoxy-
uridine.8a Low cytotoxicity leads to selectivity index val-
ues exceeding 106 for the most active compounds.8a It is
likely that the 4-pentylphenyl derivative (3c), which has
been proven to be effective against clinical VZV isolates,
will be further developed as a candidate drug.9a,c Taking
into account an interest in p-alkylphenyl furanopyrimi-
dine nucleosides due to their extraordinary antiviral
activity, we report the NMR conformational analysis
X-ray crystallographic and NMR methods are fre-
quently used to support the drug-discovery process.
Thus, the determination of conformation for com-
pounds with biological activity provides useful inform-
ation for the development of new structures with
interesting properties.1 The conformational preferences
of nucleosides may be important for their biological
roles. In viral diseases, the enzymes appear to have strict
conformational requirements. For example, there is an
increasing amount of experimental evidence that the
herpes thymidine kinase (HSV-TK) and cellular DNA
polymerases discriminate their substrates on the basis
of the nucleoside conformation, in particular the geo-
metry adopted by the furanose ring.2
Elucidation of the biological properties of 5-alkynyl uri-
dine analogs resulted in numerous activity reports3 and
4,5
detailed syntheticstudies.
It was noted that, when
Keywords: Nucleosides; Furanopyrimidine; Conformation.
*
Corresponding authors. Tel.: +1 248 3702248; fax: +1 248
3702321; e-mail: dembinsk@oakland.edu
0968-0896/$ - see front matter ꢁ 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmc.2004.11.013

1232
N. Esho et al. / Bioorg. Med. Chem. 13 (2005) 1231–1238
R
6
7
R
O
O
O
N
C
7a
5
C
I
HN
HN
N
1
4a
4
2
O
O
O
N
N
3
H C C R
Pd(PPh3)4, CuI
Et3N, DMF
"Pd"
R'O
R'O
R'O
O
O
O
or CuI, Et3N
OR'
OR'
OR'
1a R' = H
1b R' = Ac (88%)
3a R = p-CH3C6H4,
R' = H (71% from 1a)
3b R = p-CH3C6H4,
R' = Ac (58% from 1b)
3c R = p-CH3(CH2)4C6H4,
R' = H (ref. 8a)
2a R = p-CH3C6H4,
R' = H (ref. 14)
2b R = p-CH3C6H4,
R' = Ac (ref. 14)
a
a
3d R = C5H5FeC5H4,
R' = H (ref. 6b)
Scheme 1. Synthesis of furanopyrimidine nucleosides 3a and 3b. Reagents: (a) Ac2O, pyridine.
in solution for the p-tolyl-substituted furanopyrimidine
(3a). In addition, acylation of the ribose facilitated qual-
ity crystal growth, which allowed us to obtain a crystal
structure for the acetyl-protected derivative 3b.
(angle C30–C40–C50–O50); and the furanose ring pucker-
ing is specified by the pseudorotational phase angle P.
Two major furanose ring conformations are strongly
preferred for the nucleosides: C30-endo and C20-endo.16
2.2. NMR studies
2. Results and discussion
2.1. Synthesis
The nuclear Overhauser effect (NOE) is useful for the
assignment of closely related proton pairs, and allows
for determination of preferred conformations in solu-
1
19
The bicyclic furopyrimidine 3 arises at elevated tempera-
tures in the presence of Sonogashira coupling re-
agents,11 via 5-endo-dig cyclization involving the C4
pyrimidine oxygen and the acetylenic bond. Although
the presence of CuI/Et3N has been pointed out to be suffi-
cient for this reaction to occur,4c,d relevant heteroannul-
ation studies indicate an important role of palladium
as a catalyst in this process.12 Thus, the bicyclic nucleo-
side, 30,50-di-O-acetyl-3-(20-deoxy-b-D-ribofuranosyl)-6-
(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one
(3b) was prepared without isolation of the alkynyl deriva-
tive (2b) by a one-pot Sonogashira coupling4c,11 and
cyclization reaction. 30,50-Di-O-acetyl-5-iodo-20-deoxy-
uridine (1b)13,14 (1.0equiv) was combined with 4-
ethynyltoluene (1.5equiv) in the presence of Pd(PPh3)4
(0.1equiv), CuI (0.5equiv), and Et3N (1.8equiv) in
DMF (5h, 80ꢀC, Scheme 1). Workup gave 3b as a
white powder in 58% non-optimized yield. Synthesis of
nucleoside 3a was carried out in a similar manner as re-
ported previously,8a but a higher yield was achieved in
our case (71% vs 17%). 13C NMR signals for both acet-
ylated compounds 1b and 3b were assigned by an exam-
ination of coupling constants between adjacent H and C
atoms.
tion.18 For a sample of 3a in DMSO-d6 1D NOE H
NMR spectra were recorded at 20ꢀC. Assignments of
H200 (2.44ppm) and H20 (2.09ppm) were based on NOEs
to the anomericproton, H1 0. Irradiation of H10
(6.18ppm) resulted in a 3.83% enhancement of H200,
whereas the peak corresponding to H20 was not signifi-
cantly enhanced (<0.25%, Table 1). Strong NOEs
between H6/H8 of pyrimidine/purine to H20 and H30
of the 20-deoxyribose indicate that an anti conformation
is dominant, based on the studies by Seela and co-work-
ers.20 In contrast, stronger NOEs exist between H6/H8
of pyrimidine/purine and H10 when a population of
syn conformations predominates.20 In our experiment
(results summarized in Table 1), irradiation of H4 re-
sulted in NOEs at H10 (0.71%), H20 (1.20%), and H30
(0.85%). This observation is in agreement with a reverse
experiment, in which irradiation of H20 and H30 leads to
strong NOEs at H417 of furanopyrimidine (7.60% and
1.48%, respectively). This data suggests that the major-
ity of the population exists as the anti conformer. In
addition, results of the reverse experiment of H10 irradi-
Table 1. 1D NOE results for compound 3a at 20ꢀC (NOEs are given in
order of decreasing magnitude)
The conformational analyses for the nucleosides were
carried out based on parameters defined by Altona
and Sundaralingam15 and summarized by Saenger.16
Three parameters describe the primary features of the
conformation of a pyrimidine nucleoside: the glycosidic
bond torsion angle v (C2–N1–C10–O40 for pyrimidine,
or C2–N3–C10–O40 for furanopyrimidine)17 describes
the orientation of the base relative to the furanose ring;
the C40–C50 torsion angle c determines the orientation
of the 50-hydroxyl group relative to the furanose ring
Proton irradiated NOE (%)
H4
H200 (1.20), H30 (0.85), H50/H500 (0.72),
H100 (0.71)
H10
H20
H2 (3.83), H40 (0.73), H4 (0.54), H20 (0.24)
H200 (34.5), H30 (11.35), H4 (7.60),
H10 (2.33)
H200
H30
H20 (31.92), H10 (18.23), H30 (2.89),
H400 (1.60)
H2 (4.23), H50/H500 (3.21), H40 (3.04),
H200 (1.75), H4 (1.48)

N. Esho et al. / Bioorg. Med. Chem. 13 (2005) 1231–1238
1233
2.3. Crystallographic studies
Cyclic nucleoside 3b was crystallized from CHCl3/
CH3OH (layering) as colorless needles. The detailed
structure of 3b was established by X-ray crystallogra-
phy, as described in Table 4. Figure 2 shows the ORTEP
views of the molecule with the numbering scheme used
for analysis.17 Two crystallographically independent
molecules (A and B) have been found in the crystallo-
graphicasymmetricunit. Structures A and B are almost
identical in their geometry as evidenced by interatomic
distances and bond angles and by visualization of super-
imposed molecules. Selected bond lengths and angles are
summarized in Table 5, whereas all bond lengths, angles,
equivalent and anisotropicthermal parameters, and
hydrogen atom coordinates are given in the supporting
information.
A search of the CCDC database revealed few crystallo-
graphically characterized compounds with atom connec-
tivity relevant to the bicyclo furanopyrimidine motif.
Most of them embody a hydrogenated double bond of
the furan unit, thus are not congruent. When multiplic-
ity of the bond system is strictly taken into account, only
two recently reported structures remain pertinent. Struc-
tural features of the furanopyrimidine base (4),6a and
the entire nucleoside (3d),6b both ferrocene-substituted
at C6, were compared with our data for 3b.
Figure 1. A structure representing the proposed conformation of
compound 3a as depicted by 1D NOE interactions. Thicker/thinner
arrows represent stronger/weaker NOEs.
ation are in support of an anti-biased population be-
cause a weak NOE enhancement at H4 of 0.54% is ob-
served. A stronger NOE at H10 would have been
indicative of the syn conformation. The most significant
NOE interactions and the proposed conformation of
compound 3a are illustrated in Figure 1.
Table 4. Summary of crystallographic data for 3b
Molecular formula
Molecular weight
Crystal system
C22H22N2O7
426.42
Monoclinic
P21
The sugar puckers of a nucleoside most frequently adopt
either a C20-endo (S, or south) or C30-endo (N, or north)
conformation. The dominant sugar pucker can be iden-
Space group
Temperature of collection (K)
Cell dimensions [100(1) K]
100(1)
0
0
0
0
tified based on JH1 ÀH2 and JH3 ÀH4 coupling con-
stants.21 The percentages of C30-endo versus C20-endo
are calculated from the following equations: % C20-
˚
a, A
6.666(1)
12.225(1)
24.676(2)
90.00(1)
90.24(1)
90.00(1)
2010.9(4)
4
˚
b, A
˚
c, A
C30-endo =
0
0
0
0
0
0
endo = 100 · J1 ,2 /(J1 ,2 + J3 ,4 ), and
%
a, deg
b, deg
c, deg
100 À % C20-endo.21 The coupling constants observed
for compound 3a and its preferred sugar conformation
are illustrated in Tables 2 and 3. The preferred C20-endo
conformation measured at 20 and 37ꢀC implies that this
compound does not undergo a significant temperature-
dependent conformational change.
3
˚
V, A
Z
dcalc, g/cm3 (100(1) K)
Crystal dimensions, mm
Diffractometer
1.409
0.4 · 0.2 · 0.2
KUMA
KM4 CCD
MoKa
(0.71073 A)
x scan
12,736
Radiation k
Table 2. 20-Deoxyribose 1H–1H coupling constants for 3a at 20ꢀC
˚
Data collection method
Reflections measured
Range/indices (h, k, l)
Temp (ꢀC)
Coupling constants JH,H (Hz)
0
J1 ,2
0
0
J1 ,2
00
0
J2 ,3
0
00
J2 ,3
0
0
J3 ,4
0
0
J4 ,5
0
0
J4 ,5
00
À8, 7; À15,
16; À32, 31
3.43–28.44
8384
20
37
6.0
6.3
6.2
6.1
6.0
6.3
4.2
4.1
3.8
3.7
3.8
3.7
3.8
3.7
h limit, deg
Total no. of unique data
No. of observed data, I > 2r (I)
No. of variables
5854
566
Table 3. Percentage of C30-endo (N) versus C20-endo (S) conformer
and equilibrium constants (N/S) for nucleoside 3a at 20 and 37ꢀC
No. of restraints
Rint
1
0.0267
0.0720, 0.0437
R = RkFojÀjFck/RjFok (all, observed)
Temp (ꢀC)
% C30-endo (N)
% C20-endo (S)
Keq (N/S)
1=2
wR2 ¼ ðR½wðF 2o À F c Þ Š=Rw½F oŠÞ (all, observed) 0.0791, 0.0709
2
4
2
20
37
39
37
61
63
0.6
0.6
D/r (max)
Dq (max), e/A
0.275
0.217
3
˚

1234
N. Esho et al. / Bioorg. Med. Chem. 13 (2005) 1231–1238
O2
N1
C2
C7a
C12
O7
C6
C2'
C13
C14
O3'
C3'
N3
C4
C9'
C11
C16
C1'
O4'
C4a
C17
C6'
O6'
C4'
C15
C5
C5'
O5'
O7'
C7'
C8'
Figure 2. A view of the molecular structure of 3b with the crystallographical atom-labeling scheme. Displacement ellipsoids are drawn at 50%
probability level.
˚
Table 5. Selected bond lengths (A) and bond angles (deg) for molecules A and B of 3b, numbering used as for molecule A
O2–C2
O7–C6
1.236(3)
1.431(3)
1.360(3)
1.461(3)
1.420(2)
1.444(3)
1.445(3)
1.375(3)
1.310(3)
1.428(3)
1.363(3)
1.237(3)
1.427(3)
1.360(3)
1.457(3)
1.428(3)
1.445(3)
1.451(3)
1.380(3)
1.309(3)
1.426(3)
1.364(3)
N3–C10
C4–C4a
C4a–C5
C4a–C7a
C5–C6
1.483(3)
1.359(4)
1.448(3)
1.441(3)
1.346(3)
1.459(3)
1.517(3)
1.508(3)
1.529(3)
1.514(3)
1.484(3)
1.353(4)
1.439(5)
1.412(3)
1.352(3)
1.451(4)
1.519(3)
1.508(3)
1.533(3)
1.510(3)
O7–C7a
O30–C30
O40–C10
O40–C40
O50–C50
N1–C2
N1–C7a
N3–C2
N3–C4
C6–C11
C10–C20
C20–C30
C30–C40
C40–C50
O2–C2–N1
O2–C2–N3
O7–C6–C5
123.5(2)
118.7(3)
111.5(2)
114.6(2)
120.4(2)
110.4(2)
108.78(18)
110.9(2)
107.89(18)
106.60(18)
107.10(19)
109.55(19)
117.8(2)
129.2(3)
118.3(2)
113.1(2)
122.7(2)
118.9(2)
111.2(2)
114.8(2)
119.9(2)
110.4(2)
108.57(18)
111.0(2)
107.94(18)
106.50(19)
106.83(18)
109.49(19)
118.3(2)
129.6(3)
118.4(2)
113.2(2)
C2–N1–C7a
C2–N3–C4
115.6(2)
123.7(2)
114.39(19)
121.9(2)
138.3(2)
115.3(2)
106.4(2)
134.0(2)
105.52(18)
106.3(2)
121.2(2)
120.4(2)
110.24(17)
104.5(2)
104.7(2)
113.0(2)
114.8(2)
123.4(2)
114.5(2)
122.0(2)
138.4(2)
115.3(2)
106.3(2)
134.0(2)
105.59(18)
106.5(2)
120.9(2)
120.5(2)
110.36(17)
104.42(19)
105.1(2)
113.4(2)
C2–N3–C10
C4–N3–C10
C4–C4a–C5
C4–C4a–C7a
C5–C4a–C7a
C5–C6–C11
C6–O7–C7a
C6–C5–C4a
C6–C11–C12
C6–C11–C16
C10–O40–C40
C10–C20–C30
C20–C30–C40
C30–C40–C50
O7–C6–C11
O7–C7a–N1
O7–C7a–C4a
O30–C30–C20
O30–C30–C40
O40–C10–N3
O40–C10–C20
O40–C40–C30
O4–C40–C50
N1–C2–N3
N1–C7a–C4a
N3–C4–C4a
N3–C10–C20
The 20-deoxyribose ring in 3b crystallizes in the C20-endo
conformation, dominant for the 20-deoxyribose series,
with the pseudorotational phase angle P = 150.4/150.8ꢀ
(for molecules A and B, average 150.6ꢀ),22 thus locating
u = 76.1(3)ꢀ and q = 0.361(2) and u = 94.4(3)ꢀ for
(O10/O10A)23 rings, respectively.
The ribose–base distance, C10–N3, is the same for crys-
tallographically characterized furanopyrimidine nucleo-
2
2
the conformation as T1 between twist T and envelope
1
2E. By comparison, the furanose rings in 3d, adopt a rel-
atively close conformation with P = 186.0/193.5ꢀ (aver-
sides (1.483(3)/1.484(3) A of both molecules for 3b and
˚
˚
1.478(3)/1.479(2) A for 3d). Similar to 3a in solution
age 189.8ꢀ, T2 conformation) for (O10/O10A)23 rings;
and 3d in the crystalline state, the C2 carbonyl group
of 3b adopted an anti orientation toward the ribose ring:
the glycosidic bond torsion angle v (O40-C10–N3–C2) is
À161.8(2)/À162.2(2)ꢀ (À148.0/À155.4ꢀ for 3d). The fura-
nopyrimidine is planar in both independent molecules of
3b. The atoms most distorted from planarity are N3
3
a very minor contribution of C30-exo can be noticed.
The ring-puckering Cremer and Pople24 parameters are
q = 0.252(2) and u = 63.3(3)ꢀ and q = 0.251(2) and
u = 62.8(5)ꢀ for the rings of A/B molecules of 3b. The
same parameters calculated for two crystallographically
independent molecules of 3d are q = 0.363(2) and
˚
(0.026/0.024A). For comparison, the most displaced

N. Esho et al. / Bioorg. Med. Chem. 13 (2005) 1231–1238
1235
atom in 4 is C2(C23)23 0.030A. Structure 3d combines
dines 3a/b exhibited a strong purple luminescence on
TLC plates in UV light (254nm); a more detailed char-
acterization was also undertaken because fluorescent
nucleosides have practical applications. An emission
spectrum for 3a is shown in Figure 3. The wavelength
of the observed emission peak (430nm, 3a) did not vary
with excitation wavelength (kex 290 and 375nm), and
was slightly shifted to the red by comparison to the alky-
nyl precursor 2a (401nm, data not shown).14
˚
these features—the most displaced atoms are C2 (0.043
23
˚
A) and, in the second molecule, N3(N1a) (0.043A).
˚
The p-tolyl group is bound directly to the furanopyrimi-
˚
dine through a C6–C11 linkage 1.459(3)/1.451(4) A
with a slightly larger distance than the cyclopentadienyl
ring of the ferrocene substituent in 3d/4. The length of
the newly formed double bond (C5–C6) is in a typical
˚
C@C bond range (1.346(3)/1.352(3) A), similar to the
ferrocene nucleoside 3d, but shorter than for
˚
4
(1.340(3)/1.340(3) and 1.379(8) A, respectively). The
base carbon–oxygen bond lengths (C2–O2 and C7a–
3. Conclusions
˚
O7, 1.236(3)/1.237(3) and 1.360(3)/1.360(3) A) indicate
similar double- and single-bond character as observed
in 3d and 4 (1.227(3)/1.231(3) and 1.224(7), and
In summary, we have established the conformations of
an antiviral-active furanopyrimidine nucleoside by
NOE NMR spectroscopy and X-ray crystallography.
The solid state structure of the p-tolyl-substituted fura-
nopyrimidine nucleoside 3b is similar to the dominant
solution conformation of nonacylated 3a, and resembles
the ferrocene furanopyrimidine nucleoside 3d. The base
in both 3b and 3d is in the anti position, and the deoxy-
ribose ring is in the C20-endo conformation (a minor
C30-exo conformation for 3d). The aromaticrings of
the p-tolyl and ferrocene substituents (3b and 3d) lie
almost in the same plane as the bicyclic base.
˚
1.350(2)/1.355(2) and 1.355(7) A). The p-tolyl aromatic
ring lies almost in the same plane as the bicyclic base;
the dihedral angle C5–C6–C11–C16 is 8.9(4)/7.8(4)ꢀ.
When considering the whole plane, the p-tolyl ring is
twisted by 10.1/10.0ꢀ from the plane of the furanopyrimi-
dine. When viewing the structure from the p-tolyl group
toward the sugar, two subsequent slight twists between
planes of the p-tolyl, the bicyclic base, and the
C10–O40 bond are directed R (plus). The plane of the
attached cyclopentadienyl each twist in opposite direc-
tions, for the two independent molecules of 3d, by
10.3/14.3ꢀ (in 4 by 7.6ꢀ). This small difference is likely
attributed to packing forces. The C50–O50 bond is ap
to the C40–C30 bond, which can be visualized by the
O50–C50–C40–C30 torsion angle c = 179.4(2)/179.3(2)ꢀ
(A/B). By comparison, the free hydroxyl group of 3d
adopts a different conformation in which the c angle
differs by ca. 115ꢀ for the two crystallographically indepe-
ndent molecules (69.8/60.9ꢀ).6b Packing diagrams and
discussion are given in the Supplementary data.
4. Experimental section
4.1. General
Commercial chemicals were treated as follows: DMF,
distilled from CaH2 and degassed (freeze and thaw)
three times prior to use; Et3N, distilled from P2O5;
THF, distilled from Na/benzophenone; (CH3CO)2O,
distilled prior to use. 5-Iodo-20-deoxyuridine (Berry &
Associates), 4-ethynyltoluene (GFS, Lancaster), tetra-
kis(triphenylphosphine)palladium(0) and CuI 99.999%
(Aldrich), silica gel (J.T. Baker, 60–200 mesh), TLC
plates (Analtech GF, cat. number 2521 or Merck 60,
cat. number 5715), used as received. Other materials
not listed were used as received. Progress of the reac-
tions was monitored by TLC.
The electronic absorption spectrum for 3a was com-
pared to the uncyclized alkynyl uridine 2a (Fig. 3). As
expected, the absorption maxima shift to longer wave-
lengths for the fused cyclic systems, as compared to
the parent alkynyl uridine. The molar absorptivity for
3a reaches 22,000MÀ1 cmÀ1 (281nm). Furanopyrimi-
UV–visible spectra were recorded on a Cary 50 spec-
trometer. Fluorescence measurements were carried out
on an Amico-Bowman Series 2 Luminescence Spectro-
meter, cells 1 and 3mL, bandwidths of 4nm each,
PMT 650V (24ꢀC). NMR spectra were obtained on
Varian Unity 500, Mercury 400, or Bruker Avance 200
1
spectrometers. The H and 13C NMR chemical shifts
are in d and ppm, respectively, and J values are in Hz.
4.2. 3-(20-Deoxy-b-D-ribofuranosyl)-6-(4-methylphenyl)-
2,3-dihydrofuro[2,3-d]pyrimidin-2-one (3a)8a
A Schlenk flask was charged with 5-iodo-20-deoxyuri-
dine 1a (1.002g, 2.830mmol), Pd(PPh3)4 (0.654g,
0.566mmol), DMF (10mL), Et3N (0.80mL, 5.7mmol),
4-ethynyltoluene (0.82mL, 6.5mmol), and CuI
(0.054g, 0.28mmol). The mixture was stirred for 5h at
80ꢀC. TLC showed complete conversion of the sub-
strate. The solid was filtered off, the solvent removed
Figure 3. UV–vis and fluorescence (kex 290nm) spectra of 3a and
comparison to the UV–vis spectrum of 2a (CH3OH).

1236
N. Esho et al. / Bioorg. Med. Chem. 13 (2005) 1231–1238
from the filtrate (by oil pump vacuum), and the residue
kept under an oil pump vacuum for 2h. The solid was
dissolved in CHCl3 (10mL) and kept at À15ꢀC (freezer)
for 24h. The solid was filtered off, washed with CHCl3
three times, and dried by oil pump vacuum to give 3a
as a white powder (0.687g, 2.01mmol, 71%). UV–vis
90%], 449 [(M+Na)+, 33%], 427 [(M+H)+, 10%]; no
other peaks above 250 of >5%.
NMR (CDCl3): 1H (500MHz) 8.27 (s, 1H, H4), 7.66 (d,
J = 8.0, 1H, m-C6H4CH3),28 7.23 (d, J = 8.0, 2H, o-
C6H4CH3),28 6.67 (s, 1H, H5), 6.34 (dd, J = 6.0, 1.5,
1H, H10), 5.24 (q, J = 2.0, 1H, H30), 4.45–4.40 (m, 3H,
H40, H50), 2.98 (ddd, J = 14.3, 5.5, 2.8, 1H, H20), 2.40
(s, 3H, C6H4CH3), 2.12 (s, 3H, COCH3), 2.13–2.09 (m,
1H, H20), 2.08 (s, 3H, COCH3). 13C (ppm, 50MHz)
172.0 (C7a), 170.7 and 170.5 (2 COCH3), 156.6 (br s
C6), 154.7 (C2), 140.4 (i-C6H4CH3), 134.4 (d,
J = 184.9, C4), 129.9 (d, J = 158.2, m-C6H4CH3), 125.7
(p-C6H4CH3), 125.2 (br d, J = 156.4, o-C6H4CH3),
108.7 (C4a), 96.8 (d, J = 180.2, C5), 88.8 (d, J = 175.3,
C10),25 83.5 (d, J = 152.1, C40),25 74.3 (d, J = 158.2,
C30), 63.9 (t, J = 148.7, C50), 39.5 (dd, J = 139.7,
132.8, C20), 21.7 (q, J = 126.8, C6H4CH3), 21.1 (q,
J = 130.0, 2 COCH3).
(CH3OH, 4.1 · 10À5 M; nm,
e
(MÀ1 cmÀ1)) 351
(17,000), 282 (22,000). Fluorescence (CH3OH, 6 ·
10À6 M; nm) kex 290/375, kem 430/430. NMR data
matched those reported earlier.8a
4.3. 30,50-Di-O-acetyl-5-iodo-20-deoxyuridine (1b)13,14
A round bottom flask was charged with 5-iodo-20-deoxy-
uridine 1a (1.000g, 2.824mmol), pyridine (15mL), and
(CH3CO)2O (3.0mL, 32mmol). The reaction was stirred
for 16h. The solvent was removed by rotary evapora-
tion. The residue was co-evaporated with benzene/
CH2Cl2 (10/10mL), and CH2Cl2 (2 · 10mL). The resi-
due was dissolved in CH2Cl2 (250mL), and washed with
NaHCO3 (0.5M, 4 · 50mL). The organicphase was
dried over Na2SO4 and filtered. Solvent was removed
by rotary evaporation. Ethanol (ca. 1.5mL) was added
and the mixture (precipitate) was kept at À20ꢀC (free-
zer) for 24h. A white powder was collected by filtration
and dried on an oil vacuum pump to give 1b (1.085g,
2.476mmol, 88%).
4.5. NOE studies
NMR data were acquired on a Varian Unity 500MHz
spectrometer. The sealed sample was prepared in a
drybox in anhydrous DMSO-d6. Each proton listed in
Table 1 was irradiated for 1D NOE difference spectros-
copy and resonances were acquired.
1
NMR (CDCl3): H (200MHz) 8.92 (br s, 1H, N3), 7.98
(s, 1H, H6), 6.30 (dd, J = 8.2, 5.7, 1H, H10), 5.26 (dt,
J = 6.5, 2.1, 1H, H30), 4.40 and 4.37 (2d, J = 3.0 and
2.8, 2H, H50), 4.33–4.28 (m, 1H, H40), 2.56 (ddd,
J = 14.3, 5.7, 2.0 1H, H20), 2.25–2.10 (m, 1H, H20),
2.22 and 2.13 (2s, 2 · 3H, 2 COCH3); 13C (50 MHz)
170.4 and 170.3 (2 COCH3), 160.0 (d, J = 9.6, C4),
150.1 (d, J = 7.7, C2), 143.9 (dd, J = 184.9, 3.0, C6),
85.7 (dm, J = 171.6, C10),25 82.5 (dm, J = 151.7, C40),25
74.2 (dm, J = 158.3, C30), 69.2 (d, J = 4.9, C5), 64.0 (t,
J = 149.1, C50), 38.5 (dd, J = 138.5, 132.2, C20), 21.3
(q, J = 129.9, COCH3), 21.1 (q, J = 130.1, COCH3).
4.6. Crystallography
Colorless needles of 3b were grown by solvent diffusion
(layering) of a CHCl3 solution with MeOH (12 days).
Data were collected as outlined in Table 4 using a
KUMA KM4 CCD diffractometer equipped with an
Oxford Cryosystem–Cryostream cooler. Cell parameters
(100(1) K) were obtained from 3820 reflections with
3.43ꢀ < h < 28.44ꢀ. The space group was determined
from systematicabsences and subsequent least-squares
refinement. One frame checked every 50 frames showed
no crystal decay. Lorentz and polarization corrections
were applied. The structure was solved by direct tech-
niques with SHELXS and refined by full-matrix-least-
squares on F2 using SHELXL-97.29 Nonhydrogen atoms
were refined with anisotropicthermal parameters. Hydro-
gen atom positions were calculated and added to the
structure factor calculations, but were not refined. Scat-
tering factors, and D f0 and Df00 values, were taken from
the literature.30 Flack parameter for 3b was 0.5(7).31
4.4. 30,50-Di-O-acetyl-3-(20-deoxy-b-D-ribofuranosyl)-6-
(4-methylphenyl)-2,3-dihydrofuro[2,3-d]pyrimidin-2-one
(3b)26
A Schlenk flask was charged with 30,50-di-O-acetyl-5-
iodo-20-deoxyuridine 1b (0.389g, 0.888mmol), 4-ethy-
nyltoluene (0.17mL, 1.3mmol), triethylamine (0.22mL,
1.6mmol), DMF (10mL), Pd(PPh3)4 (0.102g,
0.0883mmol), and CuI (0.079g, 0.41mmol). The mixture
was stirred at 80ꢀC for 3h. DMF was removed by oil
pump vacuum (water bath) and the residue was co-evap-
orated with CH3OH (10mL). The residue was dissolved
in CHCl3/CH3OH (80:20) and filtered over a silica gel
column (15 · 2cm). The solvent was removed by rotary
evaporation. Silica gel column chromatography (hex-
ane/EtOAcgradient, 80:20 ! 65:35 ! 50:50, 35 · 2cm)
gave a white powder that was dried under oil pump
vacuum. Recrystallization from CHCl3/CH3OH (layer-
ing) gave 3b (0.221g, 0.518mmol, 58%). MS27 (ES+,
KOAc, MeOH, calcd for C22H22N2O7 426.1) 891
[(2M+K)+, 100%], 875 [(2M+Na)+, 35%], 853
[(2M+H)+, 11%], 500 (unassigned, 30%), 465 [(M+K)+,
Data for 3b (excluding structure factors) have been
deposited with the Cambridge CrystallographicData
Centre as supplementary publication CCDC-249882.
Copies of this information can be obtained free upon
application to CCDC, 12 Union Road, Cambridge
CB2 1EZ, UK. Fax: (internat.) + 44-1223/336-033;
E-mail deposit@ccdc.cam.ac.uk.
Acknowledgements
We thank the Oakland University, Research Excellence
Program in Biotechnology, NIH (grants CA111329 and

N. Esho et al. / Bioorg. Med. Chem. 13 (2005) 1231–1238
1237
Synlett 2004, 2406–2408; (c) NIS/NBS halocyclization:
Rao, M. S.; Esho, N.; Sergeant, C.; Dembinski, R. J. Org.
Chem. 2003, 68, 6788–6790.
GM054632), and Polish State Committee for Scientific
Research (grant 4 T09A14824) for support of this re-
search. NATO (grant PST.CLG.977371) is acknowl-
edged for a travel award. We are also grateful to Dr.
B. Ksebati for NMR assistance, S. Grossman and Prof.
E. Sochacka for helpful discussions.
8. (a) McGuigan, C.; Barucki, H.; Blewett, S.; Carangio, A.;
Erichsen, J. T.; Andrei, G.; Snoeck, R.; De Clercq, E.;
Balzarini, J. J. Med. Chem. 2000, 43, 4993–4997; (b)
Brancale, A.; McGuigan, C.; Andrei, G.; Snoeck, R.; De
Clercq, E.; Balzarini, J. Bioorg. Med. Chem. Lett. 2000, 10,
1215–1217; (c) McGuigan, C.; Yarnold, C. J.; Jones, G.;
Supplementary data
´
Velazquez, S.; Barucki, H.; Brancale, A.; Andrei, G.;
Snoeck, R.; De Clercq, E.; Balzarini, J. J. Med. Chem.
1999, 42, 4479–4484; (d) Srinivasan, S.; McGuigan, C.;
Andrei, G.; Snoeck, R.; De Clercq, E.; Balzarini, J.
Nucleosides, Nucleotides, Nucleic Acids 2001, 20, 763–766;
(e) Bidet, O.; McGuigan, C.; Andrei, G.; Snoeck, R.; De
Clercq, E.; Balzarini, J. Nucleosides, Nucleotides, Nucleic
Acids 2003, 22, 817–819; (f) McGuigan, C.; Brancale, A.;
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Med. Chem. Lett. 2003, 13, 4511–4513; (g) McGuigan, C.;
Carangio, A.; Snoeck, R.; Andrei, G.; De Clercq, E.;
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23, 1–5; (h) McGuigan, C.; Pathirana, R. N.; Snoeck, R.;
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Supplementary data associated with this article can
be found, in the online version, at doi:10.1016/j.bmc.
2004.11.013. Information available: NMR spectra for
compounds 3a,b, interatomicdistanecs, bond angles,
coordinates and thermal parameters, packing discussion
and diagram for compound 3b; crystallographic data are
also available as cif file.
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13
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