2′-Deoxy­immunosine: a thia­zolo[4,5-d]pyrimidine nucleoside adopting the syn conformation

The title compound [systematic name: 5-amino-3-(2-deoxy-β-D-erythro-pento­furanosyl)thia­zolo[4,5-d]pyrimidine-2,7-(3H,6H)-dione], C₁₀H₁₂N₄O₅S, exhibits a syn glycosylic bond conformation, with a torsion angle χ of 61.0 (3)°. The furan­ose moiety adopts the N-type sugar pucker (³T₄), with P = 33.0 (5)° and τ_m = 15.1 (1)°. The conformation at the exocyclic C4′—C5′ bond is +ap (trans), with the torsion angle γ = 176.71 (14)°. The extended structure is a three-dimensional hydrogen-bond network involving O—H...O and N—H...O hydrogen bonds.

S1. Comment

The development of clinically useful agents that restore and enhance the ability of the human immune system to ward off infection or other invasion challenges has become a major objective of current pharmaceutical research efforts. The AIDS epidemic and the need for adjuvant therapy to boost the immune system of the elderly and cancer patients has brought this area of immunopotentiation into sharp focus (Hadden, 1987, 1993; St Georgiev, 1990; Failli & Caggiano, 1992; Werner, 1990). Many different types of compounds have been demonstrated to possess immunostimulatory properties. Among them, the nucleoside-based guanosine derivatives are very promising (Reitz et al., 1994). In this context, 7-deazaguanosine and 7-allyl-8-oxoguanosine (loxoribine) have been extensively studied (References?) (purine numbering is used throughout this paper). Another guanosine analogue, 8-oxo-7-thiaguanosine [(IIb); immunosine, isatoribine, TOG] has been investigated in great detail and shown to possess excellent in vivo activity against a variety of DNA and RNA viruses (Nagahara et al., 1990; Smee et al., 1989; Smee, Alaghamandan, Bartlett & Robins 1990; Smee, Alaghamandan, Cottam et al., 1990). Immunosine exhibits a stimulatory effect on both cellular and humoral components of the immune response. The observed antiviral effect has been attributed primarily to the induction of α-interferon (Smee, Alaghamandan, Bartlett & Robins 1990; Smee, Alaghamandan, Cottam et al., 1990). Recently, it was found that immunosine and other guanosine analogues activates immune cells via the Toll-like receptor 7 (TLR7; Lee et al., 2003). Immunosine has also been reported to be effective at reducing the plasma virus concentration in patients with chronic hepatitis C virus (HCV) infections, with minimal side effects (Horsmans et al., 2005).

While immunosine can be readily prepared by glycosylation of the immunosine base, the synthesis of the corresponding title 2'-deoxyribonucleoside analogue, (I), encountered difficulties (Seela et al., 2007). We have developed a stereoselective synthesis for compound (I) and have incorporated this compound into oligonucleotides. The replacement of two dG residues by 2'-deoxyimmunosine within a DNA duplex resulted in the same stability as observed for the unmodified parent duplex (T_m = 323 K; Seela et al., 2007). This shows that 2'-deoxyimmunosine forms a stable base pair with 2'-deoxycytidine (Seela et al., 2007). However, compound (I) does not show the base pairing ambiguity observed for 2'-deoxy-8-oxoguanosine, (III) (Oka & Greenberg, 2005). From this context, we became interested in undertaking a single-crystal X-ray analysis of compound (I). Slow crystallization from ethanol afforded compound (I) as colourless crystals. The three-dimensional structure of (I) is shown in Fig. 1, and selected geometric parameters are listed in Table 1.

The orientation of the nucleobase relative to the sugar moiety (syn/anti) of purine nucleosides is defined by the torsion angle χ (O4'—C1'—N9—C4; IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983). The natural 2'-deoxyribonucleosides usually adopt an anti conformation. In contrast, from the crystal structure of (I), the glycosylic bond torsion angle is determined to be in the syn range, with a χ value of 61.0 (3)°. It is generally observed that the introduction of bulky substitutents at position-8 of the purine moiety switches the preference of the glycosylic torsion angle from anti to syn (Uesugi & Ikehara, 1977; Lipscomb et al., 1995). This conversion arises from steric repulsion between the 8-substituent and the 2'-deoxyribose. For the related compound, (IIa), a syn conformation of the glycosylic bond has also been reported [O4'—C1'—N9—C8 = -120.0 (2)°; Nagahara et al., 1990]. In contrast, in the crystal structure of a DNA duplex, the glycosylic bond torsion angle of compound (III) is in the anti conformation, with χ = -53.0°, when paired with 2'-deoxycytidine (Lipscomb et al., 1995). The length of the N9—C1' glycosidic bond of (I) is 1.477 (2) Å, which is longer than that of compound (IIa) [1.458 (3) Å; Nagahara et al., 1990].

The sugar moiety of nucleoside (I) shows a pseudorotation phase angle P of 33.0 (5)° with a maximum amplitude of puckering τ_m of 15.1 (1)°, which indicates a north (N) conformation (3'-endo–4'-exo, ³T₄; Rao et al., 1981). In contrast, the sugar moiety of the related compound, (IIa), adopts a south (S) conformation (2'-endo–1'-exo, ²T₁) (Nagahara et al., 1990). The torsion angle γ (O5'—C5'—C4'—C3') characterizes the orientation of the exocyclic 5'-hydroxyl group relative to the 2'-deoxyribose ring. In the crystal structure of compound (I), γ is 176.71 (14)°. This value shows that the C4'—C5' bond is in an antiperiplanar (+ap, trans) orientation. For compound (IIa), the exocyclic C4'—C5' bond adopts a synclinal (+gauche) orientation, with γ = 53.7 (2)°.

The thiazolopyrimidine ring of (I) is nearly planar; the r.m.s. deviation of the ring atoms from their calculated least-squares planes is 0.033 Å, with a maximum deviation of -0.051 (2) Å for atom C8. The exocyclic amino and oxo groups are almost coplanar with the heterocyclic ring system. Atom C1' of the sugar moiety deviates from the plane by 0.358 (3) Å. The S7—C8 and S7—C5 bond lengths are 1.765 (2) Å and 1.743 (2) Å, which are very similar to the corresponding bond lengths in the related compound (IIa) [S7—C8 = 1.764 (3) Å and S7—C5 = 1.737 (3) Å; Nagahara et al., 1990].

The structure of nucleoside (I) is stabilized by several intermolecular hydrogen bonds, leading to the formation of layered sheets (Table 2 and Fig. 2). Within the three-dimensional network, the nucleobases are arranged head-to-head and are stacked. Hydrogen bonds are mainly formed between adjacent nucleobases and sugar moieties (N1—H1···O3', N2—H2A···O5', O3'—H3'B···O6 and O5'—H5'C···O6). One further hydrogen bond is formed between neighbouring nucleobases (N2—H2B···O8). The hydrogen bonds N1—H1···O3' and N2—H2B···O8 are formed within each sheet, while the other three hydrogen bonds (N2—H2A···O5', O3'—H3'B···O6, O5'—H5'C···O6) connect neighbouring sheets. In contrast with other compounds showing a syn conformation of the glycosylic bond, such as (IIa) (Nagahara et al., 1990), no intramolecular O5'—H5'···N3 hydrogen bond was found for the crystal structure of (I).

Related literature

For related literature, see: Failli & Caggiano (1992); Flack (1983); Hadden (1987, 1993); Horsmans et al. (2005); IUPAC–IUB (1983); Lee et al. (2003); Lipscomb et al. (1995); Nagahara et al. (1990); Oka & Greenberg (2005); Rao et al. (1981); Reitz et al. (1994); Seela & Ming (2007); Sheldrick (1997); Smee et al. (1989); Smee, Alaghamandan, Bartlett & Robins (1990); Smee, Alaghamandan, Cottam, Jolley & Robins (1990); St (1990); Uesugi & Ikehara (1977); Werner (1990).

S2. Experimental

Compound (I) was synthesized by the stereoselective glycosylation of the protected immunosine base with the 2'-deoxyribose halide (Seela et al., 2007) and was crystallized from ethanol as colourless needles [m.p. 451 K (decomposition)]. For the X-ray diffraction experiment, a single-crystal was fixed at the top of a Lindemann capillary with epoxy resin.

S3. Refinement

The absolute configuration of (I) results from the Flack parameter (Flack, 1983), but also from the defined configuration of the sugar halide used in the glycosylation reaction. All H atoms were found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms were placed in geometrically idealized positions, with C—H = 0.93–0.98 Å and N—H = 0.86 Å (AFIX 93 for N2 and AFIX 43 for N1 in SHELXTL; Sheldrick, 1997), and constrained to ride on their parent atoms, with U_iso(H) = 1.2U_eq(C) = U_eq(N). The OH groups were refined as rigid groups allowed to rotate but not tip (AFIX 147), with O—H = 0.82 Å and U_iso(H) = 1.5U_eq(O).

Computing details

Data collection: XSCANS (Siemens, 1996); cell refinement: XSCANS; data reduction: SHELXTL (Sheldrick, 1997); program(s) used to solve structure: SHELXTL; program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003).

Figures

	Fig. 1. A perspective view of nucleoside (I), showing the atomic purine numbering. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as spheres of arbitrary size.
	Fig. 2. The crystal packing of (I), viewed down the a axis, showing the intermolecular hydrogen-bonding network.

5-amino-3-(2-deoxy-β-D-erythro-pentofuranosyl)thiazolo[4,5-d]pyrimidine- 2,7-(3H,6H)-dione

Crystal data

C10H12N4O5S	Z = 1
Mr = 300.30	F(000) = 156
Triclinic, P1	Dx = 1.628 Mg m^−3
Hall symbol: P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.2347 (10) Å	Cell parameters from 34 reflections
b = 7.1855 (13) Å	θ = 4.9–18.1°
c = 8.9972 (16) Å	µ = 0.29 mm^−1
α = 110.756 (12)°	T = 293 K
β = 96.827 (13)°	Needle, colourless
γ = 99.511 (19)°	0.4 × 0.2 × 0.2 mm
V = 306.28 (10) Å^3

Data collection

Bruker P4 diffractometer	Rint = 0.000
Radiation source: fine-focus sealed tube	θmax = 29.0°, θmin = 2.5°
Graphite monochromator	h = −1→7
ω/2θ scans	k = −9→9
2042 measured reflections	l = −12→12
2042 independent reflections	3 standard reflections every 97 reflections
2029 reflections with I > 2σ(I)	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.027	H-atom parameters constrained
wR(F^2) = 0.073	w = 1/[σ^2(Fo^2) + (0.0413P)^2 + 0.048P] where P = (Fo^2 + 2Fc^2)/3
S = 1.07	(Δ/σ)max < 0.001
2042 reflections	Δρmax = 0.20 e Å^−3
184 parameters	Δρmin = −0.20 e Å^−3
3 restraints	Absolute structure: Flack (1983), with 427 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.04 (6)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
N1	0.0028 (3)	0.6645 (2)	0.65633 (18)	0.0270 (3)
H1	−0.0476	0.7747	0.7051	0.032*
C2	−0.1082 (4)	0.5522 (3)	0.4954 (2)	0.0281 (3)
N2	−0.2894 (5)	0.6200 (3)	0.4258 (2)	0.0456 (5)
H2A	−0.3616	0.5540	0.3255	0.055*
H2B	−0.3347	0.7300	0.4811	0.055*
N3	−0.0390 (4)	0.3829 (2)	0.40988 (17)	0.0290 (3)
C4	0.1406 (4)	0.3251 (3)	0.49086 (19)	0.0250 (3)
C5	0.2539 (4)	0.4238 (3)	0.6543 (2)	0.0269 (3)
C6	0.1909 (4)	0.6087 (3)	0.74294 (19)	0.0246 (3)
O6	0.2899 (3)	0.7252 (2)	0.88699 (16)	0.0319 (3)
S7	0.48417 (9)	0.30299 (7)	0.71566 (5)	0.03588 (13)
C8	0.4317 (5)	0.1212 (3)	0.5157 (2)	0.0357 (4)
O8	0.5498 (5)	−0.0146 (3)	0.4733 (2)	0.0581 (6)
N9	0.2387 (4)	0.1560 (2)	0.41503 (17)	0.0289 (3)
C1'	0.2037 (4)	0.0499 (3)	0.2378 (2)	0.0278 (3)
H1'	0.2969	−0.0617	0.2153	0.033*
C2'	−0.0819 (4)	−0.0368 (3)	0.1456 (2)	0.0314 (4)
H2'A	−0.2032	−0.0206	0.2205	0.038*
H2'B	−0.1085	−0.1807	0.0793	0.038*
C3'	−0.1261 (4)	0.0858 (3)	0.0391 (2)	0.0274 (3)
H3'A	−0.2358	0.1821	0.0841	0.033*
O3'	−0.2388 (3)	−0.0390 (2)	−0.12679 (16)	0.0363 (3)
H3'B	−0.3895	−0.0996	−0.1333	0.054*
C4'	0.1499 (4)	0.2016 (3)	0.0462 (2)	0.0269 (3)
H4'	0.2085	0.1350	−0.0552	0.032*
O4'	0.3240 (3)	0.1932 (2)	0.17853 (16)	0.0322 (3)
C5'	0.1611 (5)	0.4230 (3)	0.0732 (3)	0.0359 (4)
H5'A	0.0492	0.4315	−0.0170	0.043*
H5'B	0.0964	0.4885	0.1711	0.043*
O5'	0.4255 (4)	0.5249 (3)	0.08783 (19)	0.0436 (4)
H5'C	0.4257	0.6088	0.0454	0.065*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0327 (8)	0.0205 (6)	0.0250 (6)	0.0130 (6)	0.0034 (6)	0.0029 (5)
C2	0.0295 (8)	0.0257 (7)	0.0262 (7)	0.0106 (7)	0.0021 (7)	0.0055 (6)
N2	0.0544 (12)	0.0397 (9)	0.0337 (8)	0.0304 (9)	−0.0081 (8)	0.0000 (6)
N3	0.0333 (8)	0.0279 (7)	0.0235 (6)	0.0146 (6)	0.0017 (6)	0.0049 (5)
C4	0.0286 (8)	0.0230 (7)	0.0241 (7)	0.0113 (7)	0.0070 (7)	0.0067 (6)
C5	0.0299 (8)	0.0296 (7)	0.0239 (7)	0.0155 (7)	0.0039 (6)	0.0099 (6)
C6	0.0257 (8)	0.0240 (7)	0.0237 (7)	0.0062 (6)	0.0051 (6)	0.0083 (6)
O6	0.0366 (7)	0.0292 (6)	0.0236 (5)	0.0082 (6)	0.0008 (5)	0.0037 (4)
S7	0.0439 (3)	0.0430 (2)	0.02657 (18)	0.0262 (2)	0.00454 (17)	0.01356 (16)
C8	0.0485 (12)	0.0371 (9)	0.0288 (8)	0.0261 (9)	0.0099 (8)	0.0132 (7)
O8	0.0879 (16)	0.0580 (10)	0.0428 (9)	0.0571 (12)	0.0123 (9)	0.0182 (8)
N9	0.0379 (8)	0.0273 (7)	0.0243 (6)	0.0182 (7)	0.0077 (6)	0.0077 (5)
C1'	0.0346 (9)	0.0237 (7)	0.0245 (7)	0.0118 (7)	0.0085 (7)	0.0053 (6)
C2'	0.0352 (10)	0.0259 (8)	0.0290 (7)	0.0031 (7)	0.0085 (7)	0.0067 (6)
C3'	0.0246 (8)	0.0272 (7)	0.0240 (7)	0.0051 (7)	0.0051 (6)	0.0026 (6)
O3'	0.0299 (7)	0.0391 (7)	0.0267 (6)	0.0025 (6)	0.0006 (5)	0.0010 (5)
C4'	0.0263 (8)	0.0280 (7)	0.0237 (7)	0.0052 (7)	0.0044 (6)	0.0070 (6)
O4'	0.0257 (6)	0.0398 (7)	0.0311 (6)	0.0033 (6)	0.0023 (5)	0.0163 (5)
C5'	0.0376 (11)	0.0316 (9)	0.0383 (9)	0.0041 (8)	0.0050 (8)	0.0154 (7)
O5'	0.0421 (9)	0.0425 (8)	0.0426 (7)	−0.0070 (7)	−0.0034 (7)	0.0230 (6)

Geometric parameters (Å, º)

N1—C2	1.379 (2)	C1'—O4'	1.413 (2)
N1—C6	1.381 (2)	C1'—C2'	1.530 (3)
N1—H1	0.8600	C1'—H1'	0.9800
C2—N3	1.323 (2)	C2'—C3'	1.536 (3)
C2—N2	1.325 (3)	C2'—H2'A	0.9700
N2—H2A	0.8600	C2'—H2'B	0.9700
N2—H2B	0.8600	C3'—O3'	1.4308 (19)
N3—C4	1.330 (2)	C3'—C4'	1.525 (3)
C4—N9	1.381 (2)	C3'—H3'A	0.9800
C4—C5	1.390 (2)	O3'—H3'B	0.8200
C5—C6	1.402 (3)	C4'—O4'	1.436 (2)
C5—S7	1.743 (2)	C4'—C5'	1.511 (3)
C6—O6	1.256 (2)	C4'—H4'	0.9800
S7—C8	1.765 (2)	C5'—O5'	1.422 (3)
C8—O8	1.213 (3)	C5'—H5'A	0.9700
C8—N9	1.389 (3)	C5'—H5'B	0.9700
N9—C1'	1.477 (2)	O5'—H5'C	0.8200
C2—N1—C6	123.23 (15)	N9—C1'—H1'	108.6
C2—N1—H1	118.4	C2'—C1'—H1'	108.6
C6—N1—H1	118.4	C1'—C2'—C3'	105.80 (15)
N3—C2—N2	119.79 (17)	C1'—C2'—H2'A	110.6
N3—C2—N1	122.54 (17)	C3'—C2'—H2'A	110.6
N2—C2—N1	117.67 (17)	C1'—C2'—H2'B	110.6
C2—N2—H2A	120.0	C3'—C2'—H2'B	110.6
C2—N2—H2B	120.0	H2'A—C2'—H2'B	108.7
H2A—N2—H2B	120.0	O3'—C3'—C4'	108.09 (14)
C2—N3—C4	115.40 (15)	O3'—C3'—C2'	113.65 (15)
N3—C4—N9	121.50 (15)	C4'—C3'—C2'	104.54 (15)
N3—C4—C5	125.84 (16)	O3'—C3'—H3'A	110.1
N9—C4—C5	112.64 (16)	C4'—C3'—H3'A	110.1
C4—C5—C6	118.72 (16)	C2'—C3'—H3'A	110.1
C4—C5—S7	112.27 (14)	C3'—O3'—H3'B	109.5
C6—C5—S7	128.76 (14)	O4'—C4'—C5'	108.60 (15)
O6—C6—N1	118.83 (16)	O4'—C4'—C3'	107.81 (14)
O6—C6—C5	127.07 (17)	C5'—C4'—C3'	112.62 (17)
N1—C6—C5	114.09 (15)	O4'—C4'—H4'	109.3
C5—S7—C8	90.16 (10)	C5'—C4'—H4'	109.3
O8—C8—N9	125.17 (19)	C3'—C4'—H4'	109.3
O8—C8—S7	124.10 (18)	C1'—O4'—C4'	111.66 (15)
N9—C8—S7	110.73 (14)	O5'—C5'—C4'	109.83 (19)
C4—N9—C8	114.14 (15)	O5'—C5'—H5'A	109.7
C4—N9—C1'	124.67 (15)	C4'—C5'—H5'A	109.7
C8—N9—C1'	119.31 (16)	O5'—C5'—H5'B	109.7
O4'—C1'—N9	106.88 (14)	C4'—C5'—H5'B	109.7
O4'—C1'—C2'	108.03 (15)	H5'A—C5'—H5'B	108.2
N9—C1'—C2'	115.88 (17)	C5'—O5'—H5'C	109.5
O4'—C1'—H1'	108.6
C6—N1—C2—N3	−1.3 (3)	C5—C4—N9—C1'	−165.19 (17)
C6—N1—C2—N2	179.17 (19)	O8—C8—N9—C4	−177.7 (2)
N2—C2—N3—C4	−178.8 (2)	S7—C8—N9—C4	2.2 (2)
N1—C2—N3—C4	1.7 (3)	O8—C8—N9—C1'	−12.6 (4)
C2—N3—C4—N9	−177.28 (18)	S7—C8—N9—C1'	167.28 (14)
C2—N3—C4—C5	1.3 (3)	C4—N9—C1'—O4'	61.0 (3)
N3—C4—C5—C6	−4.5 (3)	C8—N9—C1'—O4'	−102.4 (2)
N9—C4—C5—C6	174.12 (17)	C4—N9—C1'—C2'	−59.4 (2)
N3—C4—C5—S7	−179.34 (16)	C8—N9—C1'—C2'	137.13 (19)
N9—C4—C5—S7	−0.7 (2)	O4'—C1'—C2'—C3'	−5.75 (19)
C2—N1—C6—O6	176.77 (18)	N9—C1'—C2'—C3'	114.07 (16)
C2—N1—C6—C5	−1.9 (3)	C1'—C2'—C3'—O3'	130.01 (16)
C4—C5—C6—O6	−174.06 (18)	C1'—C2'—C3'—C4'	12.38 (18)
S7—C5—C6—O6	−0.2 (3)	O3'—C3'—C4'—O4'	−136.30 (16)
C4—C5—C6—N1	4.5 (2)	C2'—C3'—C4'—O4'	−14.93 (18)
S7—C5—C6—N1	178.30 (14)	O3'—C3'—C4'—C5'	103.91 (17)
C4—C5—S7—C8	1.58 (16)	C2'—C3'—C4'—C5'	−134.71 (15)
C6—C5—S7—C8	−172.56 (19)	N9—C1'—O4'—C4'	−129.23 (16)
C5—S7—C8—O8	177.7 (2)	C2'—C1'—O4'—C4'	−3.9 (2)
C5—S7—C8—N9	−2.09 (16)	C5'—C4'—O4'—C1'	134.39 (17)
N3—C4—N9—C8	177.74 (17)	C3'—C4'—O4'—C1'	12.09 (19)
C5—C4—N9—C8	−1.0 (2)	O4'—C4'—C5'—O5'	57.4 (2)
N3—C4—N9—C1'	13.5 (3)	C3'—C4'—C5'—O5'	176.71 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O3′^i	0.86	2.11	2.911 (2)	155
N2—H2A···O5′^ii	0.86	2.21	3.009 (2)	154
N2—H2B···O8^iii	0.86	2.05	2.794 (3)	145
O3′—H3′B···O6^iv	0.82	1.99	2.795 (2)	166
O5′—H5′C···O6^v	0.82	2.01	2.778 (2)	156

Symmetry codes: (i) x, y+1, z+1; (ii) x−1, y, z; (iii) x−1, y+1, z; (iv) x−1, y−1, z−1; (v) x, y, z−1.