Journal of Biomolecular Structure and Dynamics, 2014 Vol. 32, No. 5, 831–851, http://dx.doi.org/10.1080/07391102.2013.789402
Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour M. Alcolea Palafox* Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid, 28040, Spain Communicated by Ramaswamy H. Sarma (Received 8 February 2013; final version received 21 March 2013) 5-iodo-2′-deoxyuridine Nucleoside Analogue (IUdR) was the first selective antiviral nucleoside against herpes simplex virus type 1 and 2, and it was also a meaningful anticancer drug. Within a full study of this drug and its possible behaviour, previously, a comprehensive theoretical conformational analysis by MP2 and B3LYP was carried out, and all the possible stable structures were determined with full relaxation of all geometrical parameters. The search located 45 stable structures, and in all them, the whole conformational parameters (v, b, c, /, d, P, mmax) were analyzed as well as the NBO natural atomic charges. Comparisons of the conformers with those of the natural Nucleoside 2′-deoxythymidine (dT) were carried out, and the main differences between IUdR and dT were analyzed. The accuracy of the methods used was probed with the simulation of the X-ray crystal data by a tetramer form. Watson-Crick (WC) IUdR/dT···2′-deoxyadenosine pairs were analyzed for the first time using quantum chemical calculations, as well as the mispairing IUdR/dT···2′-deoxyguanosine. As result, it is observed that IUdR give rises to a slightly stronger WC pair and weaker mispairing than those with dT, therefore deforming slightly the DNA axis and difficulting the growth of the DNA virus and consequently, killing it. Keywords: 5-iodo-2′-deoxyuridine; IUdR; thymidine; antiviral; DNA base pairs
1. Introduction Nucleoside analogues have been primarily examined for their ability to inhibit reverse transcriptase, and also the ability to inhibit enzymes necessary for de novo thymidine synthesis, such as thymidylate synthase (TS) and thymidylate kinase (TK). Alternatively, they can be incorporated into a growing strand of DNA, and either cause strand termination, or produce a kink in the DNA that prevents replication (Vortherms, Dang, & Doyle, 2009). Thus, several nucleoside and nucleotide analogues have been identified as potent anticancer and antiviral agents (De Clercq & Neyts, 2004; Taft & Paula da Silva, 2006). Among these compounds, 5-iodo-2′-deoxyuridine nucleoside analogue (IUdR) (Scheme 1) was the first compound identified with antiviral activity against a number of orthopoxviruses, and it has been reported to be active both in vitro and in animal models of infection (Prichard & Kern, 2010). Treatment with IUdR inhibited viral replication of iridovirus (Chen, Zheng, & Jiang, 1999), poxviruses (including variola, vaccinia (Neyts, Verbeken, & De Clercq, 2002; Smee, Humphreys, Hurst, *Email:
[email protected] Ó 2013 Taylor & Francis
& Barnard, 2008), monkeypox, cowpox, molluscum contagiosum, orf) and ranavirus (Qin et al., 2003). IUdR has antimicrobial activities (Zander et al., 2010) alone and in combination against S. Aureus. When IUdR labelled with 125I (125IUdR) is incorporated into the DNA of mitotic tumour cells, the Auger electrons emitted during iodine decay are highly cytotoxic (Yamasaki, Moritake, & Klein, 2003; Rebischung et al., 2008). Thus, it is used as a clinical radiosensitizer (Atcher et al., 1989; Kinsella, Dobson, Mithcell, & Fornace, 1987; Seo et al., 2006; Zager et al., 2003) for the detection of DNA replication, as a marker for cell kinetic studies (Gratzner, 1982; Speth et al., 1989), and in the studies of early proliferative response to anticancer treatment (Carnochan & Brooks, 1999). The development of novel anti-herpes virus drugs that are more effective for varicella-zoster virus (VZV) and human cytomegalovirus infections and less cytotoxic against host cells is desirable. For this reason, previously we have carried out a previous study (Alcolea, 2013) on IUdR with the aims of establish the
832
M. Alcolea Palafox
Scheme 1. Molecular structure and definition of the exocyclic and endocyclic angles in IUdR nucleoside.
relationship between structure, conformational features or physicochemical properties and activity of these drugs. From our understanding, it would be interesting to analyse previously the different conformational possibilities for IUdR and compare the results to the nucleoside natural 2′-deoxythymidine (dT) in order to find the facility to change of conformation during the reaction in the active site. Also an accurate knowledge of the conformational properties of these nucleosides would be an important help for the interpretation of drug–target interactions. Different authors have analyzed the conformers of several nucleosides and nucleosides analogues (Baumgartner, Motura, Contreras, Pierini, & Briñón, 2003; Choi et al., 2003; Ponomareva, Yurenko, Zhurakivsky, Mourik, & Hovorun, 2012; Saran & Ojha, 1993a, 1993b; Yurenko, Zhurakivsky, Ghomi, Samijlenko, & Hovorun, 2008; Yurenko, Zhurakivsky, Samijlenko, & Hovorun, 2011; Yurenko, Zhurakivsky, Ghomi, Samijlenko, & Hovorun, 2007a), but no one conformational study appears on IUdR, and no one comparison dT vs. IUdR has been reported. Although calculations have been published for the uracil base (Alcolea, Iza, & Gil, 2002; Alcolea & Rastogi, 2002), thymine base (Brovarets’ & Hovorun, 2010) and for 5-iodouracil (Alcolea et al., 2010; Rastogi et al., 2010), no similar studies have been carried out previously for IUdR. Another goal of present research is a simulation of the solid-state structure. One of the reasons of this study is to confirm the validity of our calculations performed on IUdR through a comparison with the experimental Xray data. We have simulated the crystal unit cells in nucleoside analogues (Alcolea & Iza, 2012; Alcolea, 2013) and nucleobase derivatives (Alcolea et al., 2007; 2010; Rastogi & Alcolea, 2011; Ortiz, Alcolea Palafox, & Rastogi, 2012) by dimer and tetramer forms, and in general, the geometric parameters and IR and Raman
vibrational spectra were in accordance with those found experimentally. Now, we have carried out the simulation of the crystal unit cell in IUdR with a tetramer form. Nucleosides analogues containing unsaturated ribose ring structure, with lack 2′- and 3′-OH groups, are the most effective compounds because the growth of the DNA viral chain through 3′-OH is impeded. However, IUdR has this 3′-OH group and as consequence the growth is not impeded. Thus, other mechanism of inhibition should be presented in IUdR. Several authors (Camerman & Trotter, 1965; Bailey, Navarro, & Hernanz, 1999) have given a possible general explanation without details. Now, one of the aims of the present work is to carry out a detailed comparison of the molecular structure of IUdR with dT and thus to suggest a possible reason for this inhibition. This is another goal of the present manuscript. For this purpose, with the calculation of the interaction energies in the Watson– Crick (WC) pairs and mispairing pairs, the differences with dT were determined, and therefore, a possible reason for this inhibitory activity of IUdR can be given. The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases has been studied by different authors (Danilov, Anisimov, Kurita, & Hovorun, 2005). 2.
Calculations
The calculations were carried out by using the MP2 method and by using density functional methods (DFT), such as B3LYP hybrid functional. These methods appear implemented in the GAUSSIAN 03 program package (Frisch et al., 2003). DFT methods provide adequate compromise between the desired chemical accuracy and the heavy demands put on computer time and power. Moreover, DFT methods have been used satisfactory in many studies of drug design (Hoffmann & Rychlewski, 2002; Alcolea et al., 2011). Because of the iodine atom, the DGDZVP basis set was selected for all the calculations. The B3LYP method was chosen because different studies have shown that the data obtained with this level of theory are in good agreement with those obtained by other more costly computational methods as MP2 calculations and it predicts vibrational wavenumbers of DNA bases better than the HF and MP2 methods (Alcolea, 1998, 2000; Alcolea et al., 2002, 2004; Alcolea & Rastogi, 2002). The optimum geometry was determined, by minimizing the energy with respect to all geometrical parameters without imposing molecular symmetry constraints. Berny optimization under the TIGHT convergence criterion was used. Atomic charges were determined with the Natural NBO procedure (Carpenter & Weinhold, 1988; Reed, Curtiss, & Weinhold, 1988). The harmonic wavenumber computations were carried out at the same level of the respective optimization
The antiviral Nucleoside Analogue 5-iodo-2´-deoxyuridine (IUdR) process and by the analytic evaluation of the second derivative of the energy with respect to the nuclear displacement. Wavenumber calculations were performed in all the optimized conformers determined by DFT to asses that they correspond to real minimum. All the optimized structures showed positive harmonic vibrations only (true energy minimum). Relative energies were obtained by including zero-point vibrational energies (ZPE). For the calculation of the ZPE, the wavenumbers were retained unscaled. The Gibbs free energy was calculated at 298.15 K. The potential energy surface of this molecule was determined by rotation of the torsional angles v (glycosidic bond), c (C4′-C5′ bond), b (C5′-O5′ bond), e (C3′-O3′ bond) and the pseudorotation phase P. These dihedral angles simultaneously held fixed at values varying between 0° and 360° in steps of 20° in a detailed second study. All the remaining geometrical parameters were relaxed during these optimizations. All the optimized points were plotted by the SURFER program (SURFER, 1999). Thus, all local minimum were determined. All quantum mechanical computations have been performed on the alpha computer of the Computational Centre from University Complutense of Madrid. 2.1.
Interaction energies
They were computed on the B3LYP optimized structures with the DGDZVP basis set. In the WC pair and mispairing pair of IUdR and dT with 2′-deoxyadenosine (dA) and 2′-deoxyguanosine (dG) the interaction energies obtained were corrected for basis set superposition error (BSSE) using the standard counterpoise (CP) procedure (Boys & Bernardi, 1970; Alcolea et al., 2009) as follows: CP The total CP corrected interaction energy, DEAB ; between the nucleoside A (≡ IUdR or dT) and the nucleoside B (≡ dA or dG) is calculated according to: CP DEAB ¼ E int ðABÞ þ E def ðABÞ
ð1Þ
where E int ðABÞ is defined as: AB E int ðABÞ ¼ EAB ðABÞ EAAB ðABÞ EBAB ðABÞ
ð2Þ
AB and where EAB ðABÞ stands for the electronic energy at the optimized geometry of the whole system, and EAAB (AB) (or EBAB (AB)) is the electronic energy of the isolated subsystem A (or B) in the entire system AB. The deformation energy E def ðABÞ is defined as:
E def ðABÞ ¼ EAdef ðABÞ þ EBdef ðABÞ
833 ð3Þ
where the deformation energy of monomer X (≡ A or B) is: EXdef ðABÞ ¼ EXX ðABÞ EXX ðXÞ
ð4Þ
Here, the subscripts denote the molecular system, and the superscripts indicate whether the calculation is done with the basis set of the entire system (AB), or the basis set of the monomer (X). The parenthesis indicates whether the calculation is done at the optimised geometry of the entire system (AB), or at the monomer optimised geometry (X). 3. Results and discussion 3.1. Definition of the conformational angles Following the Saenger’s notation (Saenger, 1984), the atomic description of this molecule as well as the most important exocyclic and endocyclic torsional angles is defined in Scheme 1. The different conformations in IUdR can be characterized by the following five important structural parameters: (i) the glycosylic torsional angle, v(O4′–C1′–N1–C2), which determines the two orientations of the base relative to the furanose ring, denoted as the anti and syn forms. (ii) The exocyclic torsional angle b(C4′–C5′–O5′–H5′), which describes the orientation of the hydroxyl hydrogen H5′ relative to the furanose ring. (iii) The exocyclic torsional angle c(C3′–C4′–C5′–O5′), which determines the orientation of the 5′-hydroxyl group relative to the furanose ring. This ring is twisted out-of-plane in order to minimize non-bonded interactions between their substituents and located in the north (N) [C2′exo/C3′-endo] and south (S) [C2′-endo/C3′-exo] conformers. (iv) The torsional angle d(C5′–C4′–C3′–O3′), which describes the orientation of the CH2OH moiety relative to the furanose ring. Finally, (v) the torsional angle /(C2′–C3′–O3′–H3′) that determines the orientation of hydroxyl hydrogen H3′. 3.2. In the isolated state 3.2.1. Conformers and energetics An extensive conformational study was carried out and the relative calculated energies of the 45 optimum conformers appear collected in Table 1 at the B3LYP and MP2 levels, as well as a detailed collection of the most important conformational parameters of these optimized forms. The conformers were classified according to the three ranges of rotation of v: conformers C (v: 131.8 ± 11.1° by B3LYP), conformers A (v: 162.3 ± 6.4°) and conformers B (v: 74.8 ± 13.3°), Figure 1. The energy criterion by MP2 was followed for the numbering: firstly,
C2
B16 B17 B18 B19 B20 B21 B22 C1
B15
B13 B14
B10 B11 B12
B8 B9
B6 B7
B5
B4
B3
B2
B1
Conf
b
c
/
d
62.1 62.4 45.5 73.2 141.0 (61.7) (64.1) (45.5) (73.3) (143.9) “72.5” “78.2” “61.7” “80.9” “92.2” “61.3” “54.3” “49.3” “69.8” “140.1” 61.5 43.0 43.8 153.5 95.1 (62.8) (42.6) (46.0) (152.3) (92.6) 62.6 42.3 46.5 95.7 94.2 (63.8) (42.2) (48.6) (96.6) (91.0) 68.5 175.0 58.8 177.9 92.9 (66.15) (176.5) (57.3) (178.7) (95.3) 68.8 82.9 59.2 175.6 91.3 (66.4) (89.1) (57.3) (174.8) (94.5) (114.0) (174.7) (54.2) (81.9) (104.8) 70.1 60.0 178.3 86.7 93.7 (67.8) (59.9) (179.6) (87.4) (94.7) 68.3 59.1 179.1 160.2 98.8 62.5 41.0 47.3 59.7 90.3 (63.7) (40.8) (49.3) (57.2) (87.0) 68.6 60.6 178.9 60.1 91.4 65.8 80.4 69.5 178.5 150.3 71.9 42.0 71.4 78.1 81.8 (70.9) (39.3) (69.9) (78.2) (81.7) 71.1 55.5 69.4 62.2 79.3 69.9 172.8 168.5 85.7 90.4 (67.6) (172.7) (170.3) (85.2) (91.5) 70.0 65.6 173.4 85.5 92.1 (67.1) (66.7) (175.1) (86.1) (94.3) 67.7 166.3 168.1 163.6 98.2 68.0 59.1 174.9 152.6 96.1 77.8 156.4 44.5 142.3 84.2 87.6 170.7 51.1 91.0 86.9 68.9 68.3 174.6 58.3 90.8 88.2 179.3 54.2 53.7 84.7 79.5 83.8 51.0 67.9 131.3 130.4 174.1 52.3 63.7 141.4 (128.5) (175.8) (50.9) (64.2) (145.4) “126.6” “175.9” “52.6” “68.2” “144.1” 126.1 172.6 51.4 180.0 146.0 (124.1) (174.9) (50.0) (179.3) (150.7) “102.4” “164.1” “43.7” “166.3” “103.0”
v m1 34.30 (38.18) “0.03” “34.00” 6.46 (6.08) 4.03 (4.52) 8.97 (9.49) 9.15 (9.56) (38.67) 10.67 (10.43) 11.39 3.87 (4.35) 11.24 29.41 9.00 (7.91) 9.76 10.40 (9.91) 11.20 (11.31) 11.78 11.88 10.56 18.54 12.41 18.95 39.41 30.94 (33.55) “28.91” 30.18 (33.14) “33.14”
m0 22.43 (26.37) “22.37” 16.59” 10,79 (14.05) 12.16 (14.86) 9.43 (8.38) 9.98 (8.71) (32.17) 6.04 (6.75) 4.28 11.94 (14.65) 3.91 13.42 13.94 (16.41) 12.19 7.39 (8.24) 5.18 (4.54) 3.08 3.85 12.30 0.83 1.87 0.97 32.77 17.64 (19.42) “13.50” 16.11 (18.04) “44.91”
m3
32.43 20.65 (34.78) (20.89) “15.17” “20.17” “32.08” 25.18” 19.62 26.28 (22.19) (31.08) 17.21 24.62 (20.62) (29.93) 22.15 28.43 (22.08) (27.86) 22.92 29.53 (22.50) (28.47) (30.21) (12.10) 21.90 25.84 (22.26) (26.75) 21.28 24.17 16.68 23.92 (20.07) (29.20) 20.75 23.43 32.97 26.36 26.47 35.40 (27.24) (37.84) 25.96 33.85 22.62 27.46 (22.72) (28.22) 21.82 25.39 (21.46) (24.78) 20.69 22.96 21.51 24.29 27.27 35.20 29.27 30.39 20.59 22.19 28.16 28.23 30.92 13.15 31.66 22.27 (34.15) (23.82) “32.46” “25.38” 31.77 23.26 (34.69) (25.18) “9.88” “16.03”
m2 0.90 (3.16) “26.42” “1.15” 23.64 (28.64) 23.51 (28.49) 24.14 (23.08) 25.16 (23.66) (12.45) 20.49 (21.46) 18.24 22.90 (27.87) 17.57 8.28 31.33 (34.29) 29.25 22.34 (23.29) 19.62 (18.78) 16.67 18.02 30.23 20.07 15.46 17.52 12.07 3.05 (2.90) “7.66” 4.59 (4.57) “37.78”
m4 159.67 (156.38) “55.55” “159.28” 41.94 (44.75) 46.73 (47.30) 37.88 (36.25) 38.20 (36.52) (322.56) 31.74 (33.02) 28.32 46.92 (47.49) 27.80 175.39 41.34 (43.88) 39.36 33.90 (35.48) 30.14 (29.12) 25.90 27.37 38.67 19.98 23.16 16.59 143.23 166.57 (165.98) “174.64” 169.32 (168.65) “102.99”
Pa 34.58 (37.96) “26.87” “34.30” 26.37 (31.24) 25.11 (30.40) 28.06 (27.38) 29.16 (28.00) (38.05) 25.75 (26,55) 24.17 24.42 (22.69) 23.45 33.08 35.23 (37.79) 33.56 27.22 (27.90) 25.23 (24.56) 23.00 24.22 34.93 31.14 22.40 29.38 38.60 32.55 (35.20) “32.60” 32.32 (35.38) “43.97”
mmaxb E E 4E 2 E 3 4 T
T
3
3
T T
1
T
3
T
3
3
4
3
E T 3 4 T 3 E 3 E 3 E 2 1 T 2 E 2 E 2 3 T 1E 2 E 0 1 T
T
3
3
T T
3
3
4
4
4
2
T T 3 4 T 3
4
4E
4
4
2
4
4
4E
2
2
Sugar conf. 4.63 (5.32) “6.00” “7.02” 4.03 (4.64) 4.44 (5.02) 3.63 (3.67) 4.75 (5.08) (4.26) 4.06 (4.64) 3.32 5.82 (6.75) 4.66 5.14 4.41 (4.85) 4.79 3.92 (4.17) 5.71 (6.24) 3.68 5.35 4.93 4.62 6.20 5.91 6.98 7.11 (7.96) “9.51” 8.29 (9.24) “10.19”
l
3.867 3.914 3.953 4.123 5.056 7.676 7.108 0.120
4.022
3.850 3.676
2.804 3.205 3.582
1.860 3.002
1.960
2.169
1.655
1.202
“0f” “0h” 1.160
0.208
DG
(Continued)
1.087 0.846 (0.878) “16.87” “12.67”
0 0d “0e” “0g” 1.384 (2.130) 1.458 (2.168) 2.297 (2.538) 2.830 (3.434) (3.454) 2.585 (3.709) 2.747 3.105 (4.227) 3.508 3.817 3.961 (4.896) 4.352 4.625 (6.272) 4.702 (6.347) 4.896 5.056 5.522 5.591 5.922 7.196 8.231 0.403 (0.086)
c
DE
Table 1. The 45 optimum stable conformers calculated in IUdR molecule, with endocyclic and exocyclic torsional angles in degrees, pseudorotational angle P in degrees, dipole moment l (in Debye), and relative energies ΔE, and Free energies ΔG in (kcal mol1). The values are listed successively at the B3LYP/DGDZVP level, MP2/DGDZVP level (values in parentheses), simulation of the hydration with 20 water molecules and at the B3LYP/DGDZVP level (values in quotation marks and in italic), and with PCM at B3LYP/DGDZVP level (values in quotation marks).
834 M. Alcolea Palafox
ΔE = 7749.9933254 AU.
ΔE = 7754.979041 AU§.
ΔE = 9283.558162 AU.
ΔE = 7755.022147 AU.
1 AU = 627.5095 kcal/mol.
§
h
ΔG = 7755.068068 AU.
g
f
ΔG = 9283.664602 AU.
e
c
/
d
m0
m2 mmax ¼ cosP when m2 is negative, 180° is added59 to the calculated value of P.
d
c
b
a
b
m1
m2
m3
m4
Pa mmaxb
”115.3” “135.0” “42.2” “163.9” “84.9” “40.36” “17.96” “9.44” “33.50” “46.35” “78.13” “45.88” 125.8 175.7 51.1 54.6 138.9 13.54 28.35 31.34 24.20 6.89 173.61 31.53 (123.3) (177.8) (49.4) (57.1) (142.6) (14.93) (30.78) (33.94) (26.08) (7.17) (173.20) (34.18) “120.5” “179.6” “47.2” “64.2” “111.3” “44.36” “40.76” “21.81” “3.26” “29.30” “119.66” “44.01” 125.5 71.1 58.2 76.0 113.5 39.71 34.74 17.26 5.39 28.24 116.17 39.13 120.7 70.0 57.4 158.4 87.7 15.69 7.13 25.08 34.87 32.19 44.41 35.10 137.7 53.7 178.7 70.0 127.5 35.35 38.16 26.48 6.69 17.89 133.89 38.19 (135.1) (49.6) (173.4) (68.0) (145.3) (27.25) (39.25) (35.70) (20.79) (3.86) (155.72) (39.16) 128.8 52.6 176.9 176.4 140.0 29.06 37.19 30.74 14.65 8.95 147.38 36.50 128.0 96.2 54.0 175.2 146.6 17.36 31.24 32.33 23.14 3.72 167.68 33.09 124.3 69.2 58.9 57.4 101.8 39.29 30.03 10.42 12.26 32.36 105.72 38.53 134.8 82.2 66.1 174.3 130.3 33.85 36.90 25.74 6.77 16.91 134.40 36.79 132.9 58.8 176.9 60.5 93.7 38.90 24.61 2.50 20.20 37.31 93.64 39.40 141.2 92.3 70.7 173.7 137.8 29.78 37.31 30.22 13.82 9.92 145.81 36.53 142.9 70.0 65.1 51.9 137.9 23.26 35.23 32.88 20.30 1.65 158.51 35.34 (164.4) (174.7) (52.9) (148.8) (60.1) (10.04) (27.20) (32.90) (28.06) (11.48) (181.30) (32.91) 155.9 165.5 49.7 153.5 87.8 3.07 23.46 33.08 32.03 18.57 13.30 33.99 (160.2) (167.0) (48.0) (153.7) (84.6) (4.70) (27.54) (37.99) (36.31) (20.16) (11.71) (38.80) 168.7 177.3 170.6 60.9 150.7 2.63 17.75 29.72 31.92 22.16 203.07 32.30 (174.4) (179.1) (172.8) (61.3) (156.0) (9.91) (12.9) (29.11)C (35.62) (28.98) (214.52) (35.33) 164.8 56.6 164.3 61.5 149.7 4.26 23.41 32.17 30.55 16.90 191.30 32.80 (170.6) (59.1) (166.5) (61.6) (155.5) (4.36) (17.79) (31.47) (34.92) (25.03) (205.66) (34.91) 161.6 69.6 65.2 67.5 141.8 25.02 36.54 33.43 19.97 2.97 156.58 36.43 (167.3) (73.9) (65.1) (66.8) (149.6) (21.16) (36.31) (36.67) (25.52) (2.97) (165.60) (37.86) 164.1 172.1 66.7 67.8 146.2 21.15 35.01 34.69 23.51 1.71 163.84 36.11 (170.4) (169.4) (64.9) (67.9) (154.4) (13.7) (31.8) (36.7) (29.9) (10.4) (177.36) (36.74) 8164.6 43.9 71.6 70.7 78.7 4.43 19.42 34.04 37.47 26.66 25.13 37.60 163.8 53.7 70.1 54.1 75.3 4.09 19.44 33.67 36.89 26.04 24.66 37.05 164.5 72.3 75.0 61.3 141.0 25.57 36.74 33.37 19.58 3.58 155.73 36.60 (169.2) (81.0) (74.9) (62.1) (149.7) (20.90) (36.20) (36.92) (25.88) (3.34) (166.21) (38.02) 165.6 174.0 67.3 59.3 148.6 5.33 24.64 33.18 30.83 16.37 189.58 33.65
v
4 þm1 Þðm3 þm0 Þ tgP ¼ 2mðm2 ðsinð36Þþsinð72ÞÞ
A10
A7 A8 A9
A6
A5
A4
A3
C7 C8 C9 C10 C11 C12 C13 A1 A2
C4 C5 C6
C3
Conf
Table 1. (Continued)
4
3E
3
E E 2 E
2 3 T 3
E
2
E
2
3
E T 3E
3
2
0
T T 2 3 T 1E 0 1 T 3 4 T 1E 2 E 2 1 T 2 E 0 1 T 1E 0 E 2 1 T 2 E 2 3 T 3 E 3
4
Sugar conf.
DE
DG
“7.36” “11.83 » “11.25” 5.78 0.925 1.372 (6.48) (1.499) “5.27” “12.71” “7.26” 4.61 1.663 0.612 4.81 1.694 0g 5.28 2.305 0.912 (6.23) (3.922) 5.48 2.654 1.549 8.71 2.846 2.203 3.26 2.858 1.362 6.06 2.896 2.453 3.09 3.104 1.630 5.97 3.930 2.336 3.96 4.196 2.720 (7.31) (0.852) 7.04 1.37 0.756 (7.48) (1.454) 6.55 3.806 3.174 (6.56) (3.562) 6.96 3.576 2.787 (7.63) (4.006) 5.18 2.603 1.240 (5.61) (4.116) 5.30 3.035 1.825 (5.38) (4.189) 3.93 3.284 2.392 4.35 3.439 2.593 5.33 3.939 2.730 (5.60) (5.806) 3.72 4.147 3.653
l
The antiviral Nucleoside Analogue 5-iodo-2´-deoxyuridine (IUdR) 835
836
M. Alcolea Palafox Conformers A
Figure 1.
Conformers B
Conformers C
Three types of conformers determined in IUdR corresponding to the three ranges of rotation of v, with b and c 60o.
Conformer B1
Conformer C1
(a)
(b)
Figure 2. Calculated parameters in conformers B1 and C1 (global minimum of the syn and anti forms, respectively): (a) optimum bond lengths and angles and (b) natural atomic charges on the atoms.
the most stable and also the expected non-active biological syn forms (B) were numbered; secondly, those conformers found in the crystal and, by analogy with related nucleosides (Hoffmann & Rychlewski, 2002; Alcolea et al., 2009; Alcolea & Talaya, 2010; Alcolea & Iza, 2010), the expected active biological anti forms (C); and finally, the high-anti conformers (A) were listed. Conformers A were in general difficult to be optimized, and in many cases, they changed to the equivalent conformer C. Two energy criteria were considered for each conformer: the electronic energy E + ZPE correction and the Gibbs energy G. The conformers differ in general very little in energy. Thus, our 45 optimized conformers were found within
the electronic energy range ΔE = 0–8 kcal/mol and Gibbs energy range ΔG = 0–7 kcal/mol related to the global minimum, Figure 2. This range of ΔG values is similar to that reported (Yurenko et al., 2007b) in dT, 0– 7.5 kcal/mol. The stability order of the five most stable conformers by the E + ZPE criterion is: B1 > C1 > A1 > C2 > A2 → (by MP2/dgdzvp) B1 > C1 > C3 > C2 > A2 → (by B3LYP/dgdzvp) By Gibbs energy criterion is: C5 > C1 > B1 > C4 > A2 → (by B3LYP/dgdzvp)
The antiviral Nucleoside Analogue 5-iodo-2´-deoxyuridine (IUdR)
837
Figure 3. Plot with the geometry of the 12 best conformers of IUdR, and with the values of the strongest intramolecular H-bonds determined at B3LY/DGDZVP and MP2/DGDZVP levels (values in parentheses).
Six conformers are only found within the electronic energy range DE = 0–2.0 kcal/mol by MP2, five of them with v (123.3° to 164.4°) anti, mainly S-type furan puckering, with c (48–52.9°), b (167.0–177.8°) and with great variation for e angle. The ratio anti/syn form is remarkable decreased from 5.0 in the low-energy group (
