alpha-Nucleosides in biological systems. Crystal structure and conformation of alpha-cytidine

Butterfly Effect in Cytarabine: Combined NMR-NQR Experiment, Solid-State Computational Modeling, Quantitative Structure-Property Relationships and Molecular Docking Study

Cytarabine (Ara-C) is a synthetic isomer of cytidine that differs from cytidine and deoxycytidine only in the sugar. The use of arabinose instead of deoxyribose hinders the formation of phosphodiester linkages between pentoses, preventing the DNA chain from elongation and interrupting the DNA synthesis. The minor structural alteration (the inversion of hydroxyl at the 2' positions of the sugar) leads to change of the biological activity from anti-depressant and DNA/RNA block builder to powerful anti-cancer. Our study aimed to determine the molecular nature of this phenomenon. Three 1H-14N NMR-NQR experimental techniques, followed by solid-state computational modelling (Quantum Theory of Atoms in Molecules, Reduced Density Gradient and 3D Hirshfeld surfaces), Quantitative Structure-Property Relationships, Spackman's Hirshfeld surfaces and Molecular Docking were used. Multifaceted analysis-combining experiments, computational modeling and molecular docking-provides deep insight into three-dimensional packing at the atomic and molecular levels, but is challenging. A spectrum with nine lines indicating the existence of three chemically inequivalent nitrogen sites in the Ara-C molecule was recorded, and the lines were assigned to them. The influence of the structural alteration on the NQR parameters was modeled in the solid (GGA/RPBE). For the comprehensive description of the nature of these interactions several factors were considered, including relative reactivity and the involvement of heavy atoms in various non-covalent interactions. The binding modes in the solid state and complex with dCK were investigated using the novel approaches: radial plots, heatmaps and root-mean-square deviation of the binding mode. We identified the intramolecular OH···O hydrogen bond as the key factor responsible for forcing the glycone conformation and strengthening NH···O bonds with Gln97, Asp133 and Ara128, and stacking with Phe137. The titular butterfly effect is associated with both the inversion and the presence of this intramolecular hydrogen bond. Our study elucidates the differences in the binding modes of Ara-C and cytidine, which should guide the design of more potent anti-cancer and anti-viral analogues.

The α-D-anomer of 2'-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis

β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist (23T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4-N4 bond and a relatively short C-N bond in the solid state. Crystal packing is controlled by N-H...O and O-H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H...N contacts (C1'-H1' and C3'-H3'A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.

A new and potentially prebiotic α-cytidine derivative

A new α-cytidine derivative was synthesised from the prebiotic reaction of ribose aminooxazoline and dicyanoacetylene.

A new α-cytidine derivative was synthesised from the prebiotic reaction of ribose aminooxazoline and dicyanoacetylene. The tetracyclic structure of the product was confirmed by X-ray diffraction and then an alternative 6-step synthetic pathway to the product was found which was suitable for large-scale synthesis.

Exploratory Studies to Investigate a Linked Prebiotic Origin of RNA and Coded Peptides. 4th Communication

As part of an ongoing investigation into a possible linked origin of RNA and coded peptides, we have (further) investigated the potentially prebiotic synthesis of pyrimidine ribonucleosides (ribonucleotides), by stepwise nucleobase assembly on sugar (sugar phosphate) scaffolds. In this paper, we complete our description of this assembly process on aldopentose scaffolds. Treatment of D-ribose (14) and D-xylose (20) with cyanamide smoothly produces the furanosylamino-oxazolines 15 and 21, respectively (Schemes 1 and 3). Similar treatment of D-lyxose (26) also produces the furanosylamino-oxazoline 29, but as a minor component of an equilibrating mixture in which the pyranosylamino-oxazoline 28 predominates (Scheme 4). Treatment of the various amino-oxazolines with cyanoacetylene gives furanosylcytidines 16, 25, and 31, and the lyxopyranosylcytidine 30 (Schemes 1-4). Minor by-products of the cyanoacetylene reaction include imino lactone 17, acetals 19, 22, and 24, and cyanovinyl adducts 22 and 23 resulting from initial addition of nucleoside OH groups to the terminal acetylenic C-atom of cyanoacetylene (Schemes 2-4).

Stereochemical studies on nucleic acid analogues. I. Conformations of alpha-nucleosides and alpha-nucleotides: interconversion of sugar puckers via O4'-exo

The preferred conformations of ribo and deoxyribo alpha-nucleosides and alpha-nucleotides, the stereoisomers of the naturally occurring beta-isomers, are worked out by minimizing the conformational energy as a function of all the major parameters including the sugar ring conformations along the pseudorotation path. The results of the studies bring out certain distinct conformational features that are at variance with their beta counterparts. The range of glycosyl conformations are found to be not only quite restricted here but favor predominantly the anti conformation. The syn glycosyl conformation for the entire region of P values are found to be energetically less favorable, with the barrier to anti in equilibrium with syn interconversion being higher especially in alpha-ribonucleosides. The energetically preferred range of pseudorotation phase angles (P) is also considerably restricted and P values corresponding to the C1'-exo range of sugars are highly unfavorable for alpha-nucleosides, in sharp contrast to the broad range of sugar ring conformations favored by beta-isomers. While both trans congruent to 180 degrees and skew congruent to 270 degrees conformations around the C3'-O3' (phi') bond are favored for alpha-3'-nucleotides with deoxyribose sugars, ribose sugars seem to favor only the skew values of phi'. Most interestingly and in sharp contrast to beta-stereoisomers, an energy barrier is encountered at P values corresponding to O4'-endo sugars. This suggests that the possible sugar pucker interconversion between C2'-endo/C3'-exo and C3'-endo/C2'-exo in alpha-anomers could take place only through the O4'-exo region. Likewise the possible path of anti in equilibrium with syn interconversion in alpha-nucleosides is not via high anti, in sharp contrast to beta-nucleosides. These observations should be borne in mind while assigning the sugar ring conformers in alpha-nucleosides and those containing them from nmr investigations. Comparison of the results with beta-anomers seem to suggest on the whole a lack of conformational variability or the restricted nature of alpha-stereoisomers. This could be one of the reasons for its nonselection in the naturally occurring nucleic acids.

F.t.-i.r. and laser-Raman spectra of cytosine and cytidine

Fourier-transform infrared (F.t.-i.r.) and laser-Raman spectra of cytosine and cytidine in the solid state have been recorded and assignments of the frequencies made. Comparison of the observed frequencies for cytosine with those for cytidine permits identification of the bands characteristic of the sugar on the one hand, and of the pyrimidine base on the other.

Conformation and structure of 9-alpha-D-arabinofuranoxyladenine

The crystal structure of the nucleoside 9-alpha-D-arabinofuranosyladenine (C10H13N5O4) has been determined by means of three-dimensional X-ray counter data. The adenosine analog crystallizes in space group P2(1)2(1)2(1) of the orthorhombic system with eight formula units in a cell of dimensions a, 6.720(5), b, 40.188(35), c, 8.357(8) A. Hence, there are two crystallographically independent molecules in the unit cell. The structure was solved by direct methods and refined by full-matrix least-squares techniques to a final value of the conventional R-factor of 0.076 using 1173 independent intensity data. In the crystal, both independent molecules (A and B) adopt the anti conformation (for an alpha-sugar), with glycosyl torsion angles, chi, of -73 degrees and -64 degrees; these are comparable to values found in other alpha-nucleosides. The conformation about the extracyclic C(4')-C(5') bond is gauche-gauche in both molecules. The sugar pucker is C(2'0-exo-C(3')-endo, 2T3, in molecule A and C(3')-endo, 3E, in molecule B. Conformational analysis of rotation about the N(9)-C(1') glycosyl bond has been performed by use of CNDO/2 molecular orbital calculations. These calculations suggest that the observed conformation may not be the global minimum, but that it lies only 0.4 kcal x mol-1 higher in energy than the global minimum. The highest energy barrier to rotation around the glycosyl bond is calculated to be only 1.1 kcal x mol-1, which is comparable to the value calculated for adenosine.

Conformational studies of alpha- and beta-pyrimidine 2'-deoxyribonucleosides in the syn and anti conformation

Proton magnetic resonance studies of a series of pyrimidine alpha- and beta-2'-deoxyribosides in 2H2O have been carried out at 250 MHz. The H-H coupling constants and chemical shifts are discussed in terms of the molecular conformation. Methyl substitution at the 6-position of the base leads to rotation from the anti to the syn conformation in both anomeric species. In both series, the 2'endo pucker is preferred when the base is anti. Rotation into the syn conformation leads to a shift towards the 3'endo pucker, the shift being larger in the alpha-series. In the alpha-series, a correlation between the ring pucker and the C(4')-C(5') conformer distribution is revealed. Changes in geminal coupling constant, J2'2", are noted in the alpha-series and related to the sugar pucker.

The crystal and molecular structure of 9-alpha-D-arabinofuranosyladenine

The glycosyl torsional angles in two crystallographically-independent molecules of alpha-araA are -73 and -64 degrees, both of which are in the "anti" region. The sugar conformations are C(3')-endo and C(2')-exo-C(3')-endo.