Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR

Accurate pKa Determination for a Heterogeneous Group of Organic Molecules

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energetics of gas-phase protonation. The electrostatic contribution to the solvation energies of protonated and deprotonated compounds were calculated by solving the Poisson equation using atomic charges generated by fitting the electrostatic potential derived from the molecular wave functions in vacuum. The combination of gas-phase and electrostatic solvation energies by means of the thermodynamic cycle enabled us to compute pKa values for the 26 compounds, which cover six distinct chemical groups (carboxylic acids, benzoic acids, phenols, imides, pyridines and imidazoles). The computational procedure for determining pKa values is accurate and transferable with a root-mean-square deviation of 0.53 and 0.57 pKa units and a maximum error of 1.0 pKa and 1.3 pKa units for Becke-half&half and B3LYP DFT functionals, respectively.

Molecular recognition in purinergic receptors. 1. A comprehensive computational study of the h-P2Y1-receptor

P2Y receptors (P2Y-Rs) are attractive pharmaceutical targets due to their involvement in the modulation of many tissues and organs. The lack of experimental structural data on P2Y-Rs impedes structure-based drug design. The need to elucidate the receptor's molecular recognition, together with the limitations of previous receptor models, triggered the construction of a new molecular model for the h-P2Y1-R. Therefore, a h-P2Y1-R model was constructed by homology modeling using the 2.6 A crystal structure of bovine rhodopsin as a template and subsequently refined by constrained molecular dynamics (MD) simulations in a fully hydrated lipid bilayer environment. ATP was docked into the receptor binding site, followed by binding site refinement using Monte Carlo and MD simulations. Analysis of the h-P2Y1-R-ATP complex suggests that the triphosphate moiety is tightly bound by a multitude of interactions possibly including a Mg2+ ion, the ribose ring is not involved in specific interactions, and the adenine ring is bound via N1, N7, and N6. The molecular recognition of the h-P2Y1-R was further probed by ATP derivatives modified on the adenine ring, and correlated with EC50 values for these derivatives. Analysis of receptor:ligand complexes and quantum mechanical studies on model compounds support the role of both steric and electronic effects in improving H-bonding (via N1 and N6) and pi-stacking interactions. The computed h-P2Y1-R model was validated with respect to our previous biochemical results. We believe that this new model of the h-P2Y1-R provides the means for understanding phenomena such as the ligand's potency and receptor subtype selectivity.

Molecular recognition in purinergic receptors. 2. Diastereoselectivity of the h-P2Y1-receptor

In the companion paper, part 1, we described the construction of an improved molecular model for the h-P2Y1 receptor (h-P2Y1-R) and proposed a rational for the stereoelectronic selectivity of the receptor. Here, we extend our studies on the molecular recognition of the h-P2Y1-R to the exploration of the diastereoselectivity of this receptor. For this purpose, we implemented an integrative approach combining synthesis, spectral analysis, biochemical assays, and computational analysis. Specifically, we selected and synthesized novel ATP analogues bearing a chiral center on the phosphate chain. We analyzed the conformation of the chiral ATP analogues in solution by 1H/13C NMR and assigned the absolute configuration of the diastereoisomers. The coordination mode of these analogues with a Mg2+ ion was evaluated by 31P NMR. These chiral analogues were biochemically evaluated and found to be potent h-P2Y1-R ligands. An EC50 difference of ca. 20-fold was observed between the diastereoisomers. Their spectral absolute configuration assignment was confirmed by comparison of the biochemical results to those of ATP-alpha-S diastereoisomers whose chirality is known. Finally, a computational analysis was performed for the elucidation of molecular recognition employing molecular mechanics (docking) studies on the receptor:ligands complexes. On the basis of the current results, we hypothesize that h-P2Y1-R's chiral discrimination originates from the requirement that the nucleotide analogue interacts with a Mg2+ ion within the receptor binding site. This Mg2+ ion is possibly coordinated with both Asp204 and the ATP's alpha, beta, gamma-phosphates in a Lambda configuration.

Characterization and elucidation of coordination requirements of adenine nucleotides complexes with Fe(II) ions

In spite of the significant role of iron ions-nucleotide complexes in living cells, these complexes have been studied only to a limited extent. Therefore, we fully characterized the ATP:Fe(II) complex including stoichiometry, geometry, stability constants, and dependence of Fe(II)-coordination on pH. A 1:1 stoichiometry was established for the ATP:Fe(II) complex based on volumetric titrations, UV and SEM/EDX measurements. The coordination sites of ferrous ions in the complex with ATP, established by 1H-, 31P-, and 15N-NMR, involve the adenine N7 as well as P(alpha), P(beta), and P(gamma). Coordination sites remain the same within the pH range of 3.1-8.3. By applying fluorescence monitored Fe(II)-titration, we established a logK value of 5.13 for the Fe(ATP)2- complex, and 2.31 for the Fe(HATP)-complex. Ferrous complexes of ADP3- and AMP2- were less stable (log K 4.43 and 1.68, respectively). The proposed major structure for the Fe(ATP)2- complex is the 'open' structure. In the minor 'closed' structure N7 nitrogen is probably coordinated with Fe(II) through a bridging water molecule. The electronic and stereochemical requirements for Fe(II)-coordination with ATP4- were probed using a series of modified-phosphate or modified-adenine ATP analogues. We concluded that: Fe(II) coordinates solely with the phosphate-oxygen atom, and not with sulfur, amine, or borane in the cases of phosphate-modified analogues of ATP; a high electron density on N7 and an anti conformation of the adenine-nucleotide are required for enhanced stability of ATP analogues:Fe(II) complexes as compared to ATP complexes (up to more than 100-fold); there are no stereochemical preferences for Fe(II)-coordination with either Rp or Sp isomers of ATP-alpha-S or ATP-alpha-BH3 analogues.

Gas-phase hydrogen/deuterium exchange of adenine nucleotides

Gas-phase hydrogen/deuterium exchange reactions of (de)protonated (sodiated) adenosine-5'-mono-, di- and triphosphate ions with CD(3)OD, CD(3)CO(2)D and ND(3) were achieved using a combination of electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry. The reaction kinetics are dependent on factors such as the charge state, the phosphate chain length, the properties of the exchange reactants and the sodium content. The results indicate that the overall H/D exchange may involve specific sites even if endowed with high energetic barriers. The enhanced reactivity exhibited by adenosine polyphosphate ions compared with adenosine-5'-monophosphate suggests a critical role of the polyphosphate chain in rendering conformationally accessible remote H-donor sites. Low-energy collision-induced dissociation of (sodiated) adenine nucleotides anions supports the aptitude of the (poly)phosphate chain in probing distant sites via the intermediacy of a cyclic structure.

Estimating pKa values for pentaoxyphosphoranes

pKa values are estimated independently, by two entirely different methods, for the ionizations of the apical and equatorial OH groups of two representative hydroxyphosphoranes. A bond length-pKa correlation based on crystal structures of cyclohexanol derivatives gives values of 13.5 +/- 1.5 and 8.62 +/- 1.87, respectively, for the apical and equatorial OH groups of tetracyclohexyloxyhydroxyphosphorane, and an ab initio molecular dynamics calculation gives values of 14.2 and 9.8 for the corresponding first ionizations of pentahydroxyphosphorane.