Structure of Cyclic Nucleoside Phosphonate Ester Prodrugs: An Inquiry

Crystal structure, Hirshfeld surface analysis, inter-molecular inter-action energies, energy frameworks and DFT calculations of 4-amino-1-(prop-2-yn-1-yl)pyrimidin-2(1H)-one

In the title mol-ecule, C7H7N3O, the pyrimidine ring is essentially planar, with the propynyl group rotated out of this plane by 15.31 (4)°. In the crystal, a tri-periodic network is formed by N-H⋯O, N-H⋯N and C-H⋯O hydrogen-bonding and slipped π-π stacking inter-actions, leading to narrow channels extending parallel to the c axis. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (36.2%), H⋯C/C⋯H (20.9%), H⋯O/O⋯H (17.8%) and H⋯N/N⋯H (12.2%) inter-actions, showing that hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions. The mol-ecular structure optimized by density functional theory (DFT) calculations at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The HOMO-LUMO behaviour was also elucidated to determine the energy gap.

Synthesis and crystal structure of benzyl 5-oxo-5-phenyl-2-(quinolin-2-yl)pentanoate, C27H23NO3

C27H23NO3, monoclinic, P21 (no. 4), a = 5.8236(4) Å, b = 16.7277(13) Å, c = 10.5963(7) Å, β = 96.022(2)°, V = 1026.55(13) Å3, Z = 2, R gt(F) = 0.0396, wR ref(F 2) = 0.0953, T = 153(2) K.

Evolution of an amino acid based prodrug approach: stay tuned

Certain acyclic nucleoside phosphonates (ANPs) such as (S)-HPMPC (cidofovir, Vistide) and (S)-HPMPA have been shown to be active against a broad spectrum of DNA and retroviruses. However, their poor absorption as well as their toxicity limit the utilization of these therapeutics in the clinic. Nucleoside phosphonates are poorly absorbed primarily due to the presence of the phosphonic acid group, which ionizes at physiological pH. When dosed intravenously they display dose-limiting nephrotoxicity due to their accumulation in the kidney. To overcome these limitations, nucleoside phosphonate prodrug strategies have taken center stage in the development pathway and a number of different approaches are at various stages of development. Our efforts have focused on the development of ANP prodrugs in which a benign amino acid promoiety masks a phosphonate P-OH via a hydroxyl side chain. The design of these prodrugs incorporates multiple chemical groups (the P-X-C linkage, the amino acid stereochemistry, the C-terminal and N-terminal functional groups) that can be tuned to modify absorption, pharmacokinetic and efficacy properties with the goal of improving overall prodrug performance.