Polymerases have a structurally highly conserved negatively charged amino acid motif that is strictly required for Mg 2+ cation-dependent catalytic incorporation of (d)NTP nucleotides into nucleic acids. Based on these characteristics, a nucleoside monophosphonate scaffold, α-carboxy nucleoside phosphonate (α-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that α-CNPs mimic the dNTP binding through a carboxylate oxygen, two phosphonate oxygens, and base-pairing with the template. In particular, the carboxyl oxygen of the α-CNP acts as the potential equivalent of the α-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the α-CNP chelate Mg 2+ , mimicking the chelation by the β-and γ-phosphate oxygens of dNTPs. α-CNPs (i) do not require metabolic activation (phosphorylation), (ii) bind directly to the substrate-binding site, (iii) chelate one of the two active site Mg 2+ ions, and (iv) reversibly inhibit the polymerase catalytic activity without being incorporated into nucleic acids. In addition, α-CNPs were also found to selectively interact with regulatory (i.e., allosteric) Mg 2+ -dNTP-binding sites of nucleos(t)ide-metabolizing enzymes susceptible to metabolic regulation. α-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active-or regulatory-site inhibitors with therapeutic potential. The polymerization of nucleotides by Escherichia coli DNA polymerase I represents a general model for catalytic action of nucleic acid polymerases (SI Appendix, Fig. S1) (1, 2). According to this model, there is a universal role for the Mg 2+ cation to interact with three phosphate oxygens of dNTP. The highly conserved consensus motifs in every polymerase active site consist of either aspartate or glutamate residues that chelate Mg 2+ through three additional coordination bonds during polymerization (2, 3). The crucial role of the metal cofactor and structurally conserved active site architecture in polymerases has also been demonstrated by validating Mg 2+ as a target for the design of antiviral drugs, not only against HIV RT but also, among others, against HIV integrase, HIV ribonuclease H (RNase H), and influenza-encoded endonuclease (4, 5). Hence, it should be feasible to design a universal but simplified (d)NTP mimic that binds efficiently to a wide variety of DNA/RNA polymerases.It was hypothesized that a universal nucleoside triphosphate mimic should contain three major indispensable entities: (i) a nucleobase part (i.e., to achieve optimal Watson-Crick basepairing with the template overhang), (ii) a replacement of the triphosphate moiety that should enable efficient Mg 2+ -directed coordination, and (iii) a variable linker between the nucleobase and the modified triphosphate to mimic the pentose entity present in natural (d)NTPs. For the triphosphate part, we chose an α-carboxy phosphonate entity that is chemically stable in physiolog...

The synthesis of the first series of a new class of nucleoside phosphonate analogues is described. Addition of a carboxyl group at the α position of carbocyclic nucleoside phosphonate analogues leads to a novel class of potent HIV reverse transcriptase (RT) inhibitors, α-carboxy nucleoside phosphonates (α-CNPs). Key steps in the synthesis of the compounds are Rh-catalyzed O-H insertion and Pd-catalyzed allylation reactions. In cell-free assays, the final products are markedly inhibitory against HIV RT and do not require phosphorylation to exhibit anti-RT activity, which indicates that the α-carboxyphosphonate function is efficiently recognized by HIV RT as a triphosphate entity, an unprecedented property of nucleoside monophosph(on)ates.

A novel 1:1 cocrystal between p-toluenesulfonamide and triphenylphosphine oxide has been prepared and structurally characterized. This 1:1 cocrystal was observed to form during solid state grinding experiments, with subsequent formation of a known 3:2 cocrystal in the presence of excess sulfonamide. Both cocrystals are stable in the solid state. The ternary phase diagram for the two coformers was constructed in two different solvents: acetonitrile and dichloromethane. Examination of these diagrams clarified solution crystallization of both the newly discovered 1:1 cocrystal and the previously reported 3:2 cocrystal, and identified regions of stability for each cocrystal in each solvent. The choice of solvent was found to have a significant effect on the position of the solid state regions within a cocrystal system.

α-Carboxy nucleoside phosphonates (α-CNPs) are modified nucleotides that represent a novel class of nucleotide-competing reverse transcriptase (RT) inhibitors (NcRTIs). They were designed to act directly against HIV-1 RT without the need for prior activation (phosphorylation). In this respect, they differ from the nucleoside or nucleotide RTIs [N(t)RTIs] that require conversion to their triphosphate forms before being inhibitory to HIV-1 RT. The guanine derivative (G-α-CNP) has now been synthesized and investigated for the first time. The (L)-(+)-enantiomer of G-α-CNP directly and competitively inhibits HIV-1 RT by interacting with the substrate active site of the enzyme. The (D)-(−)-enantiomer proved inactive against HIV-1 RT. In contrast, the (+)- and (−)-enantiomers of G-α-CNP inhibited herpes (i.e. HSV-1, HCMV) DNA polymerases in a non- or uncompetitive manner, strongly indicating interaction of the (L)-(+)- and the (D)-(−)-G-α-CNPs at a location different from the polymerase substrate active site of the herpes enzymes. Such entirely different inhibition profile of viral polymerases is unprecedented for a single antiviral drug molecule. Moreover, within the class of α-CNPs, subtle differences in their sensitivity to mutant HIV-1 RT enzymes were observed depending on the nature of the nucleobase in the α-CNP molecules. The unique properties of the -CNPs make this class of compounds, including G-α-CNP, direct acting inhibitors of multiple viral DNA polymerases.

As α-carboxy nucleoside phosphonates (α-CNPs) have demonstrated a novel mode of action of HIV-1 reverse transcriptase inhibition, structurally related derivatives were synthesized, namely the malonate 2, the unsaturated and saturated bisphosphonates 3 and 4, respectively and the amide 5. These compounds were evaluated for inhibition of HIV-1 reverse transcriptase in cell-free assays. The importance of the α-carboxy phosphonoacetic acid moiety for achieving reverse transcriptase inhibition, without the need for prior phosphorylation, was confirmed. The malonate derivative 2 was less active by two orders of magnitude than the original α-CNPs, while displaying the same pattern of kinetic behavior; interestingly the activity resides in the “L”-enantiomer of 2, as seen with the earlier series of α-CNPs. A crystal structure with an RT/DNA complex at 2.95 Å resolution revealed the binding of the “L”-enantiomer of 2, at the polymerase active site with a weaker metal ion chelation environment compared to 1a (T-α-CNP) which may explain the lower inhibitory activity of 2.