Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics.

ABSTRACT: 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, ?-carboxy nucleoside phosphonate (?-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that ?-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 ?-CNP acts as the potential equivalent of the ?-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the ?-CNP chelate Mg(2+), mimicking the chelation by the ?- and ?-phosphate oxygens of dNTPs. ?-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, ?-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. ?-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active- or regulatory-site inhibitors with therapeutic potential.

SUBMITTER: Balzarini J 

PROVIDER: S-EPMC4371953 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature