1. Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics
- Author
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Johan Vande Voorde, Jubi John, Eddy Arnold, Nuala M. Maguire, Jean A. Bernatchez, Jan Balzarini, Alan Ford, Sandra Liekens, Sergio E. Martinez, Niki Mullins, Anita R. Maguire, Kalyan Das, Marianne Ngure, Matthias Götte, Lieve Naesens, Wim Dehaen, Sarah Keane, and Youngju Kim
- Subjects
Cell Extracts ,Models, Molecular ,Stereochemistry ,Molecular Sequence Data ,Allosteric regulation ,Organophosphonates ,DNA-Directed DNA Polymerase ,chemistry.chemical_compound ,Allosteric Regulation ,Drug Resistance, Viral ,Humans ,heterocyclic compounds ,Nucleotide ,chemistry.chemical_classification ,Multidisciplinary ,Base Sequence ,biology ,Nucleotides ,Chemistry ,Active site ,Nucleosides ,Stereoisomerism ,Biological Sciences ,Phosphonate ,HIV Reverse Transcriptase ,Kinetics ,Enzyme ,Mutation ,Biocatalysis ,Nucleic acid ,biology.protein ,Nucleoside triphosphate ,Reverse Transcriptase Inhibitors ,Nucleoside ,HeLa Cells - 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, 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. ispartof: Proceedings of the National Academy of Sciences of the United States of America vol:112 issue:11 pages:3475-3480 ispartof: location:United States status: published
- Published
- 2015