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Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3475-80. doi: 10.1073/pnas.1420233112. Epub 2015 Mar 2.

Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics.

Author information

1
Rega Institute for Medical Research and jan.balzarini@rega.kuleuven.be.
2
Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8020;
3
Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada;
4
Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
5
Department of Chemistry and School of Pharmacy, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland; and.
6
Department of Chemistry, KU Leuven, B-3000 Leuven, Belgium;
7
Rega Institute for Medical Research and.
8
Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC H3A 1A3, Canada.

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.

KEYWORDS:

(deoxy)nucleoside triphosphate mimic; HIV reverse transcriptase; allosteric inhibition; alpha-carboxy nucleoside phosphonate; herpes virus DNA polymerase

PMID:
25733891
PMCID:
PMC4371953
DOI:
10.1073/pnas.1420233112
[Indexed for MEDLINE]
Free PMC Article

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