Balzarini, J;Das, K;Bernatchez, JA;Martinez, SE;Ngure, M;Keane, S;Ford, A;Maguire, N;Mullins, N;John, J;Kim, Y;Dehaen, W;Vande Voorde, J;Liekens, S;Naesens, L;Gotte, M;Maguire, AR;Arnold, E

2015

March

Proceedings of The National Academy of Sciences of The United States of America

Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics

Validated

Altmetric: 2 ()

HIV-1 REVERSE-TRANSCRIPTASE PROTEIN-COUPLED RECEPTORS POLYMERASE TRANSLOCATION THYMIDINE KINASE DNA-POLYMERASES 647V CELLS IN-VITRO MECHANISM INHIBITION ACTIVATION

112

3475

3480

Polymerases have a structurally highly conserved negatively charged amino acid motif that is strictly required for Mg2+ cation-dependent catalytic incorporation of (d)NTP nucleotides into nucleic acids. Based on these characteristics, a nucleoside monophosphonate scaffold, alpha-carboxy nucleoside phosphonate (alpha-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that alpha-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 alpha-CNP acts as the potential equivalent of the alpha-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the alpha-CNP chelate Mg2+, mimicking the chelation by the beta- and gamma-phosphate oxygens of dNTPs. alpha-CNPs (i) do not require metabolic activation (phosphorylation), (ii) bind directly to the substrate-binding site, (iii) chelate one of the two active site Mg2+ ions, and (iv) reversibly inhibit the polymerase catalytic activity without being incorporated into nucleic acids. In addition, alpha-CNPs were also found to selectively interact with regulatory (i.e., allosteric) Mg2+-dNTP-binding sites of nucleos(t)ide-metabolizing enzymes susceptible to metabolic regulation. alpha-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active- or regulatory-site inhibitors with therapeutic potential.

WASHINGTON

0027-8424

10.1073/pnas.1420233112