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Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8596-601. doi: 10.1073/pnas.1421733112. Epub 2015 Jun 29.

Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase γ.

Author information

1
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
2
Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555;
3
Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322;
4
Center for AIDS Research, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322; Veterans Affairs Medical Center, Decatur, GA 30033.
5
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520; ywyin@utmb.edu karen.anderson@yale.edu.
6
Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555; Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555; ywyin@utmb.edu karen.anderson@yale.edu.

Abstract

Nucleoside analog reverse transcriptase inhibitors (NRTIs) are the essential components of highly active antiretroviral (HAART) therapy targeting HIV reverse transcriptase (RT). NRTI triphosphates (NRTI-TP), the biologically active forms, act as chain terminators of viral DNA synthesis. Unfortunately, NRTIs also inhibit human mitochondrial DNA polymerase (Pol γ), causing unwanted mitochondrial toxicity. Understanding the structural and mechanistic differences between Pol γ and RT in response to NRTIs will provide invaluable insight to aid in designing more effective drugs with lower toxicity. The NRTIs emtricitabine [(-)-2,3'-dideoxy-5-fluoro-3'-thiacytidine, (-)-FTC] and lamivudine, [(-)-2,3'-dideoxy-3'-thiacytidine, (-)-3TC] are both potent RT inhibitors, but Pol γ discriminates against (-)-FTC-TP by two orders of magnitude better than (-)-3TC-TP. Furthermore, although (-)-FTC-TP is only slightly more potent against HIV RT than its enantiomer (+)-FTC-TP, it is discriminated by human Pol γ four orders of magnitude more efficiently than (+)-FTC-TP. As a result, (-)-FTC is a much less toxic NRTI. Here, we present the structural and kinetic basis for this striking difference by identifying the discriminator residues of drug selectivity in both viral and human enzymes responsible for substrate selection and inhibitor specificity. For the first time, to our knowledge, this work illuminates the mechanism of (-)-FTC-TP differential selectivity and provides a structural scaffold for development of novel NRTIs with lower toxicity.

KEYWORDS:

HIV reverse transcriptase; drug efficacy and toxicity; human mitochondrial DNA polymerase; mitochondrial toxicity; nucleoside reverse transcriptase inhibitors

PMID:
26124101
PMCID:
PMC4507203
DOI:
10.1073/pnas.1421733112
[Indexed for MEDLINE]
Free PMC Article

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