PMID: 26124101 , Related PDB ids: 5C51, 5C52, 5C53
Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW
Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8596-601. doi:, 10.1073/pnas.1421733112. Epub 2015 Jun 29.
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 gamma), causing unwanted mitochondrial toxicity. Understanding the structural and mechanistic differences between Pol gamma 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 gamma 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 gamma 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.