Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2′-deoxycytidine

• Published in: Proceedings of the National Academy of Sciences - PNAS 2014-08, Vol.111 (32), p.E3252-E3259
• Main Authors: Li, Deyu, Fedeles, Bogdan I, Singh, Vipender, Peng, Chunte Sam, Silvestre, Katherine J, Simi, Allison K, Simpson, Jeffrey H, Tokmakoff, Andrei, Essigmann, John M
• Format: Article
• Language: English
• Subjects: Anti-HIV Agents - chemistry; Anti-HIV Agents - pharmacology; antiretroviral properties; antiviral agents; Azacitidine - analogs & derivatives; Azacitidine - chemistry; Azacitidine - pharmacology; Bacteriophage M13 - drug effects; Bacteriophage M13 - genetics; Bacteriophage M13 - physiology; Base Pairing; Biological Sciences; cell culture; Cells; Correlation analysis; Deoxycytidine - analogs & derivatives; Deoxycytidine - chemistry; Deoxycytidine - pharmacology; drugs; genome; Genome, Viral - drug effects; HIV - drug effects; HIV - genetics; HIV - physiology; Human immunodeficiency virus; Humans; innate immunity; Isomerism; Magnetic Resonance Spectroscopy; Models, Chemical; Molecules; Mutagenesis; mutagenicity; Mutagens - chemistry; Mutagens - pharmacology; nuclear magnetic resonance spectroscopy; nucleic acids; nucleosides; nucleotides; Organic chemicals; patients; PNAS Plus; Spectrophotometry, Infrared; Temperature; tissue culture; virus replication; Virus Replication - drug effects; Virus Replication - genetics
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1405635111

Viral lethal mutagenesis is a strategy whereby the innate immune system or mutagenic pool nucleotides increase the error rate of viral replication above the error catastrophe limit. Lethal mutagenesis has been proposed as a mechanism for several antiviral compounds, including the drug candidate 5-aza-5,6-dihydro-2′-deoxycytidine (KP1212), which causes A-to-G and G-to-A mutations in the HIV genome, both in tissue culture and in HIV positive patients undergoing KP1212 monotherapy. This work explored the molecular mechanism(s) underlying the mutagenicity of KP1212, and specifically whether tautomerism, a previously proposed hypothesis, could explain the biological consequences of this nucleoside analog. Establishing tautomerism of nucleic acid bases under physiological conditions has been challenging because of the lack of sensitive methods. This study investigated tautomerism using an array of spectroscopic, theoretical, and chemical biology approaches. Variable temperature NMR and 2D infrared spectroscopic methods demonstrated that KP1212 existed as a broad ensemble of interconverting tautomers, among which enolic forms dominated. The mutagenic properties of KP1212 were determined empirically by in vitro and in vivo replication of a single-stranded vector containing a single KP1212. It was found that KP1212 paired with both A (10%) and G (90%), which is in accord with clinical observations. Moreover, this mutation frequency is sufficient for pushing a viral population over its error catastrophe limit, as observed before in cell culture studies. Finally, a model is proposed that correlates the mutagenicity of KP1212 with its tautomeric distribution in solution.