title: A transient kinetic approach to investigate nucleoside inhibitors of mitochondrial DNA polymerase gamma.
abstract: Nucleoside analogs play an essential role in treating human immunodeficiency virus (HIV) infection since the beginning of the AIDS epidemic and work by inhibition of HIV-1 reverse transcriptase (RT), a viral polymerase essential for DNA replication. Today, over 90% of all regimens for HIV treatment contain at least one nucleoside. Long-term use of nucleoside analogs has been associated with adverse effects including mitochondrial toxicity due to inhibition of the mitochondrial polymerase, DNA polymerase gamma (mtDNA pol gamma). In this review, we describe our efforts to delineate the molecular mechanism of nucleoside inhibition of HIV-1 RT and mtDNA pol gamma based upon a transient kinetic approach using rapid chemical quench methodology. Using transient kinetic methods, the maximum rate of polymerization (k(pol)), the dissociation constant for the ground state binding (K(d)), and the incorporation efficiency (k(pol)/K(d)) can be determined for the nucleoside analogs and their natural substrates. This analysis allowed us to develop an understanding of the structure activity relationships that allow correlation between the structural and stereochemical features of the nucleoside analog drugs with their mechanistic behavior toward the viral polymerase, RT, and the host cell polymerase, mtDNA pol gamma. An in-depth understanding of the mechanisms of inhibition of these enzymes is imperative in overcoming problems associated with toxicity.
authors.affiliation: Yale University School of Medicine, Department of Pharmacology, 333 Cedar Street, P.O. Box 208066, New Haven, CT 06520-8066, USA. karen.anderson@yale.edu
authors.forename: Karen S
authors.initials: KS
authors.lastname: Anderson
mesh_terms: D000074002:DNA Polymerase gamma; D004261:DNA Replication / Q000187:drug effects; D004272:DNA, Mitochondrial / Q000096:biosynthesis*; D004259:DNA-Directed DNA Polymerase / Q000235:genetics; D004791:Enzyme Inhibitors / Q000494:pharmacology* / Q000633:toxicity; D054303:HIV Reverse Transcriptase / Q000037:antagonists & inhibitors; D006801:Humans; D066298:In Vitro Techniques; D007700:Kinetics; D008954:Models, Biological; D019384:Nucleic Acid Synthesis Inhibitors; D009705:Nucleosides / Q000494:pharmacology* / Q000633:toxicity; D010597:Pharmacogenetics / Q000639:trends; D020641:Polymorphism, Single Nucleotide; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology
chemical_list: D004272:DNA, Mitochondrial; D004791:Enzyme Inhibitors; D019384:Nucleic Acid Synthesis Inhibitors; D009705:Nucleosides; D018894:Reverse Transcriptase Inhibitors; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D000074002:DNA Polymerase gamma; D004259:DNA-Directed DNA Polymerase; C413027:POLG protein, human