A Cell-Based Strategy To Assess Intrinsic Inhibition Efficiencies of HIV-1 Reverse Transcriptase Inhibitors

Abstract

During HIV-1 reverse transcription, there are increasing opportunities for nucleos(t)ide (NRTI) or nonnucleoside (NNRTI) reverse transcriptase (RT) inhibitors to stop elongation of the nascent viral DNA (vDNA). In addition, RT inhibitors appear to influence the kinetics of vDNA synthesis differently. While cell-free kinetic inhibition constants have provided detailed mechanistic insight, these assays are dependent on experimental conditions that may not mimic the cellular milieu. Here we describe a novel cell-based strategy to provide a measure of the intrinsic inhibition efficiencies of clinically relevant RT inhibitors on a perstop-site basis. To better compare inhibition efficiencies among HIV-1 RT inhibitors that can stop reverse transcription at any number of different stop sites, their basic probability, p, of getting stopped at any potential stop site was determined. A relationship between qPCR-derived 50% effective inhibitory concentrations (EC 50 s) and this basic probability enabled determination of p by successive approximation. On a per-stop-site basis, tenofovir (TFV) exhibited 1.4-fold-greater inhibition efficiency than emtricitabine (FTC), and as a class, both NRTIs exhibited an 8-to 11-fold greater efficiency than efavirenz (EFV). However, as more potential stops sites were considered, the probability of reverse transcription failing to reach the end of the template approached equivalence between both classes of RT inhibitors. Overall, this novel strategy provides a quantitative measure of the intrinsic inhibition efficiencies of RT inhibitors in the natural cellular milieu and thus may further understanding of drug efficacy. This approach also has applicability for understanding the impact of viral polymerase-based inhibitors (alone or in combination) in other virus systems.T he HIV-encoded reverse transcriptase (RT) enzyme catalyzes the initiation, elongation, and termination of viral DNA (vDNA) synthesis through an ordered multistep process known as reverse transcription (Fig. 1A) (1, 2). This process, by which single-stranded HIV-1 RNA is converted to double-stranded HIV-1 DNA, follows a series of successive events whereby the product of each nucleoside incorporation serves as a substrate for the following reaction until the end of the genomic template is reached. First, minus-strand vDNA synthesis is initiated inefficiently from a primer-binding site (PBS) by a cell-derived tRNA 3Lys primer, resulting in the formation of minus-strand strong-stop vDNA product (3). Initiation is then followed by a processive mode of vDNA synthesis with continued elongation (4). Subsequent steps in reverse transcription involve selective degradation of genomic vRNA, minus-strand transfer, initiation of plus-strand vDNA from polypurine tracts (PPT and cPPT), formation of plus-strand strong-stop vDNA product, plus-strand transfer, and continued minus-and plus-strand vDNA synthesis until the end of the template is reached and full-length viral double-stranded DNA (dsDNA) is formed (5).Due to its essential role in ...

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

“…To date, monitoring of HIV-1 RT progression in infected cells has primarily been accomplished by measuring reverse transcription products of various length with quantitative PCR (qPCR) using primer-probe sets that uniquely measure shorter or longer (early and late, respectively) cDNA products12,13,14. While this qPCR approach is appropriate to determine intrinsic efficiencies of the reverse transcription process in cellular systems, the output is of relatively low resolution, with no sequence information being derived.…”