HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection

Abstract

Nucleoside analogs (NAs) are used to treat numerous viral infections and cancer. They compete with endogenous nucleotides (dNTP/NTP) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension. To date, an integrated mathematical model that could allow the analysis of their mechanism of action, of the various resistance mechanisms, and their effect on viral fitness is still lacking. We present the first mechanistic mathematical model of polymerase inhibition by NAs that takes into account the reversibility of polymerase inhibition. Analytical solutions for the model point out the cellular- and kinetic aspects of inhibition. Our model correctly predicts for HIV-1 that resistance against nucleoside analog reverse transcriptase inhibitors (NRTIs) can be conferred by decreasing their incorporation rate, increasing their excision rate, or decreasing their affinity for the polymerase enzyme. For all analyzed NRTIs and their combinations, model-predicted macroscopic parameters (efficacy, fitness and toxicity) were consistent with observations. NRTI efficacy was found to greatly vary between distinct target cells. Surprisingly, target cells with low dNTP/NTP levels may not confer hyper-susceptibility to inhibition, whereas cells with high dNTP/NTP contents are likely to confer natural resistance. Our model also allows quantification of the selective advantage of mutations by integrating their effects on viral fitness and drug susceptibility. For zidovudine triphosphate (AZT-TP), we predict that this selective advantage, as well as the minimal concentration required to select thymidine-associated mutations (TAMs) are highly cell-dependent. The developed model allows studying various resistance mechanisms, inherent fitness effects, selection forces and epistasis based on microscopic kinetic data. It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment.

In Vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis

“…The relative fitness estimated for the individual isolates ranged from 59% to 79% for the distinct isolates, which is generally consistent with previous in vivo estimates [46] and predictions from mechanistic mathematical models of HIV-1 DNA polymerization [7].…”

“…Mutations resulting from exposure to one RT inhibitor may alter the phenotype of mutations selected by another RT inhibitor, through functional or conformational perturbation of the enzyme. Epistasis in HIV-1 has been studied in the absence of drugs [47] and after application of single drugs [7], [48]. Due to the complexity of the laboratory work required and the many possible permutations resulting from a variety of parameters, passage experiments using multiple drugs simultaneously have not yet been studied in detail.…”

“…Lamivudine (3 TC) is the most commonly used NRTI. Its triphosphate (3 TC-TP) competes with endogenous deoxycytosine triphosphate for incorporation into the nascent viral DNA during reverse transcription, where it inhibits HIV DNA elongation [7]. Adefovir (ADV) is an adenosine-monophosphate analogue, which in diphosphate form, acts as a chain-terminator competing with deoxyadenosine triphosphate for incorporation into viral DNA.…”

“…NVP resistance mutations within the NNRTI binding pocket decrease NVP binding to RT by means of steric hindrance [10]. Lamivudine (3 TC) resistance conferred by the M184V mutation, decreases the affinity of 3 TC-TP for the primer/template complex during reverse transcription [7]. In contrast, ADV (and tenofovir) resistance selectively decreases incorporation of ADV phosphonate into viral DNA [11], [12], associated with mutations at K70E and K65R.…”

Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance

“…Thereby, residue R72 in Q151M (or Q151Mc) RT may slow down the rate of release of PPi for ddNTP incorporation versus that for dNTP incorporation and contribute to ddNTP discrimination. While biochemical and structural information helps provide an understanding of the phenotypic characteristics of drug resistance mutations, there are several complex factors, such as the distribution of infected cell types and evolutionary dynamics, that influence infectivity, the effects of drug resistance, and compensatory mutations (44); statistical analysis of the fitness of a large number of HIV variants demonstrated the existence of epistasis in HIV (45). The Q151M mutation provides a strong example of a primary mutation that leads to fitness defects in HIV-1 RT, as reflected by deleterious effects on polymerase catalysis and the viral replication rate, that become entrenched upon accompaniment by the compensatory mutations A62V, V75I, F77L, and F116Y in Q151Mc to restore enzymatic and viral fitness.…”