Molecular Mechanism of Antagonism between the Y181C and E138K Mutations in HIV-1 Reverse Transcriptase

Oliveira

et al. 2014

J Virol

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Clinical resistance to rilpivirine (RPV), a novel nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI), is associated an E-to-K mutation at position 138 (E138K) in RT together with an M184I/V mutation that confers resistance against emtricitabine (FTC), a nucleoside RT inhibitor (NRTI) that is given together with RPV in therapy. These two mutations can compensate for each other in regard to fitness deficits conferred by each mutation alone, raising the question of why E138K did not arise spontaneously in the clinic following lamivudine (3TC) use, which also selects for the M184I/V mutations. In this context, we have investigated the role of a N348I connection domain mutation that is prevalent in treatment-experienced patients. N348I confers resistance to both the NRTI zidovudine (ZDV) and the NNRTI nevirapine (NVP) and was also found to be associated with M184V and to compensate for deficits associated with the latter mutation. Now, we show that both N348I alone and N348I/ M184V can prevent or delay the emergence of E138K under pressure with RPV or a related NNRTI, termed etravirine (ETR). N348I also enhanced levels of resistance conferred by E138K against RPV and ETR by 2.2-and 2.3-fold, respectively. The presence of the N348I or M184V/N348I mutation decreased the replication capacity of E138K virus, and biochemical assays confirmed that N348I, in a background of E138K, impaired RT catalytic efficiency and RNase H activity. These findings help to explain the low viral replication capacity of viruses containing the E138K/N348I mutations and how N348I delayed or prevented the emergence of E138K in patients with M184V-containing viruses.

Section: Discussionsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 99%

The Connection Domain Mutation N348I in HIV-1 Reverse Transcriptase Enhances Resistance to Etravirine and Rilpivirine but Restricts the Emergence of the E138K Resistance Mutation by Diminishing Viral Replication Capacity

Oliveira

et al. 2014

J Virol

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“…We also wished to provide mechanistic insight into reasons for the favored selection of E138K versus other E138 mutations in the ECHO and THRIVE clinical studies. E138V was also chosen for study because it had been observed in patients who failed ETR-containing therapy in the DUET studies (23) and in cell culture under ETR pressure (34,35) and has not previously been characterized.…”

mentioning

confidence: 99%

Effect of Mutations at Position E138 in HIV-1 Reverse Transcriptase and Their Interactions with the M184I Mutation on Defining Patterns of Resistance to Nonnucleoside Reverse Transcriptase Inhibitors Rilpivirine and Etravirine

Antimicrob Agents Chemother

Asahchop

et al. 2013

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Impacts of mutations at position E138 (A/G/K/Q/R/V) alone or in combination with M184I in HIV-1 reverse transcriptase (RT) were investigated. We also determined why E138K is the most prevalent nonnucleoside reverse transcriptase inhibitor mutation in patients failing rilpivirine (RPV) therapy. Recombinant RT enzymes and viruses containing each of the above-mentioned mutations were generated, and drug susceptibility was assayed. Each of the E138A/G/K/Q/R mutations, alone or in combination with M184I, resulted in decreased susceptibility to RPV and etravirine (ETR). The maximum decrease in susceptibility to RPV was observed for E138/R/Q/G by both recombinant RT assay and cell-based assays. E138Q/R-containing enzymes and viruses also showed the most marked decrease in susceptibility to ETR by both assays. The addition of M184I to the E138 mutations did not significantly change the levels of diminution in drug susceptibility. These findings indicate that E138R caused the highest level of loss of susceptibility to both RPV and ETR, and, accordingly, E138R should be recognized as an ETR resistance-associated mutation. The E138K/Q/R mutations can compensate for M184I in regard to both enzymatic fitness and viral replication capacity. The favored emergence of E138K over other mutations at position E138, together with M184I, is not due to an advantage in either the level of drug resistance or viral replication capacity but may reflect the fact that E138R and E138Q require two distinct mutations to occur, one of which is a disfavorable G-to-C mutation, whereas E138K requires only a single favorable Gto-A hypermutation. Of course, other factors may also affect the concept of barrier to resistance.

“…Recently, deep sequencing analysis of patients who suffered from RPV virologic failure in the phase III studies ECHO and THRIVE showed that K101E and E138K rarely occurred on the same genome (65). However, no natural antagonism seems to exist between K101E and E138K; thus, the occurrence of other mutational pairs associated with NNRTI resistance, such as Y181C and E138K, may be in part a matter of chance in the context of RT enzymes that are functional and commensurate with viral replication capacity (55). In conclusion, enzymatic and cell-based assays show that K101E can play a significant role in resistance to RPV.…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, antagonism seems to exist between E138K and Y181C, and the mechanisms involved have been reported (54,55). In the present study, we have compared the effects of the K101E and E138K substitutions on drug susceptibility using the Monogram PhenoSense HIV RT assay.…”

Section: Discussionmentioning

confidence: 99%

Role of the K101E Substitution in HIV-1 Reverse Transcriptase in Resistance to Rilpivirine and Other Nonnucleoside Reverse Transcriptase Inhibitors

Antimicrob Agents Chemother

Huang³

et al. 2013

Self Cite

Resistance to the recently approved nonnucleoside reverse transcriptase inhibitor (NNRTI) rilpivirine (RPV) commonly involves substitutions at positions E138K and K101E in HIV-1 reverse transcriptase (RT), together with an M184I substitution that is associated with resistance to coutilized emtricitabine (FTC). Previous biochemical and virological studies have shown that compensatory interactions between substitutions E138K and M184I can restore enzyme processivity and the viral replication capacity. Structural modeling studies have also shown that disruption of the salt bridge between K101 and E138 can affect RPV binding. The current study was designed to investigate the impact of K101E, alone or in combination with E138K and/or M184I, on drug susceptibility, viral replication capacity, and enzyme function. We show here that K101E can be selected in cell culture by the NNRTIs etravirine (ETR), efavirenz (EFV), and dapivirine (DPV) as well as by RPV. Recombinant RT enzymes and viruses containing K101E, but not E138K, were highly resistant to nevirapine (NVP) and delavirdine (DLV) as well as ETR and RPV, but not EFV. The addition of K101E to E138K slightly enhanced ETR and RPV resistance compared to that obtained with E138K alone but restored susceptibility to NVP and DLV. The K101E substitution can compensate for deficits in viral replication capacity and enzyme processivity associated with M184I, while M184I can compensate for the diminished efficiency of DNA polymerization associated with K101E. The coexistence of K101E and E138K does not impair either viral replication or enzyme fitness. We conclude that K101E can play a significant role in resistance to RPV. The reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) is crucial for HIV-1 replication and has been an important target of antiretroviral (ARV) therapy (1). Both nucleos(t)ide reverse transcriptase inhibitors [N(t)RTIs] and nonnucleoside reverse transcriptase inhibitors (NNRTIs) are key components of ARV therapy (2), which has led to significant declines in HIV-associated morbidity and mortality (3,4). N(t)RTIs that act as competitive inhibitors and cause chain termination of the growing viral DNA chain include zidovudine (AZT, ZDV), didanosine (ddI), stavudine (d4T), lamivudine (3TC), emtricitabine (FTC), abacavir (ABC), and tenofovir (TFV). In contrast, NNRTIs act allosterically by binding to the NNRTI binding pocket (BP) located 10 Å from the polymerase active site (3) and include earlier drugs, such as nevirapine (NVP), delavirdine (DLV), and efavirenz (EFV), and newer products, such as etravirine (ETR) and rilpivirine (RPV). However, the rapid replication rate of HIV-1 and the error-prone nature of its RT can drive the development of resistance to all ARVs currently in use (5).The earlier NNRTIs, such as NVP and EFV, have a low genetic barrier for development of resistance, and cross-resistance among NNRTIs is common (6, 7). Recently, however, several newer NNRTIs that are diarylpyrimidine (DAPY) compounds, ETR (8, 9) and RPV ...