Extent and importance of cross-resistance to efavirenz after nevirapine failure

Recent Advances in the Design and Development of Non-nucleoside Reverse Transcriptase Inhibitor Scaffolds

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have always been an important part of the anti-HIV-1 combination therapy known as combination antiretroviral therapy (cART) since 1996. The use of NNRTIs for about 22 years has led to some mutations in the residues that compose the reverse transcriptase active site, resulting in the emergence of drug-resistant viruses. Thus, the search for new potent NNRTIs with an improved safety profile and activity against drug-resistant HIV strains is indispensable, and many hit and lead NNRTIs have been discovered in the last decade. This review provides an overview of the development in this field from 2013 to August 2018.

Time to Viremia for Patients Taking their First Antiretroviral Regimen and the Subsequent Resistance Profiles

BACKGROUND

The resistance profiles for patients on first-line antiretroviral therapy (ART) regimens after viremia have not been well studied in community clinic settings in the modern treatment era.

OBJECTIVE

To determine time to viremia and the ART resistance profiles of viremic patients.

METHODS

HIV-positive patients aged ≥16 years initiating a three-drug regimen were retrospectively identified from 01/01/06 to 12/31/12. The regimens were a backbone of two nucleoside reverse transcriptase inhibitors (NRTIs) and a third agent: a protease inhibitor (PI), non-nucleoside reverse transcriptase inhibitor (NNRTI), or an integrase inhibitor (II). Time to viremia was compared using a proportional hazards model, adjusting for demographic and clinical factors. Resistance profiles were described in those with baseline and follow-up genotypes.

RESULTS

For 653 patients, distribution of third-agent use and viremia was: 244 (37%) on PIs with 80 viremia, 364 (56%) on NNRTIs with 84 viremia, and 45 (7%) on II with 11 viremia. Only for NNRTIs, time to viremia was longer than PIs (p = 0.04) for patients with a CD4 count ≥200 cells/mm(3). Of the 175 with viremia, 143 (82%) had baseline and 37 (21%) had follow-up genotype. Upon viremia, emerging ART resistance was rare. One new NNRTI (Y181C) mutation was identified and three patients taking PI-based regimens developed NRTI mutations (M184 V, M184I, and T215Y).

CONCLUSIONS

Time to viremia for NNRTIs was longer than PIs. With viremia, ART resistance rarely developed without PI or II mutations, but with a few NRTI mutations in those taking PI-based regimens, and NNRTI mutations in those taking NNRTI-based regimens.

Discovery of the Aryl-phospho-indole IDX899, a Highly Potent Anti-HIV Non-nucleoside Reverse Transcriptase Inhibitor

Here, we describe the design, synthesis, biological evaluation, and identification of a clinical candidate non-nucleoside reverse transcriptase inhibitors (NNRTIs) with a novel aryl-phospho-indole (APhI) scaffold. NNRTIs are recommended components of highly active antiretroviral therapy (HAART) for the treatment of HIV-1. Since a major problem associated with NNRTI treatment is the emergence of drug resistant virus, this work focused on optimization of the APhI against clinically relevant HIV-1 Y181C and K103N mutants and the Y181C/K103N double mutant. Optimization of the phosphinate aryl substituent led to the discovery of the 3-Me,5-acrylonitrile-phenyl analogue RP-13s (IDX899) having an EC50 of 11 nM against the Y181C/K103N double mutant.

Resistance patterns selected by nevirapine vs. efavirenz in HIV-infected patients failing first-line antiretroviral treatment: a bayesian analysis

Background

WHO recommends starting therapy with a non-nucleoside reverse transcriptase inhibitor (NNRTI) and two nucleoside reverse transcriptase inhibitors (NRTIs), i.e. nevirapine or efavirenz, with lamivudine or emtricitabine, plus zidovudine or tenofovir. Few studies have compared resistance patterns induced by efavirenz and nevirapine in patients infected with the CRF01_AE Southeast Asian HIV-subtype. We compared patterns of NNRTI- and NRTI-associated mutations in Thai adults failing first-line nevirapine- and efavirenz -based combinations, using Bayesian statistics to optimize use of data.

Methods and Findings

In a treatment cohort of HIV-infected adults on NNRTI-based regimens, 119 experienced virologic failure (>500 copies/mL), with resistance mutations detected by consensus sequencing. Mutations were analyzed in relation to demographic, clinical, and laboratory variables at time of genotyping. The Geno2Pheno system was used to evaluate second-line drug options. Eighty-nine subjects were on nevirapine and 30 on efavirenz. The NRTI backbone consisted of lamivudine or emtricitabine plus either zidovudine (37), stavudine (65), or tenofovir (19). The K103N mutation was detected in 83% of patients on efavirenz vs. 28% on nevirapine, whereas Y181C was detected in 56% on nevirapine vs. 20% efavirenz. M184V was more common with nevirapine (87%) than efavirenz (63%). Nevirapine favored TAM-2 resistance pathways whereas efavirenz selected both TAM-2 and TAM-1 pathways. Emergence of TAM-2 mutations increased with the duration of virologic replication (OR 1.25–1.87 per month increment). In zidovudine-containing regimens, the overall risk of resistance across all drugs was lower with nevirapine than with efavirenz, whereas in tenofovir-containing regimen the opposite was true.

Conclusions

TAM-2 was the major NRTI resistance pathway for CRF01_AE, particularly with nevirapine; it appeared late after virological failure. In patients who failed, there appeared to be more second-line drug options when zidovudine was combined with nevirapine or tenofovir with efavirenz than with alternative combinations.

Efavirenz-based combination antiretroviral therapy after peripartum single-dose nevirapine

Single-dose nevirapine (sdNVP) reduces mother-to-child HIV transmission, but induces NVP resistance and subsequent NVP-based combination antiretroviral therapy (cART) may fail. Some resistance mutations affect NVP more than efavirenz (EFV). We evaluated virological suppression of EFV-based cART in women after sdNVP. A retrospective analysis matched 107 women who had received sdNVP within the 24 months before cART (cases) with women who had never received sdNVP (controls). By total cohort (intention-to-continue treatment) at week 96, 65% of cases and 73% of controls had a viral load (VL) <400 copies/mL and 63% of cases and 64% of controls had VL <25 copies/mL. At weeks 48 and 96, women starting cART less than six months after sdNVP (n = 20) had VL <400 copies/mL of 90% and 75%, respectively compared with 90% and 70%, respectively, for controls. Overall 172 (80%) women reached week 96. EFV-based cART, in field conditions, was effective for women after sdNVP, even within six months of sdNVP.

Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors

OBJECTIVES

K103N, the most common nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutation in patients with transmitted resistance and in patients receiving a failing NNRTI-containing regimen, is fully susceptible to the new NNRTI, etravirine. Therefore, we sought to determine how often NNRTI-resistant mutations other than K103N occur as minority variants in plasma samples for which standard genotypic resistance testing detects K103N alone.

METHODS

We performed ultradeep pyrosequencing (UDPS; 454 Life Sciences a Roche Company, Branford, CT) of plasma virus samples from 13 treatment-naive and 20 NNRTI-experienced patients in whom standard genotypic resistance testing revealed K103N but no other major NNRTI-resistance mutations.

RESULTS

Samples from 0 of 13 treatment-naive patients vs. 7 of 20 patients failing an NNRTI-containing regimen had minority variants with major etravirine-associated NNRTI-resistant mutations (P = 0.03, Fisher exact test): Y181C (7.0%), Y181C (3.6%) + G190A (3.2%), L100I (14%), L100I (32%) + 190A (5.4%), K101E (3.8%) + G190A (4.9%), K101E (4.0%) + G190S (4.8%), and G190S (3.1%).

CONCLUSIONS

In treatment-naive patients, UDPS did not detect additional major NNRTI-resistant mutations suggesting that etravirine may be effective in patients with transmitted K103N. In NNRTI-experienced patients, UDPS often detected additional major NNRTI-resistant mutations suggesting that etravirine may not be fully active in patients with acquired K103N.

Comparison of genotypic resistance profiles and virological response between patients starting nevirapine and efavirenz in EuroSIDA

OBJECTIVE

To compare virological outcome and genotypic resistance profiles in HIV-1-infected patients starting non-nucleoside reverse transcriptase inhibitor (NNRTI)-containing regimens.

METHODS

NNRTI-naive patients were included who started treatment with nevirapine (NVP) or efavirenz (EFV) with genotypic resistance test results available at time of initiation (baseline). Virological failure was defined as two consecutive values > 500 copies/ml after starting the regimen. Cox models were used to investigate time to virological failure (the first of two values).

RESULTS

A total of 759 patients were included (13% antiretroviral-naive): 389 initiated NVP and 370 initiated EFV. Baseline IAS-USA NNRTI resistance mutations were detected in 3%. Using the Rega algorithm (version 7.1) to interpret resistance, 460 (64%) patients had resistance (full or intermediate) to at least one drug they were starting (69% NVP, 60% EFV, P = 0.011); 287 (74%) NVP and 168 (45%) EFV patients experienced virological failure after treatment initiation, P < 0.001. After adjustment for previous antiretroviral use, previous AIDS, year started NNRTI, CD4 cell count (baseline, nadir), viral load (baseline, maximum), and baseline drug resistance (measured by Rega), the relative hazards (EFV versus NVP) of virological failure was 0.50, 95% confidence interval: 0.39-0.65, P < 0.001. At time of virological failure, comparable levels of NNRTI resistance were detected. The K103N mutation emerged more in patients failing EFV and Y181C in patients failing NVP.

CONCLUSIONS

NVP may be associated with an inferior virological outcome compared to EFV in NNRTI-naive patients with extensive resistance to other drug classes. The profile of NNRTI resistance mutations when virologically failing an NNRTI-containing regimen appears to depend on the NNRTI the patients fail.

Impact of drug resistance genotypes on CD4+ counts and plasma viremia in heavily antiretroviral-experienced HIV-infected patients

The number of HIV-infected individuals with prior multiple treatment failures is increasing as time passes by. The success of antiretroviral therapy in these patients is often compromised by the selection of drug-resistant viruses. Despite initial concerns, a rebound in AIDS cases among heavily treatment-experienced patients failing virologically their antiretroviral therapy has not occurred yet. In a multicenter study conducted in Spain, HIV-infected patients were assessed with prior failure to antiretrovirals from the three main drug families who presented during the last semester of the year 2003 with plasma HIV-RNA values above 1,000 copies/ml, despite good treatment adherence. The relationships between CD4+ T cell counts, viral loads and drug-resistant genotypes were examined. A total of 273 patients were identified in 12 centers (78% male, median age: 41 years). The mean viral load was 50,438 copies/ml and the mean CD4+ count was 328 cells/mul. Only 19.5% had less than 200 CD4+ T cells/mul. Most patients (95%) were receiving nucleoside reverse transcriptase inhibitors (NRTI) in their last antiretroviral regimen, while 63% were treated with protease inhibitors (PI) and 27% on non-nucleoside reverse transcriptase inhibitors (NNRTI). Overall, 97.4% had at least one drug resistance mutation (87.2% for NRTI, 68.5% for NNRTI, and 92.7% for PI). Using the virtual phenotype, resistance to three or more drugs within each class was recognized in 45.8% for NRTI, 40.7% for NNRTI, and 44.7% for PI. Moreover, cross-resistance to compounds from two or three drug families was recognized in 41% and 19.4% of patients, respectively. Nearly half of the patients had plasma HIV-RNA below 10,000 copies/ml and they showed significantly higher CD4 + counts than those with greater viremia (408 versus 259 cells/mul; P < 0.001). Patients with higher plasma viremia had significantly more drug resistance mutations than those with lower viremia. No favorable effect on viral load could be recognized for individual drug resistance mutations known to reduce viral fitness in vitro (i.e., rtM184V, rtL74V, rtK65R, proD30N, or proI50L). In summary, a large proportion of treatment-experienced patients failing their current antiretroviral regimen carry viruses with broad cross-resistant genotypes. Nearly half of the patients with these multi-drug resistant viruses had < 10,000 HIV-RNA copies/ml and 80% have more than 200 CD4 + T cells/mul. Thus, maintaining treatment HIV-infected individuals failing virologically and harboring drug-resistant viruses might ameliorate immunological deterioration until new drugs became available. J. Med. Virol. 77:23-28, 2005. (c) 2005 Wiley-Liss, Inc.

Efavirenz Versus Nevirapine in Current Clinical Practice: A Prospective, Open-Label Observational Study

An open-label, observational, prospective 18-month survey was conducted to compare the efficacy and tolerability of the 2 available nonnucleoside reverse transcriptase inhibitors (NNRTIs) in all possible indications of current clinical practice. A broad range of clinical and laboratory variables accounting for drug efficacy and tolerability (with special emphasis on metabolic and hepatic toxicity) were measured in 287 evaluable patients treated with efavirenz, compared with 258 subjects taking nevirapine for 18 months. A separate efficacy analysis was performed in 154 antiretroviral-naive subjects, 298 patients experienced with 2-7 prior anti-HIV lines who abandoned protease inhibitors (PIs), and 103 subjects entering a salvage regimen containing at least 4 drugs, including PIs. Antiretroviral-naive patients experienced greater efavirenz activity at 3-12 months (maximum HIV RNA drop =-2.4 log(10) copies/mL), associated with a significantly higher rate of complete viral suppression, while immunologic results proved significant only after 6-9 months. When assessing experienced patients and those on rescue regimens, a similar and progressively blunted laboratory response was achieved, on the ground of a worse baseline virologic and immunologic profile, and duration of prior anti-HIV therapy. Both first-month (4.2 and 4.3% for efavirenz and nevirapine, respectively) and overall discontinuation rates (11.5 and 12%, respectively) proved similar, but a profound difference emerged as to the different spectrum of untoward events: central nervous system (CNS) disturbances, persisting metabolic abnormalities, and possibly gynecomastia and laboratory pancreatic abnormalities for efavirenz vs. immediate allergy and increased hepatotoxicity (regardless of chronic infection with hepatitis B or C virus and methadone use) for nevirapine. A limited virologic and immunologic advantage of efavirenz was observed in the first 12-month assessment of antiretroviral-naive patients, whereas all other examined situations did not disclose relevant efficacy differences between efavirenz and nevirapine throughout the 18-month comparison. Although the short- and long-term toxicity and withdrawal rates of the 2 drugs were comparable, the different pathways prompting allergic, metabolic, liver, and CNS disturbances observed with NNRTIs deserve careful investigation, to prevent toxicity of these relevant antiretroviral compounds.

Long-Term Virological Response to Multiple Sequential Regimens of Highly Active Antiretroviral Therapy for HIV Infection

Objective

Information about the virological response to sequential highly active antiretroviral therapy (HAART) for HIV infection is limited. The virological response to four consecutive therapies was evaluated in the Swiss HIV Cohort.

Design

Retrospective analysis in an observational cohort.

Methods

1140 individuals receiving uninterrupted HAART for 4.8 ±0.6 years were included. The virological response was classified as success (<400 copies/ml), low-level (LF: 400–5000 copies/ml) or high-level failure (HF: >5000 copies/ml). Potential determinants of the virological response, including patient demographics, treatment history and virological response to previous HAART regimens were analysed using survival and logistic regression analyses.

Results

40.1% failed virologically on the first (22.0% LF; 18.1% HF), 35.1% on the second (14.2% LF; 20.9% HF), 34.2% on the third (9.9% LF; 24.3% HF) and 32.7% on the fourth HAART regimen (9% LF; 23.7% HF). Nucleoside pre-treatment (OR: 2.34; 95% CI: 1.67–3.29) and low baseline CD4 T-cell count (OR: 0.79/100 cells rise; 95% CI: 0.72–0.88) increased the risk of HF on the first HAART. Virological failure on HAART with HIV-1 RNA levels exceeding 1000 copies/ml predicted a poor virological response to subsequent HAART regimens. A switch from a protease inhibitor- to a non-nucleoside reverse transcriptase inhibitor-containing regimen significantly reduced the risk of HF. Multiple switches of HAART did not affect the recovery of CD4 T lymphocytes.

Conclusion

Multiple sequential HAART regimens do not per se reduce the likelihood of long-term virological suppression and immunological recovery. However, early virological failure increases significantly the risk of subsequent unfavourable virological responses. The choice of a potent initial antiretroviral drug regimen is therefore critical. This study has been presented in part at the 10th Conference on Retroviruses & Opportunistic Infections. Boston, Mass., USA, 2003. Abstract #571.

New patterns of HIV-1 resistance during HAART

HIV-1 resistance and subsequent virologic failure occur in a substantial proportion of HIV-infected patients receiving HAART regimens. In the present article, we summarize new data on resistance to current and forthcoming antiretroviral drugs which will help in the interpretation of the results of resistance tests and the individualization of therapy. Nucleoside analog mutations (NAMs) (M41L, D67N, K70R, L210W, T215Y/F and K219Q/E) are associated with reduced susceptibility to most nucleoside analogs and the nucleotide tenofovir. This recently approved drug has shown a reduced virologic response in the presence of three or more NAMs, including M41L or L210W, as well as in the presence of T69 insertions. Hypersusceptibility (IC50 < 0.5) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) has recently been described in association with increased resistance to nucleoside analogs, and it seems to enhance the immunologic and virologic reponses in patients receiving efavirenz-containing regimens. New protease inhibitors (PIs) have a lower cross-resistance profile, although more clinical data are needed to establish appropriate PI sequencing to promote sustained virologic success. Cross-resistance between amprenavir (APV) and lopinavir (LPV/r) in the presence of only four APV-related mutations has been described, suggesting that phenotypic tests should be applied before prescribing LPV/r to APV-experienced patients. Resistance to the new entry inhibitor class compound T-20 (enfuvirtide) has also been detected.

Changes in Viral Load in People with Virological Failure who Remain on the Same Haart Regimen

Objectives

To assess the rate of change in viral load and CD4 count over time in HIV-infected patients experiencing virological failure on a HAART regimen.

Design

Study population included patients from EuroSIDA, a large, multicentre, observational study enrolling HIV-infected patients across Europe.

Methods

Median change in viral load and CD4 count per month were estimated using the viral load and CD4 measurements obtained over a 12-month period after confirmed virological failure between 3 and 4 log10 copies/ml in a population of 488 HIV-infected patients who were left on a failing HAART regimen.

Results

The estimated median viral load change in our study population was 0.024 log10 copies/ml per month, statistically different from 0 (P=0.0001). In 20.9% of the patients studied viral load showed a tendency to decrease, in 47.8% showed a tendency to increase by a positive rate no higher than 0.04 log10 copies/ml per month and in the remaining 31.3% showed a tendency to increase by a rate greater than 0.04 log10 copies/ml per month. On average, CD4 counts were estimated to remain stable (decrease at a slow rate of about –0.53 cells/μl per month).

Conclusions

In patients that remained on a stable, but virologically failing HAART regimen (with viral load ranging 1000–10000 copies/ml), the viral load over the ensuing 12-month period increased at a relatively slow rate. In contrast, the CD4 count remained stable, possibly because of partial but sustained viral suppression below the viral load natural set-point. The time-course of selecting more replication-competent virus in patients with virological failure remains to be fully clarified.