Use of viral resistance patterns to antiretroviral drugs in optimising selection of drug combinations and sequences

Fluorine in anti-HIV drugs approved by FDA from 1981 to 2023

Human immunodeficiency virus (HIV) is the etiological agent of acquired immunodeficiency syndrome (AIDS). Nowadays, FDA has approved over thirty antiretroviral drugs grouped in six categories. Interestingly, one-third of these drugs contain different number of fluorine atoms. The introduction of fluorine to obtain drug-like compounds is a well-accepted strategy in medicinal chemistry. In this review, we summarized 11 fluorine-containing anti-HIV drugs, focusing on their efficacy, resistance, safety, and specific roles of fluorine in the development of each drug. These examples may be of help for the discovery of new drug candidates bearing fluorine in their structures.

Antiretroviral therapy adherence among treatment-naive HIV-infected patients

OBJECTIVE

To determine the incidence of antiretroviral therapy (ART) adherence among treatment-naive HIV-infected patients and to evaluate the impact of single-tablet regimen (STR) on ART adherence among this population.

DESIGN

Retrospective cohort study.

METHODS

We used a nationally representative sample of IQVIA LRx Lifelink individual level pharmacy claims database during 2011-2016, and defined adult patients with index date (first complete ART regimen prescription fill date) after 30 June 2011 as treatment naïve. We estimated ART adherence, measured as the proportion of days covered during 1 year following the index date. We conducted multivariable analysis to identify the factors associated with optimum adherence (≥90% proportion of days covered). We also compared adherence between patients prescribed STR and multiple-tablet regimens among those prescribed integrase strand transfer inhibitor-based or nonnucleoside reverse transcriptase inhibitor-based regimens.

RESULTS

Overall 42.9% of the patients were optimally adherent. Adherence was significantly lower among blacks, Hispanics and patients in low-income communities. Adjusting for the covariates, patients on STR had higher incidence of optimum adherence compared with those on multiple-tablet regimens among patients on integrase strand transfer inhibitor-based regimens [49 vs. 24%, relative risk, 2.16 (95% confidence interval: 1.96-2.26)], but no significant difference was observed among those on nonnucleoside reverse transcriptase inhibitor-based regimen [45 vs. 45%, relative risk, 1.12 (95% confidence interval: 0.99-1.26)].

CONCLUSION

Low ART adherence observed among treatment-naive patients in this nationally representative study suggests the need for public health interventions to improve adherence among this population.

Discovery and Development of the Anti-Human Immunodeficiency Virus Drug, Emtricitabine (Emtriva, FTC)

The HIV/AIDS epidemic, which was first reported on in 1981, progressed in just 10 years to a disease afflicting 10 million people worldwide including 1 million in the US. In 1987, AZT was approved for treating HIV/AIDS. Unfortunately, its clinical usefullness was severly limited by associated toxicities and the emergence of resistance. Three other drugs that were approved in the early 1990s suffered from similar liabilities. In 1990, the Liotta group at Emory University developed a highly diastereoselective synthesis of racemic 3'-thia-2',3'-dideoxycytidine and 3'-thia-2',3'-5-fluorodideoxycytidine and demonstrated that these compounds exhibited excellent anti-HIV activity with no apparent cytotoxicity. Subsequently, the enantiomers of these compounds were separated using enzyme-mediated kinetic resolutions and their (-)-enantiomers (3TC and FTC, respectively) were found to have exceptionally attractive preclinical profiles. In addition to their anti-HIV activity, 3TC and FTC potently inhibit the replication of hepatitis B virus. The development of FTC, which was being carried out by Burroughs Wellcome, had many remarkable starts and stops. For example, passage studies indicated that the compound rapidly selected for a single resistant mutant, M184V, and that this strain was 500-1000-fold less sensitive to FTC than was wild-type virus. Fortunately, it was found that combinations of AZT with either 3TC or FTC were synergistic. The effectiveness of AZT-3TC combination therapy was subsequently demonstrated in four independent clinical trials, and in 1997, the FDA approved Combivir, a fixed dose combination of AZT and 3TC. In phase 1 clinical trials, FTC was well tolerated by all subjects with no adverse events observed. However, the development of FTC was halted by the aquistition of Wellcome PLC by Glaxo PLC in January 1995. In 1996, Triangle Pharmaceuticals licensed FTC from Emory and initiated a series of phase I/II clinical studies that demonstrated the safety and efficacy of the drug. In August 1998, FTC was granted "Fast Track" status, based primarily on its potential for once daily dosing. While the outcomes of two subsequent phase III trials were positive, a third phase III clinical trial involving combinations of 3TC or FTC with stavudine and neviripine had to be terminated due to serious liver-related adverse events. Although analysis of the data suggested that the liver toxicity was due to neviripine, the FDA decided that the study could not be used for drug registration. Ultimately, in January 2003, Gilead Sciences acquired Triangle Pharmaceuticals and completed the development of FTC (emtricitabine), which was approved for once a day, oral administration in July 2003. A year later, Truvada, a once a day, oral, fixed dose combination of emtricitabine and tenofovir disoproxyl fumarate received FDA approval and quickly became the accepted first line therapy when used with a third antiretroviral agent. In July 2006, the FDA approved Atripla, a once a day, oral, fixed dose combination of emtricitabine, tenofovir disoproxyl fumarate, and efavirenz, which represented the culmination of two decades of research that had transformed AIDS from a death sentence to a manageable chronic disease.

To sequence or not to sequence?

There is now incontrovertible evidence that a combination of two nucleoside analogues is superior to AZT monotherapy for the treatment of HIV infection. There is also evidence that a range of antiretroviral combinations can produce profound drops in plasma HIV viral load, often below the detectable limits of the assay. A lower rate of viral replication is associated with delays in the selection of viral mutants resistant to drugs; the principal reason for therapeutic failure. These highly effective combinations are likely to delay clinical events and considerably improve the prognosis in HIV-infected individuals. Using mathematical modelling techniques to assess the half-life of plasma virus infectious cells and proviral DNA, one group has gone so far as to suggest it may be possible to stop therapy after several years, as the virus will have been eliminated. More sanguine investigators, however, believe that this is unlikely, as some infected cellular compartments may have long half-lives and the virus may persist, or even continue to replicate slowly, in sanctuary sites, such as the CNS and genital tract, poorly penetrated by drugs. Thus, some virologists and clinicians believe that it is crucially important to give initial therapy with the strongest possible combination of drugs to achieve an 'undetectable' plasma viral load and that, providing compliance is good, this will lead to a prolonged therapeutic effect. In these circumstances no sequencing issues arise. Others, however, continue to believe that, in due course, the virus is likely to evade drug pressure. In these circumstances, consideration of a sequence of drugs, to avoid initial and subsequent therapy from squandering future therapy options through, principally, cross-resistance, becomes an important issue. None of the issues discussed in this review has been tested by controlled clinical trials but they generate hypotheses requiring urgent evaluation.

Antiretroviral therapies in HIV-1 infection

Recent progress in our understanding of the viral dynamics and immunobiology of HIV infection, coupled with the introduction of a new generation of antiretroviral agents, has led to significant advances in the medical management of HIV infection. Eleven antiretroviral drugs are currently licensed in the United States, and eight are licensed in Europe. These include the nucleoside reverse transcriptase inhibitors (AZT, ddI, ddC, 3TC and d4T); the non-nucleoside reverse transcriptase inhibitors (nevirapine and delavirdine) and the protease inhibitors (saquinavir, indinavir and ritonavir). This report summarises recent developments in the use of antiretroviral therapies and the main treatment strategies under evaluation in current trials. These strategies include the evaluation of novel antiretroviral agents; combinations to achieve maximal viral suppression; optimal sequencing of antiretroviral agents; and subtraction therapy. However, many important issues in the use of antiretroviral therapies remain unresolved, including the optimal role of new agents, such as protease inhibitors (PIs), and the use of triple combination therapy in initial and subsequent treatment regimens; when therapy should be changed; which alternative agents should then be used; and the most appropriate methods for monitoring the efficacy of therapy.

Viral resistance patterns selected by antiretroviral drugs and their potential to guide treatment choice

Massive viral turnover and reverse transcriptase's high error rate create the potential for drug-resistant viral variants to appear rapidly under the selective pressure of antiretroviral therapy. Loss of antiviral effect in treatment-adherent persons is most commonly coincident with the appearance of viral mutants with reduced drug sensitivity. Thus, detection of viral resistance may represent an early marker of therapy failure. Similarly, control of viral replication in the plasma compartment, as defined by plasma viral load below the levels of assay quantification, is associated with a sustained therapeutic response and delayed development of viral resistance. Information on patterns of resistance to and cross-resistance between antiretroviral agents is increasingly well characterised and represents an important consideration when deciding how to combine and/or sequence antiretrovirals to achieve optimal antiviral effects. Given the limited number of antiretrovirals presently available or in advanced development, it is important not to limit future therapeutic options by using therapies early in the treatment sequence which may select for cross-resistant viral variants and hence potentially reduce the magnitude of therapeutic response when treatment is changed to another member of that drug class. However, no studies using resistance to guide clinical decision making have been reported to date and available sequencing studies have focused largely on switching or adding therapies to patients experienced with zidovudine monotherapy. Thus, no resistance driven treatment algorithm is currently available.

Impact of early versus late adherence to highly active antiretroviral therapy on immuno-virological response: a 3-year follow-up study

OBJECTIVE

To assess the impact of different patterns of adherence to highly active antiretroviral therapy (HAART), in particular, the relative impact of early and late adherence, on long-term immuno-virological response in HIV-infected individuals started on a protease inhibitor-containing regimen.

DESIGN

Clinical, immuno-virological and self-reported adherence data were collected at 4 (M4), 12 (M12), 20 (M20), 28 (M28) and 36 (M36) months after HAART initiation in the French APROCO cohort.

METHODS

A standardized self-administered questionnaire classified patients as non-adherent, moderately or highly adherent at each visit. Stable viral suppression at both M28 to M36, and a CD4 cell increase > 200 between M0 and M36 were used as outcome measures.

RESULTS

Of the 582 patients followed regularly through M36, 360 patients had complete adherence data. Although 59.2% were highly adherent at M4, only 25.8% maintained consistent high adherence throughout the follow-up. High adherence at M4 was independently associated with both stable viral suppression at M28-M36 [OR (95% CI): 2.8 (1.4-5.5)] and a CD4 cell increase > 200 during the same period [OR (95% CI): 3.9 (1.7-9.7)]. However, 'moderately adherent' patients between M12 and M36 had the same likelihood [OR (95% CI): 1.9 (1.1-3.2)] as patients who were always high adherent [OR (95% CI): 1.9 (1.1-3.2)] of achieving stable viral load suppression, relative to those who reported non-adherence episodes.

CONCLUSION

Optimizing adherence in the early months of treatment is crucial to ensure long-term immuno-virological high adherence during follow-up have a less negative impact. Priority should be given to interventions aimed to improve adherence in the early months of HAART.

Reverse transcriptase mutations in HIV-1 infected patients treated with two nucleoside analogues: the SMART study

Resistance to nucleoside reverse transcriptase inhibitors (NRTIs) was studied in 527 HIV-1-infected patients, 342 responder and 185 non-responder to two NRTIs. Responders were followed for one year to assess the incidence of clinical failure. The prevalence of the 215Y/F substitution was higher among non-responder, compared to responder patients (33.7&#x0025 vs. 17&#x0025, P = 0.0005), whereas the prevalence of the 184V and of the 70R mutations was comparable between these two groups. The 74V substitution was never observed and the 75T mutation was detected in only two subjects non-responder to a stavudine including regimen. Reduced susceptibility to didanosine or stavudine was infrequent. Reduced susceptibility to zidovudine was observed in 25&#x0025 of individuals failing a zidovudine including regimen, whereas reduced susceptibility to lamivudine was detected in all subjects failing a lamivudine including regimen. In the prospective analysis, patients with undetectable viral load at enrollment had a lower incidence of failure rate over one year compared to those with detectable HIV-RNA at entry (P &#x003C 0.0001). A detectable viral load at enrollment was the only independent variable that predicted clinical failure over one year (P &#x003C 0.0001).

Zidovudine and stavudine sequencing in HIV treatment planning: findings from the CHORUS HIV cohort

BACKGROUND

Optimal sequencing of zidovudine and stavudine in antiretroviral therapy has not been elucidated.

OBJECTIVE

To examine the impact of the sequence of therapeutic regimens containing zidovudine and stavudine on HIV-1 RNA and CD4 lymphocyte counts over 12 months.

DESIGN

Observational, multicenter, longitudinal cohort study.

SETTING

Four large outpatient, HIV practices participating in the community-based Collaborations in HIV Outcomes Research-U.S. (CHORUS) cohort study.

PARTICIPANTS

940 HIV-infected patients.

METHODS

Comparison of HIV-1 RNA and CD4 lymphocyte responses in patients sequenced from zidovudine to stavudine or from stavudine to zidovudine using repeated measures regression models fit to outcomes by application of generalized estimating equation (GEE) methodology.

RESULTS

Patients treated with zidovudine prior to stavudine (n = 834) achieved a greater mean drop from baseline HIV-1 RNA (p = .01) and higher proportion of undetectable HIV-1 RNA results (p = .05) over 12 months than those sequenced from stavudine to zidovudine (n = 106). CD4+ lymphocyte increases did not differ between the groups (p = .6).

CONCLUSIONS

Prior zidovudine therapy was not associated with long-term attenuation of HIV-1 RNA or CD4 response to subsequent stavudine-containing regimens. Zidovudine before stavudine may have benefit in a strategic long-term therapeutic plan.

Characterization of novel human hepatoma cell lines with stable hepatitis B virus secretion for evaluating new compounds against lamivudine- and penciclovir-resistant virus

L-Nucleoside analogs are new therapeutic agents for treatment of chronic hepatitis B. However, their clinical application was limited by the emergence of viral resistance. It is important to develop a new system to evaluate drug cross-resistance and to test new agents that may overcome resistant virus. In this report, three cell lines HepG2-WT10, HepG2-SM1, and HepG2-DM2 are presented; these cell lines were established by transfection of HepG2 cells with unique fully functional 1.1x hepatitis B virus (HBV) genomes: wild-type HBV-adr and its L526M and L526MM550V variants, respectively. We have demonstrated that these genomes have different susceptibilities to lamivudine [L(-)SddC] and penciclovir (PCV). By examining HBV RNA transcription, antigen expression, progeny DNA replication, and viral susceptibilities to L(-)SddC, PCV, and other nucleoside analogs, it is concluded that the cell lines are able to stably produce L(-)SddC- and PCV-sensitive and -resistant HBV virions. In addition, the relative susceptibilities of the wild-type and mutant HBV produced from the stably transfected cell lines to several anti-HBV nucleoside analogs were also examined and found to be about the same as those found by using a transient infection system. PMEA [9-(2-phosphonylmethoxytehyl)-adenine] and QYL685 are able to suppress L(-)SddC- and PCV-resistant HBV. In conclusion, this cell culture system is a novel and useful tool for evaluating anti-HBV compounds and biologics.

Dynamics of dominance of a dipeptide insertion in reverse transcriptase of HIV-1 from patients subjected to prolonged therapy

A small proportion (0.8%) of individuals of a cohort of HIV-1 infected patients subjected to prolonged therapy with nucleoside analogues included a recently recognised dipeptide insertion in their RT (Ser-Ser or Ser-Gly between RT codons 69 and 70). To study the dynamics of dominance of genomes with this genetic change, sequential HIV-1 isolates from two patients were analyzed with regard to consensus sequences and complexity of mutant spectra. The two patients displayed completely different, complex evolutionary patterns leading to temporary dominance of dipeptide insertions. In one patient, a virus very closely related to an ancestor virus from the same patient overtook the population at late times, displacing genomes encoding a Ser-Ser insertion. In another patient the sequential dominance of genomes with Ser-Ser insertion-->no insertion-->Ser-Gly insertion was observed. These three types of genomes coexisted in the mutant spectrum of one HIV-1 isolate. Complexity was also reflected in the shape of phylogenetic trees derived with genomes from the mutant spectrum at each time point. The results suggest that HIV-1 genomes encoding a dipeptide insertion between RT codons 69 and 70 do not show a clear selective advantage over other genomes lacking the insertion. Such an absence of a clear selective advantage will favor that such genomes encoding this RT insertion become dominant only in a transient fashion, and following disparate kinetics in different patients.

Mutations in the human immunodeficiency virus type 1 reverse transcriptase gene observed in stavudine and didanosine strains obtained by in vitro passages

We have selected a human immunodeficiency virus type 1 (HIV1) using the technique of in vitro selection to generate variants that are resistant to didanosine and/or stavudine. After serial passages of the Lai strain of HIV1 in MT-2 cells in increased concentrations of didanosine-stavudine association, 2 novel mutations in reverse transcriptase at codon 57 (Asp-->His) and at codon 98 (AIa-->Val) were observed. These mutations were associated with an 11.5-fold increase in the didanosine and a 4.5-fold increase in the stavudine 50% inhibitory concentration.

Long-read direct infrared sequencing of crude PCR products for prediction of resistance to HIV-1 reverse transcriptase and protease inhibitors

Patients infected with human immunodeficiency virus type 1 (HIV-1) are being treated with a number of different combinations of antiretroviral compounds that target the essential viral enzymes reverse transcriptase and protease. Different sets of HIV-1 mutations that confer drug resistance have been well defined; they allow reasonable prediction of the drug sensitivity pattern from analysis of the HIV-1 genotype in vivo. Since periodical monitoring of genotypic resistance is expected to improve clinical management in a large number of infected patients, practical and cost-effective methods are highly desirable to set at least medium-scale sequencing in clinical diagnostic settings. We present a complete protocol for direct sequencing of HIV-1 reverse transcriptase and protease-coding regions. Features making the system amenable to routine clinical use include: 1. Highly robust presequencing steps (plasma RNA extraction, reverse transcription, and nested PCR); 2. Direct use of the crude unpurified PCR product as the sequencing template; and 3. Use of infrared-labeled sequencing primers consistently allowing long reads, thus obviating the need for sequencing of both DNA strands.

Lamivudine in the Management of Adults with Human Immunodeficiency Virus Type 1 Infection

Lamivudine is a nucleoside analogue reverse transcriptase inhibitor of human immunodeficiency virus type 1 (HIV-1), HIV-2 and hepatitis B virus which demonstrates in vitro activity with a high therapeutic index in a range of T lymphocyte and haematopoietic precursor cell lines. It is synergistic in vitro with a range of other antiretrovirals including other nucleoside analogues, non-nucleoside reverse transcriptase inhibitors and protease inhibitors, in two- and three-way combinations and is active against virus resistant to zidovudine and most other antiretrovirals. It exhibits excellent oral bioavailability and penetrates the CSF. In clinical use, lamivudine exhibits limited antiretroviral activity as a monotherapy, but in two-and three-drug combinations with other antiretrovirals it provides potent antiretroviral activity and significantly delays clinical events. Adverse events appear infrequent and are generally mild and self-limiting. Resistance to lamivudine develops rapidly in vitro and in vivo but may delay the development of zidovudine resistance. Dual zidovudine-lamivudine resistance is well documented both in vitro and in vivo although the mutation at codon 184 of reverse transcriptase characteristic of lamivudine resistance may, in some cases, transiently ‘reverse’ zidovudine resistance mediated through codons 215 and 41. Owing to concerns regarding selection of virus with cross-resistance to other nucleoside analogues (ddl, ddC and possibly abacavir), whether to use lamivudine in initial or second-line regimens is currently under debate.

An Integrated “Care Path” Approach: Useful for Implementation and Coordination of New Care Guidelines for Treatment of HIV Infections

Recently, the 1997 revised guidelines were published for the treatment of HIV-infected patients. These guidelines, while having a dramatic effect on the morbidity and mortality associated with HIV infection, will require the implementation of a coordinate interdisciplinary “Care Path” for each patient. This review presents updated information on the HIV life cycle and the latest approach to antiretroviral therapy. The new approach to therapy is to utilize combination antiretroviral therapy including two retroviral inhibitors with a protease inhibitor. Further, the importance of viral load has become a primary indicator of prognosis and therapy efficacy. The CD4 cell count is important, but it is of secondary significance in treatment effectiveness measurement and indication of disease progress. The complexity of the new guidelines increases the need for a well-planned interdisciplinary “Critical Path” which is then utilized for development of a patient-specific “Care Path.”

RNA virus mutations and fitness for survival

RNA viruses exploit all known mechanisms of genetic variation to ensure their survival. Distinctive features of RNA virus replication include high mutation rates, high yields, and short replication times. As a consequence, RNA viruses replicate as complex and dynamic mutant swarms, called viral quasispecies. Mutation rates at defined genomic sites are affected by the nucleotide sequence context on the template molecule as well as by environmental factors. In vitro hypermutation reactions offer a means to explore the functional sequence space of nucleic acids and proteins. The evolution of a viral quasispecies is extremely dependent on the population size of the virus that is involved in the infections. Repeated bottleneck events lead to average fitness losses, with viruses that harbor unusual, deleterious mutations. In contrast, large population passages result in rapid fitness gains, much larger than those so far scored for cellular organisms. Fitness gains in one environment often lead to fitness losses in an alternative environment. An important challenge in RNA virus evolution research is the assignment of phenotypic traits to specific mutations. Different constellations of mutations may be associated with a similar biological behavior. In addition, recent evidence suggests the existence of critical thresholds for the expression of phenotypic traits. Epidemiological as well as functional and structural studies suggest that RNA viruses can tolerate restricted types and numbers of mutations during any specific time point during their evolution. Viruses occupy only a tiny portion of their potential sequence space. Such limited tolerance to mutations may open new avenues for combating viral infections.

RNA virus fitness

RNA viruses constitute the most abundant group of pathogens of man, animals and plants. They share high mutation rates which are in the range 10(-3) to 10(-5) misincorporations per nucleotide site and round of copying. This is due to the absence or low efficiency of proofreading-repair or postreplicative repair activities associated with replicating RNA. Populations of RNA viruses are extremely heterogeneous and form dynamic mutant swarms termed viral quasispecies. This genetic organisation implies that any individual mutant has only a fleeting existence; that is, RNA viral genomes are statistically defined but individually indeterminate. RNA viruses are able to accommodate their average nucleotide sequences to changes in environment. A parameter used to quantitate adaptation is fitness, or the relative ability of a virus to produce infectious progeny. Repeated transfers of one or a few particles (bottleneck events) generally lead to fitness losses. In contrast, large population passages allow competitive optimisation of mutant genomes and fitness gains. Of relevance to medical practice is the ability of viral quasispecies to overcome selective pressures imposed by vaccines and antiviral agents. Particularly dramatic have been the systematic isolations of HIV-1 mutants resistant to antiretroviral inhibitors in treated individuals. In addition to the ability of HIV-1 quasispecies to generate many mutant genomes in short times, calculations of mutation frequencies in the pol gene of HIV-1 populations have documented that mutations related to resistance to antiretroviral inhibitors preexist in the mutant swarms of HIV-1 quasispecies. It is not possible at present to anticipate whether a suitable drug cocktail may be capable of sustained inhibition of HIV-1 replication without selection of mutants resistant to the combination of antiviral agents. Copyright 1997 John Wiley & Sons, Ltd.