Pharmacogenomics of HIV

The antiretroviral treatment of HIV infection has expanded tremendously in the last few years. This trend is mainly a result of new assays, genetic advances and recombinant DNA technologies providing new insights into HIV virology, pathology and resistance mechanisms. Since 1995, the use of highly active antiretroviral therapy (HAART) as a combination of substances directed against various steps in the viral life cycle, has led to significant decreases in the morbidity and mortality associated with HIV infections. The ability to quantify viral load and to perform sequence analyses represent valuable tools both for understanding the pathogenic actions of the virus and for clinical drug monitoring of HIV-infected patients. Laboratory tests have been developed and validated to help predict which antiviral substances may be more effective to control viral replication in a given patient. Genotypic and phenotypic assays have been developed to assess HIV antiviral resistance. The ability to predict drug response from a certain genotypic or phenotypic setting with respect to drug absorption, drug metabolism and drug elimination is continually evolving. This may lead to significant changes in drug plasma concentrations and may affect the efficacy and toxicity of antivirals. More recently, drug/drug interactions and mutation/drug correlations have been discovered. However, the optimal usage of pharmacogenetic and pharmacogenomic tools in the clinic still remains to be defined. This review summarizes mechanisms of drug bioavailability with respect to pharmacogenomics and discusses the impact and clinical benefit of 'personalized' HIV therapy.     

Impact of clade diversity on HIV-1 virulence,antiretroviral drug sensitivity and drug resistance

HIV-1 infection is characterized by genetic diversity wherein distinct viral subtypes (clades A, B, C, D, E, F, G, K and O) are expanding in different geographical regions. This article deals with the topic of HIV-1 subtype diversity in the context of sensitivity to antiretroviral drugs, drug resistance and viral fitness. Increasing evidence suggests that all clades of HIV probably display similar sensitivity to antiviral drugs. However, viruses from some subtypes and/or geographical regions may have a greater propensity to develop resistance against certain drugs than do other viral variants. In addition, differences in regard to replication capacity or fitness may exist among various HIV subtypes and differences in this regard may potentially become magnified under conditions of drug resistance. Immunological pressures may also play an important role in the evolution of viral subtypes that may impact on ultimate drug resistance profiles.     

Mechanism of HIV antiretroviral drugs progress toward drug resistance

The rapid replication rate of HIV-1 RNA and its inherent genetic variation have led to the production of many HIV-1 variants with decreased drug susceptibility. The capacity of HIV to develop drug resistance mutations is a major obstacle to long-term effective anti-HIV therapy. Incomplete suppression of viral replication with an initial drug regimen diminishes the clinical benefit to the patient and may promote the development of broader drug resistance that may cause subsequent treatment regimens to be ineffective. The increased clinical use of combination antiretroviral treatment for HIV-1 infection has led to the selection of viral strains resistant to multiple drugs, including strains resistant to all licensed nucleoside analog RT inhibitors and protease inhibitors. Therefore, it is important to understand the influence of such mutations on viral properties such as replicative fitness, fidelity, and mutation rates. Although research continues to improve our understanding of resistance, leading to refined treatment strategies and, in some cases, improved outcome, resistance to antiretroviral therapy remains a major cause of treatment failure among patients living with HIV-1.     

Pharmacological resistance to antiretroviral drugs

Pharmacological resistance is the decreased susceptibility of human immunodeficiency virus (HIV) to antiviral drugs without evidence of genotypic or phenotypic resistance. It may be caused by a decreased activation of drugs and/or decreased drug penetration into compartments where viral replication occurs. Several issues related to drug activation and penetration into body compartments in light of pharmacological resistance are discussed in this paper. The affinity of antiviral drugs for the multidrug transporter P-glycoprotein (Pgp) and the potential clinical significance of research in this area are also presented.     

Cellular proteins (cyclin dependent kinases) as potential targets for antiviral drugs

Several pharmacological inhibitors that are specific for cellular cyclin-dependent kinases (cdks) have recently been found to repress viral replication in vitro. Thus, replication of human cytomegalovirus, herpes simplex virus, and HIV-1 is repressed by pharmacological cdk inhibitors (PCIs). Replication of several other viruses requires cdks that are sensitive to PCIs. Interestingly, some of the PCIs that have antiviral activity in vitro are being tested in animal models and in human clinical trials as anti-cancer agents, showing little toxicity in vivo. Thus, PCIs have the potential to become antiviral drugs for clinical use. As PCIs repress viral replication by targetting cellular proteins, they would constitute a novel group of antivirals. They could be active against several unrelated viruses, and viral mutants that are resistant to conventional antiviral drugs, and could be used in combination with any antiviral drug that targets a viral protein. For viral diseases whose pathological mechanism requires cdks, such as virus-induced tumours, PCIs would repress both the aetiological agent and the pathogenic mechanism. In this review, the biochemical, cellular and antiviral activities of PCIs in vitro and their toxicity in vivo are discussed. Other cellular proteins that are required for viral replication could also be targets for new antiviral drugs.     

Bioinformatics approach to predicting HIV drug resistance

The emergence of drug resistance remains one of the most challenging issues in the treatment of HIV-1 infection. The extreme replication dynamics of HIV facilitates its escape from the selective pressure exerted by the human immune system and by the applied combination drug therapy. This article reviews computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genotypic and phenotypic data. Genotypic assays are based on the analysis of mutations associated with reduced drug susceptibility, but are difficult to interpret due to the numerous mutations and mutational patterns that confer drug resistance. Phenotypic resistance or susceptibility can be experimentally evaluated by measuring the inhibition of the viral replication in cell culture assays. However, this procedure is expensive and time consuming.     

Laboratory markers of antiviral activity

Quantitative assays for viral nucleic acids have been instrumental in monitoring the response of patients to various antiviral therapies. The level of viraemia is predictive of clinical outcome in that a reduced risk of progression to AIDS or death was observed with lower plasma human immunodeficiency virus (HIV) RNA levels. Rebound in viral levels often signals therapeutic failures, some of which are associated with the development of drug resistance. Quantitative plasma assays for HIV, hepatitis C virus (HCV), cytomegalovirus (CMV) and hepatitis B virus (HBV) have been developed. Over time, modifications to these assays have been required to meet new demands. For example, as antiviral therapies have become more effective, HIV and HCV assays of greater sensitivity are required in order to follow patients for longer periods of time and to fully assess the extent of viral suppression. For HIV-1, a large percentage of patients treated with combination therapies had viral loads that were below the detection limit of the ultrasensitive assay (50 copies/ml). To assess the residual viral burden in this patient population an assay to quantify HIV-1 proviral DNA in peripheral blood mononuclear cells was developed. Studies to date indicate that proviral DNA remains easily detectable despite undetectable plasma RNA and may be useful in monitoring this patient population. To increase assay throughput, a new generation of quantitative assays that will provide real-time detection and a 6 log10 detection range from a single amplification is under development.     

Polyanions--a lost chance in the fight against HIV and other virus diseases?

Polyanions are known to exhibit potent antiviral activity in vitro, and may represent future therapeutic agents. This review summarizes literature reports, pertinent to anionic polymers as antiviral agents. The in vitro antiviral effects of numerous polyanionic compounds (sulphated polysaccharides, negatively charged serum albumin and milk proteins, synthetic sulphated polymers, polymerized anionic surfactants and polyphosphates) are described. This class of antiviral agent exhibits several unique properties that are not shared by other presently known antiviral agents: (i) a remarkable broad-spectrum antiviral activity against HIV-1, HIV-2 and a series of other enveloped viruses; (ii) the ability to inhibit syncytium formation between HIV-infected and normal CD4 T lymphocytes, a mechanism that drastically enhances HIV infectivity; and (iii) a low induction of viral drug-resistance. There is increasing evidence that polyanions interfere with the fusion process, a vital step in the viral replication cycle. The inhibition of virus-cell fusion appears to be the source of the antiviral activity of polyanions. In vivo, the pharmacological properties of polyanions result in a low bioavailability of the drugs to their viral targets, and hence a poor antiviral activity in vivo. It is suggested that polyanions must be used in combination with drug delivery systems in order to become therapeutically useful antiviral agents. Some drug delivery systems are briefly discussed.     

In Vitro Drug Combination Studies of Letermovir (AIC246, MK-8228) with Approved Anti-Human Cytomegalovirus (HCMV) and Anti-HIV Compounds in Inhibition of HCMV and HIV Replication

Despite modern prevention and treatment strategies, human cytomegalovirus (HCMV) remains a common opportunistic pathogen associated with serious morbidity and mortality in immunocompromised individuals, such as transplant recipients and AIDS patients. All drugs currently licensed for the treatment of HCMV infection target the viral DNA polymerase and are associated with severe toxicity issues and the emergence of drug resistance. Letermovir (AIC246, MK-8228) is a new anti-HCMV agent in clinical development that acts via a novel mode of action and has demonstrated anti-HCMV activity in vitro and in vivo. For the future, drug combination therapies, including letermovir, might be indicated under special medical conditions, such as the emergence of multidrug-resistant virus strains in transplant recipients or in HCMV-HIV-coinfected patients. Accordingly, knowledge of the compatibility of letermovir with other HCMV or HIV antivirals is of medical importance. Here, we evaluated the inhibition of HCMV replication by letermovir in combination with all currently approved HCMV antivirals using cell culture checkerboard assays. In addition, the effects of letermovir on the antiviral activities of selected HIV drugs, and vice versa, were analyzed. Using two different mathematical techniques to analyze the experimental data, (i) additive effects were observed for the combination of letermovir with anti-HCMV drugs and (ii) no interaction was found between letermovir and anti-HIV drugs. Since none of the tested drug combinations significantly antagonized letermovir efficacy (or vice versa), our findings suggest that letermovir may offer the potential for combination therapy with the tested HCMV and HIV drugs.     

HIV-1 genetic variation and drug resistance development

Up until 10 years ago, basic and clinical HIV-1 research was mainly performed on HIV-1 subtype B that predominated in resource-rich settings. Over the past decade, HIV-1 care and therapy has been scaled up substantially in Latin America, Africa and Asia. These regions are largely dominated by non-B subtype infections, and especially the African continent is affected by the HIV pandemic. Insight on the potency of antiviral drugs and regimens as well as on the emergence of drug resistance in non-B subtypes was lacking triggering research in this field, also partly driven by the introduction and spreading of HIV-1 non-B subtypes in Europe. The scope of this article was to review and discuss the state-of-the-art on the impact of HIV-1 genetic variation on the in vitro activity of antiviral drugs and in vivo response to antiviral therapy; as well as on the in vitro and in vivo emergence of drug resistance.     

HIV-1 replication cycle

The HIV-1 is a formidable pathogen with establishment of a persistent infection based on the ability to integrate the proviral genome into chronically infected cells, and by the rapid evolution made possible by a high mutation rate and frequent recombination during the viral replication. HIV-1 has a variety of novel genes that facilitate viral persistence and regulation of HIV replication, but this virus also usurps cellular machinery for HIV replication, particularly during gene expression and virion assembly and budding. Recent success with antiretroviral therapy may be limited by the emergence HIV drug resistance and by toxicities and other requirements for successful long-term therapy. Further investigation of HIV-1 replication may allow identification of novel targets of antiretroviral therapy that may allow continued virus suppression in patients of failing current regiments, particularly drugs that target HIV-1 entry and HIV-1 integration.     

Antiviral therapy of chronic hepatitis B: can we clear the virus and prevent drug resistance?

Antiviral therapy of chronic HBV infection remains a clinical challenge. Once this infection has been-established, the viral genome persists for life, either as an integrated genome or as episomal covalently closed circular DNA (cccDNA). The latter is the source of renewed viral replication in case of immune depression or after antiviral drug withdrawal. The mechanisms of clearance of infected cells involve CD8+ cell-mediated cytolytic and non-cytolytic pathways. Antiviral therapy, using nucleoside analogues that inhibit the viral polymerase, induces a slow depletion of intrahepatic cccDNA. The persistence of low-grade viral replication under antiviral therapy may then lead to the selection of drug-resistant mutants. New assays have been developed to study the functional consequences of these polymerase mutations in terms of replication capacity and drug susceptibility. Together with the development of new HBV polymerase inhibitors and novel immunostimulatory approaches, this should lead to the design and evaluation of rational treatment combinations for a better control of viral replication and prevention of drug resistance.     

Estimates of intracellular delay and average drug efficacy from viral load data of HIV-infected individuals under antiretroviral therapy

We analyse viral load data of five patients under ritonavir monotherapy using a model of HIV dynamics under antiretroviral therapy that includes both drug pharmacokinetics and the intracellular delay from the time of cell infection to viral production. Using this approach we separate pharamacokinetic from intracellular delays, and obtain new estimates of intracellular delay and the antiviral efficacy of ritonavir. We find the average intracellular delay to be 1 day, in agreement with experiments. The average viral generation time is now estimated at 2 days, resulting in approximately 180 replication cycles per year. The model also reveals that ritonavir monotherapy is approximately 65% as efficacious as a recently used potent four-drug therapy, suggesting that selection for drug resistance may be facilitated by the relatively low efficacy of individual drugs, contributing in part to the inherent limitations of current therapies in combating HIV-1 infection.