Biochemical studies on the mechanism of human immunodeficiency virus type 1 reverse transcriptase resistance to 1-(beta-D-dioxolane)thymine triphosphate

SYBR Green II Dye-Based Real-Time Assay for Measuring Inhibitor Activity Against HIV-1 Reverse Transcriptase

There are arrays of in vitro assays to quantify the activity of HIV-1 reverse transcriptase (HIV-1 RT). These assays utilize either chemically customized/labelled nucleotides, or TaqMan probes, or radiolabeled nucleotides/primers. Although several real-time PCR assays exist commercially for measuring the RT activity, which are usually used for quantifying the viral titres, these assays are not optimized for measuring the inhibitory concentrations (IC50) of HIV-1 RT inhibitors. Moreover, a recently established inorganic pyrophosphate-coupled enzyme assay cannot be employed for studying nonphosphorylated nucleoside reverse transcriptase inhibitors (NRTIs). In the present study, we have developed a novel one-step assay with native nucleotide substrates and SYBR Green II dye to determine IC50 values of triphosphorylated NRTIs against HIV-1 RT. Using exact batches of wild-type and mutant RT, and triphosphorylated NRTIs, we showed that our method gave IC50 values for inhibitors similar to that of an earlier published colorimetric assay with BrdUTP substrate (CABS). Our assay should be suitable for high-throughput screening of antiretroviral drugs and could also be suitable for studying drug resistance profiles. Additionally, we also used our assay to study inhibition by AZT in its nonphosphorylated form by supplementing the reaction mixture with necessary kinases and ATP.

The nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and protease inhibitors in the treatment of HIV infections (AIDS)

The majority of the drugs currently used for the treatment of HIV infections (AIDS) belong to either of the following three classes: nucleoside reverse transcriptase inhibitors (NRTIs), nonnucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs). At present, there are 7 NRTIs, 5 NNRTIs, and 10 PIs approved for clinical use. They are discussed from the following viewpoints: (i) chemical formulae; (ii) mechanism of action; (iii) drug combinations; (iv) clinical aspects; (v) preexposure prophylaxis; (vi) prevention of mother-to-child transmission; (vii) their use in children; (viii) toxicity; (ix) adherence (compliance); (x) resistance; (xi) new NRTIs, NNRTIs, or PIs in (pre)clinical development; and (xii) the prospects for a "cure" of the disease.

Design and synthesis of novel 1',3'-dioxolane 5'-deoxyphosphonic acid purine analogues as potent antiviral agents

Electronic parameters of 1',3 '-oxygen play significant roles in steering the conformation of nucleoside phosphonic acid analogues. To investigate the relationship of two oxygen atoms with antiviral enhancement, novel 1',3 '-dioxolane 5 '-deoxyphosphonic acid purine analogues were synthesized via de novo acyclic stereoselective route from acrolein and glycolic acid. The synthesized nucleoside phosphonic acid analogues 14 and 19 were subjected to antiviral screening against several viruses, such as HIV-1, HSV-1, HSV-2, and HCMV. The guanine analogue 19 exhibits in vitro anti-HIV-1 activity similar to that of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA) in MT-4 cells.

Phosphoramidate prodrugs of (-)-β-D-(2R,4R)-dioxolane-thymine (DOT) as potent anti-HIV agents

BACKGROUND

Nucleoside reverse transcriptase inhibitors (NRTIs) are an effective class of agents that has played a vital role in the treatment of HIV infections. (-)-β-D-(2R,4R)-dioxolane-thymine (DOT) is a thymidine analogue that is active against wild-type and NRTI-resistant HIV-1 mutants. It has been shown that the anti-HIV activity of DOT is limited due to poor monophosphorylation.

METHODS

To further enhance the anti-HIV activity of DOT, an extensive structure-activity relationship analysis of phosphoramidate prodrugs of DOT monophosphate was undertaken. These prodrugs were evaluated for anti-HIV activity using Hela CD4 β-gal reporter cells (P4-CCR5 luc cells).

RESULTS

Among the synthesized prodrugs, the 4-bromophenyl benzyloxy l-alanyl phosphate derivative of DOT was the most potent, with a 50% effective concentration of 0.089 μM corresponding to a 75-fold increase in activity relative to the parent nucleoside DOT with no increased cytotoxicity. The metabolic stability of a selected number of potent DOT phosphoramidates was also evaluated in simulated gastric fluid, simulated intestinal fluid, human plasma and liver S9 fractions.

CONCLUSIONS

A series of new phosphoramidate prodrugs of DOT were prepared and evaluated as inhibitors of HIV replication in vitro. Metabolic stability studies indicated that these DOT phosphoramidate derivatives have the potential to show acceptable stability in the gastrointestinal tract, but they metabolize rapidly in the liver.

Selection and characterization of HIV-1 with a novel S68 deletion in reverse transcriptase

Resistance to human immunodeficiency virus type 1 (HIV-1) represents a significant problem in the design of novel therapeutics and the management of treatment regimens in infected persons. Resistance profiles can be elucidated by defining modifications to the viral genome conferred upon exposure to novel nucleoside reverse transcriptase (RT) inhibitors (NRTI). In vitro testing of HIV-1LAI-infected primary human lymphocytes treated with β-D-2',3'-dideoxy-2',3'-didehydro-5-fluorocytidine (DFC; Dexelvucitabine; Reverset) produced a novel deletion of AGT at codon 68 (S68Δ) alone and in combination with K65R that differentially affects drug response. Dual-approach clone techniques utilizing TOPO cloning and pyrosequencing confirmed the novel S68Δ in the HIV-1 genome. The S68Δ HIV-1 RT was phenotyped against various antiviral agents in a heteropolymeric DNA polymerase assay and in human lymphocytes. Drug susceptibility results indicate that the S68Δ displayed a 10- to 30-fold increase in resistance to DFC, lamivudine, emtricitabine, tenofovir, abacavir, and amdoxovir and modest resistance to stavudine, β-d-2',3'-oxa-5-fluorocytidine, or 9-(β-D-1,3-dioxolan-4-yl)guanine and remained susceptible to 3'-azido-3'-deoxythymidine, 2',3'-dideoxyinosine (ddI), 1-(β-D-dioxolane)thymine (DOT) and lopinavir. Modeling revealed a central role for S68 in affecting conformation of the β3-β4 finger region and provides a rational for the selective resistance. These data indicate that the novel S68Δ is a previously unrecognized deletion that may represent an important factor in NRTI multidrug resistance treatment strategies.

Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine

Twenty-five years ago, nucleoside analog 3'-azidothymidine (AZT) was shown to efficiently block the replication of HIV in cell culture. Subsequent studies demonstrated that AZT acts via the selective inhibition of HIV reverse transcriptase (RT) by its triphosphate metabolite. These discoveries have established the first class of antiretroviral agents: nucleoside and nucleotide reverse transcriptase inhibitors (NRTIs). Over the years that followed, NRTIs evolved into the main component of antiretroviral drug combinations that are now used for the treatment of all populations of HIV infected patients. A total of thirteen NRTI drug products are now available for clinical application: eight individual NRTIs, four fixed-dose combinations of two or three NRTIs, and one complete fixed-dose regimen containing two NRTIs and one non-nucleoside RT inhibitor. Multiple NRTIs or their prodrugs are in various stages of clinical development and new potent NRTIs are still being identified through drug discovery efforts. This article will review basic principles of the in vitro and in vivo pharmacology of NRTIs, discuss their clinical use including limitations associated with long-term NRTI therapy, and describe newly identified NRTIs with promising pharmacological profiles highlighting those in the development pipeline. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, volume 85, issue 1, 2010.

Antiviral agents acting as DNA or RNA chain terminators

Nucleoside or nucleotide analogue inhibitors of viral replication almost act as chain terminators during DNA (DNA- and retroviruses) or RNA (RNA viruses) synthesis. Following intracellular phosphorylation, by viral and/or cellular kinases, the 5'-triphosphate metabolites (or 2'-diphosphate metabolites in the case of acyclic nucleoside phosphonate analogues) compete with the natural substrate in the DNA or RNA polymerization reaction. Obligatory chain terminators (e.g., acyclovir) do not offer the 3'-hydroxyl function at the riboside moiety of the molecule. Nucleoside analogues that possess a hydroxyl function at a position equivalent of the 3'-hydroxyl position may act as chain terminators if this hydroxyl group is conformationally constrained (e.g., ganciclovir) or sterically hindered to enter into a phosphodiester linkage with the incoming nucleotide. In case that the 3'-hydroxylgroup is correctly positioned, chain elongation may be hampered through steric hindrance from neighboring substituents (e.g., 2'-C-methyl or 4'-azido nucleoside inhibitors of HCV replication). Here, we review the molecular mechanism of action and the clinical applications of the nucleosides and nucleotides acting as chain terminators. A further discussion of clinical applications in combination therapy can be found in Chap. 12.

5'-O-Aliphatic and amino acid ester prodrugs of (-)-beta-D-(2R,4R)-dioxolane-thymine (DOT): synthesis, anti-HIV activity, cytotoxicity and stability studies

A series of (-)-beta-D-(2R,4R)-dioxolane-thymine-5'-O-aliphatic acid esters as well as amino acid esters were synthesized as prodrugs of (-)-beta-D-(2R,4R)-dioxolane-thymine (DOT). The compounds were evaluated for anti-HIV activity against HIV-1(LAI) in human peripheral blood mononuclear (PBM) cells as well as for their cytotoxicity in PBM, CEM and Vero cells. Improved anti-HIV potency in vitro was observed for the compound 2-4 (5'-O-aliphatic acid esters) without increase in cytotoxicity in comparison to the parent drug. Chemical and enzymatic hydrolysis of the prodrugs was also studied, in which the prodrugs exhibited good chemical stability with the half-lives from 3 h to 54 h at pH 2.0 and 7.4 phosphate buffer. However, the prodrugs were relatively labile to porcine esterase with the half-lives from 12.3 to 48.0 min.

Mechanisms of resistance to nucleoside analogue inhibitors of HIV-1 reverse transcriptase

Human immunodeficiency virus (HIV) reverse transcriptase (RT) inhibitors can be classified into nucleoside and nonnucleoside RT inhibitors. Nucleoside RT inhibitors are converted to active triphosphate analogues and incorporated into the DNA in RT-catalyzed reactions. They act as chain terminators blocking DNA synthesis, since they lack the 3'-OH group required for the phosphodiester bond formation. Unfortunately, available therapies do not completely suppress viral replication, and the emergence of drug-resistant HIV variants is facilitated by the high adaptation capacity of the virus. Mutations in the RT-coding region selected during treatment with nucleoside analogues confer resistance through different mechanisms: (i) altering discrimination between nucleoside RT inhibitors and natural substrates (dNTPs) (e.g. Q151M, M184V, etc.), or (ii) increasing the RT's phosphorolytic activity (e.g. M41L, T215Y and other thymidine analogue resistance mutations), which in the presence of a pyrophosphate donor (usually ATP) allow the removal of chain-terminating inhibitors from the 3' end of the primer. Both mechanisms are implicated in multi-drug resistance. The excision reaction can be modulated by mutations conferring resistance to nucleoside or nonnucleoside RT inhibitors, and by amino acid substitutions that interfere with the proper binding of the template-primer, including mutations that affect RNase H activity. New developments in the field should contribute towards improving the efficacy of current therapies.