Molecular Modeling Approach to Understanding the Mode of Action ofl-Nucleosides as Antiviral Agents

Abstract

Antiretroviral therapy for the treatment of human immunodeficiency virus type 1 (HIV-1) infection has proven effective in extending the life and enhancing the quality of life of patients with AIDS (25). Thus far, six nucleoside reverse transcriptase (RT) inhibitors (NRTIs), four protease inhibitors, and three non-NRTIs have been approved by the Food and Drug Administration. In particular, NRTIs continue to be the mainstay of antiretroviral therapy (24, 31). For example, triple-combination therapy, consisting of zidovudine (AZT) (3Ј-azido-3Ј-deoxythymidine) (9,17,18,21,28) , 33, 34), and a protease inhibitor, is being used as the primary regimen for AIDS treatment (11,15). Therefore, a complete understanding of the mechanism of action of NRTIs at the molecular level continues to be an important scientific objective for design and development of more effective and less toxic agents.The NRTIs bear structural features common to 2Ј,3Ј-dideoxynucleosides, and the majority of the approved drugs have the natural D configurations: AZT, ddC (2Ј,3Ј-dideoxycytidine) (1, 5, 46), ddI (2Ј,3Ј-dideoxyinosine) (8, 12, 29, 47), d4T (2Ј,3Ј-didehydro-2Ј,3Ј-dideoxythymidine) (16,22), and abacavir (1592U89; succinate) (10, 38). Since the discovery of 3TC, however, a number of nucleosides with the unnatural L configuration have emerged as potent antiviral agents. Both 3TC and FTC [(Ϫ)-␤-L-2Ј,3Ј-dideoxy-5-fluoro-3Ј-thiacytidine] show potent antiviral activity against HIV and hepatitis B virus, with favorable pharmacokinetic and toxicity profiles (20,43). Therefore, structural features and conformational preferences of the D and L enantiomers, as well as their interactions with the target enzymes, have been the critical issue to be studied (4,26,27,39,40,43).The activation of nucleoside RT inhibitors involves two major events: phosphorylation by kinases and the interaction of the deoxynucleoside triphosphate (dNTP) with the RT (14,30,35). The antiviral activity of 2Ј,3Ј-dideoxynucleosides is dependent on their phosphorylation by cellular kinases in the cytoplasm to the corresponding 5Ј-triphosphates. These triphosphates compete with the corresponding endogenous nucleoside triphosphates at the catalytic site of the HIV-1 RT, and also, upon incorporation into the nascent DNA strand the nucleotides act as chain terminators of the DNA elongation. The initial phosphorylation of nucleosides requires several cellular kinases, such as thymidine kinase, deoxycytidine kinase, and adenosine kinase, and the activities of these kinases depend on the nature of the heterocyclic base as well as the structure and stereochemistry of the carbohydrate moiety (36).However, as three-dimensional structures of these kinases have not yet been determined, it is difficult to envision how the initial phosphorylation is carried out for unnatural nucleosides, such as L-nucleosides, without compromising the stereochemical requirements of the enzymes and/or the nucleosides. Furthermore, the active conformation of the 5Ј-triphosphates at the site of the RT is not well u...

Inhibitory activity of dioxolane purine analogs on wild-type and lamivudine-resistant mutants of hepadnaviruses

“…48 Obtention of the crystal structure of HBV polymerase and determination of its interaction with dNTP or analogs may help in the understanding of resistance or susceptibility to new inhibitors. 49 In summary, L-FMAU was shown to be mainly an inhibitor of the DNA-dependent DNA polymerase activity leading to a decrease of infectious virus production, whereas dioxolane purine analogs were shown to inhibit both wild-type and 3TC-resistant mutant RT. Our results allowed us to gain new information regarding the mechanism of action of recently discovered nucleoside analogs that may be valuable for the design and evaluation of new combination treatments of chronic HBV infection to prevent or delay the emergence of drug-resistant mutants.…”

Mechanism of viral persistence and resistance to nucleoside and nucleotide analogs in chronic Hepatitis B virus infection

“…The potency of the antiviral effect may depend on pharmacokinetics properties including, intestinal absorption, distribution into the infected liver, cellular uptake, efficiency of intracellular phosphorylation, half-life of the triphosphate form, excision from newly synthesized viral DNA, as well as on the selectivity index of the drug that may prevent the use of optimal doses to reach a more potent antiviral effect (Bridges and Cheng, 1995;Colacino, 1996;Lee and Chu, 2001;Urban et al, 2001). In the clinical setting, host determinants such as compliance, severity of the liver disease and associated disorders may also influence antiviral efficacy.…”

Differential Maintenance of the M184V Substitution in the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 by Various Nucleoside Antiretroviral Agents in Tissue Culture

“…The M184V mutation can also be selected by structurally related compounds, such as (Ϫ)-beta-2Ј,3Ј-dideoxy-5-fluoro-3Ј-thiacytidine (FTC; emtricitabine) (12,28), as well as by several structurally unrelated NRTIs, such as abacavir (ABC) (18,30). Two other NRTIs that less frequently select for M184V are ddI and ddC, and both ddI and ABC retain clinical efficacy against viruses that contain the M184V substitution (13,16,60).…”