Parent Nucleoside Research Articles

Potent nonclassical nucleoside antiviral drugs based on the N,N-diarylformamidine concept.

New formamidine-3TC (3TC = 2',3'-dideoxy-3'-thiacytidine) analogues have been synthesized through various methods, and their antiviral activities (HIV, HBV) have been evaluated in vitro. Anti-HIV-1 in acutely infected MT-4 cells and peripheral blood monocellular cells (PBMCs) showed that compounds substituted by N,N-diarylformamidine side chains at the 4-N nucleic base position (compounds 3 and 8-11) had at least equivalent anti-HIV activity as 3TC (EC50 = 0.5 and 11.6 microM, respectively). Moreover, the newly synthesized compounds demonstrated higher anti-HBV activity (EC50 ranging from 0.01 to 0.05 microM) compared to the parent nucleoside 3TC (EC50 = 0.2 microM). It should be underlined that these new promising derivatives inhibited HIV in cells of a macrophage lineage, which are known to be cellular reservoir for HIV. These results were particularly of interest, since the antiviral activities appeared not to be mediated through the formamidine bond hydrolysis and consequently the release of free 3TC. These new analogue series were found to be highly stable to hydrolysis even after prolonged incubation in different biological media (t(1/2) ranged from 48 to 120 h). This enzymatic stability, coupled to the fact that no delay in the antiviral response was observed compared to the free 3TC antiviral response, suggest that this new N,N-diarylformamidine nucleoside series should not be considered as classical prodrugs.

Phosphoramidate Protides of 2′,3′‐Dideoxy‐3′‐fluoroadenosine and Related Nucleosides with Potent Activity Against HIV and HBV.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Phosphoramidate Protides of Carbocyclic 2′,3′‐Dideoxy‐2′,3′‐Didehydro‐7‐Deazaadenosine with Potent Activity Against HIV and HBV

Synthesis of phosphoramidate protides of carbocyclic D‐ and L‐2′,3′‐dideoxy‐2′,3′‐didehydro‐7‐deazaadenosine by treatment of the nucleoside with phosphorochloridates in the presence of pyridine and t‐BuMgCl is described. Several of these protides showed significantly improved antiviral potency over the parent nucleosides against both HIV and HBV.

Investigations of Nucleoside H‐Phosphonamidate in the Design of Nucleotide Prodrug

AbstractFor Abstract see ChemInform Abstract in Full Text.

Rigid, Conjugated, Fluoresceinated Thymidine Triphosphates: Syntheses and Polymerase Mediated Incorporation into DNA Analogues.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Phosphoramidate Protides of 2′,3′-Dideoxy-3′-fluoroadenosine and Related Nucleosides with Potent Activity Against HIV and HBV

Syntheses of phosphoramidate protides of several 2′,3′-dideoxy-3′-fluoroadenosine derivatives by treatment of the nucleoside with phosphorochloridates in the presence of pyridine and t-BuMgCl is described. Several of these protides showed significantly improved antiviral potency over the parent nucleoside against HIV and HBV. Especially marked was the improvement in potency of phosphoramidate protides of 2′,3′-dideoxy-3′-fluoroadenosine against both HIV and HBV.

Investigations of Nucleoside H-Phosphonamidate in the Design of Nucleotide Prodrug

The synthesis, anti-HIV activity and stability studies of a H-phosphonamidate derivative of 3′-azido-2′,3′-dideoxythymidine (AZT) incorporating a N,N-diisopropylamino residue as first model of alkylamino group are reported. The results demonstrate that such phosphorylated structure exerts its biological effects via chemical hydrolysis into the corresponding H-phosphonate, precursor of the parent nucleoside.

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues.

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.

Conformational Studies of Novel Antiretroviral Analogs of Zidovudine

Conformational properties of three novel zidovudine analogs, namely 3′-azido-3′-deoxy-5′-O-isonicotinoylthymidine (AZT-Iso, 2), (−)-trans-(5S,6S)-5-bromo-6, 5′-epoxy-5,6-dihydro-3′-azido-3′-deoxythymidine (3) and (+)-trans-(5R,6R)-5-bromo-6,5′-epoxy-5,6-dihydro-3′-azido-3′-deoxythymidine (4), have been investigated by AM1 calculations and NMR studies, and compared with those of the parent nucleoside (AZT, 1). Based on the results obtained the following correlation may be established, a) AZT and AZT-Iso exhibit a conformational behavior analog to other pyrimidinic nucleosides, displaying a dynamic equilibrium in solution where the two conformers (North and South) undergo a constant transformation. b) Compounds 3 and 4 show a different conformational profile. The estimate of the pseudorotation phase angle reveals the rigid structures of the latter compounds, which do not evidence conformational equilibrium in solution; theazide group being the only group free to rotate. c) Diastereoisomers 3 and 4 exhibit an extra conformational parameter compared with other pyrimidinic nucleosides: the chair or boat conformation in the third ring formed between the sugar and the base. In all cases, a reasonable correlation was obtained between theoretical and NMR spectroscopic data.

Synthesis of 2'-C-beta-fluoromethyluridine.

[reaction: see text] 2'-C-beta-Fluoromethyluridine (17) represents both a potentially important biological agent and a tool for biochemical analysis. Here we describe the first synthesis of this compound starting from uridine. The key steps include protection of the uracil base with methoxyethoxymethyl (MEM) chloride, conversion to the corresponding 2'-C-alpha-epoxide, and regioselective opening of the oxirane ring with potassium fluoride/hydrogen fluoride. Subsequent acetylation of the 3'- and 5'-hydroxyl groups enables MEM removal using B-bromocatecholborane. Deacetylation generates the parent nucleoside, 2'-C-beta-flurormethyluridine.

Cellular pharmacology of D-d4FC, a nucleoside analogue active against drug-resistant HIV.

The backbone of effective highly active antiretroviral therapy regimens for the treatment of HIV infections currently contains at least two nucleosides. Among the features that influence the potency of each component of a regimen and the overall efficacy of the combination are the cellular uptake and bioconversion of nucleoside analogues to their active triphosphate form, and the extent of possible interactions in these steps that might occur when more than one nucleoside is used in a regimen. D-d4FC (Reverset), a new cytidine analogue with the ability to inhibit many nucleoside-resistant viral variants, was examined for these parameters. In phytohemaglutinin-stimulated human peripheral blood mononuclear cells, D-d4FC was taken up in a rapid (8 h to 50% maximal value), saturable (plateau above 10 microM parent nucleoside concentration) process, resulting in levels of D-d4FC triphosphate that should provide potent antiviral activity against a variety of virus genotypes. Based on measurement of antiviral effects in cell culture, additive and in some cases, synergistic interactions were observed with protease inhibitors, non-nucleoside reverse transcriptase inhibitors or other nucleosides, including cytidine analogues.

Enhancement of nucleoside cytotoxicity through nucleotide prodrugs.

A common reason for the lack of cytotoxicity of certain nucleosides is thought to be their inability to be initially activated to the monophosphate level by a nucleoside kinase or other activating enzyme. In a search for other nucleosides that might be worthwhile anticancer agents, we have begun to examine the utilization of monophosphate prodrugs in order to explore whether any enhanced cytotoxicity might be found for the prodrugs of candidate nucleosides that have little or no cytotoxicity. To that end, 5'-bis(pivaloyloxymethyl) phosphate prodrugs of two weakly cytotoxic compounds, 8-aza-2'-deoxyadenosine (5) and 8-bromo-2'-deoxyadenosine (9), have been prepared. These prodrugs (8 and 12) were examined for their cytotoxicity in CEM cells and were found to possess significantly enhanced cytotoxicity when compared with the corresponding parent nucleosides. Further cell culture experiments were conducted to gain insight into the mechanisms of cytotoxicity of these two prodrugs, and those data are reported.

Synthesis and studies of 3′- C-trifluoromethyl nucleoside analogues bearing adenine or cytosine as the base

3′-Deoxy-3′- C-CF 3, 2′,3′-dideoxy-3′- C-CF 3 and 2′,3′-unsaturated-3′- C-CF 3 nucleoside derivatives of adenosine and cytidine have been synthesized. All these derivatives were prepared by glycosylation of adenine and uracil with a suitable peracylated 3-trifluoromethyl sugar precursor. The resulting protected nucleosides were subject to appropriate chemical modifications to afford the target nucleoside derivatives. Additionally, the chemical stability in acidic and neutral media of the 2′,3′-dideoxy-3′- C-CF 3 and 2′,3′-unsaturated-3′- C-CF 3 nucleoside derivatives of adenosine was compared to that of their parent nucleosides 2′,3′-dideoxyadenosine (ddA) and 2′,3′-dideoxy-2′,3′-didehydroadenosine (d 4A). Our results confirm that addition of a trifluoromethyl group at C-3′ on such nucleoside derivatives appears to confer increased chemical stability toward acid-catalyzed cleavage of the glycosidic bond comparatively to their parent counterparts. When evaluated for their antiviral activity in cell culture experiments, two compounds, namely, 2′,3′-dideoxy-3′- C-CF 3-adenosine and 2′,3′-dideoxy-2′,3′-didehydro-3′- C-CF 3-cytidine exhibited moderate anti-HBV activity with EC 50 values of 10 and 5 μM, respectively.

Synthesis and biological investigations of 5-substituted pyrimidine nucleosides coupled to a dihydropyridine/pyridinium salt redox chemical delivery system.

The syntheses, antiviral activities, and partition coefficients (P) of 3'-O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-coupled nucleosides are described. These novel compounds were designed in an effort to enhance the lipophilicity, and thereby the delivery to the CNS, without compromising the anti-HSV-1 activity of the parental nucleosides. We have previously reported the synthesis of 3'-O-(1-methyl-1,4-dihydropyridyl-3- carbonyl) analogs of 5-iodo-(5), 5-vinyl-(6), and (E)-5-(2-iodovinyl)-2'-deoxyuridines (7). We now report the synthesis of 5-iodo-3'-O-(1-methyl-1,4-dihydropyridyl-3- carbonyl)-5'-O-acetyl-2'-deoxyuridine (15) and 3'-O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-2'-deoxyuridine (17). Quarternization of the 3'-O-(3-pyridylcarbonyl) compounds (10,12) using iodomethane afforded the corresponding 1-methyl pyridinium salts (13,14) which were reduced with sodium dithionite to yield the corresponding 3'-O-1-methyl-1,4-dihydropyridyl-3-carbonyl compounds (15,16). The deprotection of 3'-O-(1-methyl-1,4-dihydropyridyl- 3-carbonyl)-5'-O-t-butyldimethylsilyl-2'-deoxyuridine (16) with Bu4N+F- afforded 3'-O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-2'-deoxyuridine (17). Compounds 5-7 and 15 were evaluated for their antiviral activity in vitro against HSV-1, HSV-2, HCMV, and VZV, and were found to retain anti-HSV-1, HSV-2 and VZV activity as compared to their parental nucleosides (1-3). In addition, the cellular toxicity of 3'-O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-coupled compounds (5-7 and 15) was found to be lower than the parent nucleosides. The lipophilicity of compounds (5-7,15,17) are enhanced substantially, compared to the parent nucleosides, as indicated by an increase in corresponding P values (1-octanol-water) upon replacement of the C-3' hydroxyl by 1-methyl-1,4-dihydropyridyl-3-carbonyl moiety.

Increase of the adenallene anti-HIV activity in cell culture using its bis( tBuSATE) phosphotriester derivative

The bis( S-pivaloyl-2-thioethyl) phosphotriester derivative of 9-(4′-hydroxy-1′,2′-butadienyl)adenine (adenallene) was synthesized. This mononucleotide prodrug proved to be more effective than the parent nucleoside in inhibiting HIV-1 replication in several human T4 lymphoblastoid cell lines.

Bicyclic nucleoside inhibitors of varicella-zoster virus (VZV): Pd-catalysed synthesis of 5-aryl derivatives and their biological evaluation.

We have recently reported the discovery of an entirely new category of potent antiviral agents based on novel deoxynucleoside analogues with unusual fluorescent bicyclic furano base moieties. In order to probe structure activity relationships we prepared a series of 5-aryl derivatives of the lead structures. We herein report the synthesis, characterization, and antiviral evaluation of these novel compounds. 5-Aryl derivatives of the parent nucleosides were synthesized from the corresponding alkynyl deoxyuridines using a simple, versatile and efficient one-step conversion, based on a palladium-catalysed cyclization. As previously noted for the lead compounds, a long alkyl side-chain on the base moiety is essential for antiviral activity. Even with the optimal (C8-C10) side-chain, most of the present compounds are markedly less active than their parent structures. However, some of the synthesized compounds still retained antiviral activity at non-cytotoxic concentrations, being only two- to fivefold less active than the current clinical agent acyclovir. Possible reasons for this structure activity relationship are discussed.

2'-C-cyano-2'-deoxy-1-beta-D-arabino-pentofuranosylcytosine: a novel anticancer nucleoside analog that causes both DNA strand breaks and G(2) arrest.

The mechanism of 2'-C-cyano-2'-deoxy-1-beta-D-arabino-pentofuranosylcytosine (CNDAC) action was investigated in human lymphoblastoid CEM cells and myeloblastic leukemia ML-1 cells. CNDAC was metabolized to its 5'-triphosphate and incorporated into DNA, which was associated with inhibition of DNA synthesis. After incubation of cells with [(3)H]CNDAC, metabolites were detected in 3'-->5' phosphodiester linkage and at the 3' terminus of cellular DNA. Specific enzymatic hydrolysis of DNA demonstrated that the parent nucleoside and its 2'-epimer 2'-C-cyano-2'-deoxy-2-ribo-pentofuranosylcytosine accounted for approximately 65% of the total analogs incorporated into DNA and essentially all of the drug in the 3'-->5' phosphodiester linkage. In contrast, all detectable radioactivity at 3' termini was associated with 2'-C-cyano-2',3'-didehydro-2',3'-dideoxycytidine. This de facto DNA chain-terminating nucleotide arises from an electronic characteristic and cleavage of the 3'-phosphodiester bond subsequent to the addition of a nucleotide to the incorporated CNDAC moiety by beta-elimination, a process that generates a single strand break in DNA. Investigation of the biological consequences of these actions indicated that, after incubation with cytostatic concentrations of CNDAC, cell cycle progression was delayed during S phase, but that cells arrested predominantly in the G(2) phase. This differed from the S phase-arresting actions of ara-C and gemcitabine, other deoxycytidine analogs that inhibit DNA replication but do not cause strand breaks. Thus, once incorporated into DNA, the CNDAC molecule appears to act by a dual mechanism that 1) delays the progress of further DNA replication, but 2) upon addition of a deoxynucleotide results in the conversion of the incorporated analog to a de facto DNA chain terminator at the 3' terminus of a single strand break. It is likely that DNA strand breaks trigger cell cycle arrest in G(2).

The role of therapeutic drug monitoring in treatment of HIV infection.

Looking back over the development of antiretroviral therapies (ART) for the treatment of HIV infection, probably the turning point in generating a belief that there were real grounds for optimism of ‘therapeutic success’ came with the introduction of protease inhibitors (PIs) in 1995. As a component of antiretroviral therapy, PIs produced a dramatic decrease in mortality and morbidity in HIV infection [1] most clearly demonstrated by the reduction of opportunistic infections and hospital admissions. Today, a triple drug combination regimen containing nucleoside reverse transcriptase inhibitors (NRTIs) plus PIs or non-nucleoside reverse transcriptase inhibitors (NNRTIs) constitutes the standard of care for patients commencing therapy (see Table 1). Table 1 Currently licensed antiretrovirals. Despite its success, combination ART still lacks sufficient potency and durability. Large prospective studies [2] suggest that up to 50% of HIV-positive patients will fail to achieve adequate suppression of plasma HIV RNA (i.e. < 50 copies/ml) with any of the current ART regimens. Even if this is achieved, viral rebound develops in a significant proportion of patients within 1 year of follow-up [3–5]. For example, in the Swiss cohort study [3], rebound HIV viraemia (from < 400 copies/ml to detectable) was approximately 10% per year in ART-naive patients commencing therapy and 20% in ART-experienced patients switching therapy. Although 80% of ART-naive patients achieved viral load below 400 copies/ml at 6 months, this was only sustained in 66% at 30 months and treatment changes were necessary in approximately half of patients by 24 months. In the Frankfurt cohort [4], over half of patients developed viral rebound within 12 months of achieving undetectable RNA. There are also a growing number of patients who fail treatment despite exposure to most antiretroviral agents and consequently receive salvage therapy, which may include ‘mega-ART’ regimens. Such regimens are associated with increased potential for toxicity and serious drug interactions. In this context, some of the most pressing clinical pharmacology questions are: Why do some patients fail treatment regardless of the regimen selected? How can existing therapies be improved or optimized? Will the new drugs in development show significant advantage? Treatment failure is clearly multifactorial, and may include the development of antiviral resistance, poor adherence to therapy and pharmacokinetic reasons. This review will focus on pharmacokinetic variability as an important consideration in treatment failure and current approaches to address the problem. Pharmacokinetic variability is particularly important in relation to PIs – a group of peptidomimetic drugs with considerable inter and intra-individual variability in plasma levels and marked potential for drug interactions leading to reduced or elevated PI plasma concentrations [6, 7]. Reduced concentrations will potentially compromise efficacy while elevated concentrations will predispose to adverse events. When considering the role of therapeutic drug monitoring (TDM) in antiretroviral therapy, the primary focus is therefore on PIs. However before proceeding to develop the arguments for TDM of PIs it is important to highlight the main issues around plasma concentrations of the other two main classes of antiretrovirals. For NRTIs, establishing a relationship between plasma concentration and antiviral effect has been difficult simply because it is the intracellular triphosphate anabolite that is the active moiety (Figure 1). Plasma concentrations of parent nucleosides and intracellular concentrations of triphosphates show only a weak correlation. Figure 2 displays data from studies with zidovudine (ZDV) and lamivudine (3TC) [8, 9]. Therefore meaningful data would require cell separation (i.e. to generate peripheral blood mononuclear cells, PBMCs), a technique which is time consuming, followed by analysis of the active triphosphate, a procedure that is currently available only in a handful of laboratories. This effectively precludes the routine use of TDM for NRTIs in clinical practice until such time as a more rapid throughput analytical system is developed. Figure 1 Activation pathways of nucleoside analogues. Figure 2 The relationship between intracellular nucleoside triphosphate and plasma concentration of parent drug for (a) zidovudine (ZDV) and (b) lamivudine (3TC) (○ 150 mg. • 300 mg). Note the weak correlation between area under the curve in cells ... Data from pharmacokinetic studies of NNRTIs indicate that two of the drugs, efavirenz and nevirapine, have a prolonged half-life, normally achieve adequate steady-state plasma concentrations during a dosing interval and have pharmacokinetics which are less variable than those of PIs. Although we would not entirely rule out a role for TDM of NNRTIs in some circumstances (e.g. in relation to CNS side-effects of efavirenz), presently attention is focused on PIs.

POTENT IN VITRO ANTICANCER ACTIVITIES OF RING-EXPANDED (“FAT”) NUCLEOSIDES CONTAINING THE IMIDAZO[4,5-E][1,3]DIAZEPINE RING SYSTEM

The ring-expanded (“fat”) nucleoside, 4,8-diamino-6-imino-6H-1-β-D-ribo- furanosylimidazo[4,5-e][1,3]diazepine (1) and its 2′,3′,5′-tri-O-benzoyl derivative (2) exhibited potent broad spectrum anticancer activities in vitro against a wide variety of human tumor cell lines. The tribenzoyl derivative 2 was found to be considerably more active than the parent nucleoside 1. Further studies using human prostate cancer cells PC-3 and DU-145 suggest that the treatment of exponentially growing culture cells with 1 and 2 leads to marked loss of cell viability in a dose-dependent manner.

In Vitro and In Vivo Metabolism and Pharmacokinetics of bis [(T-Butyl)-S-acyl-2-thioethyl]-β-L-2′,3′-dideoxy-5-fluorocytidine Monophosphate

Exposure to 10 & M L-FddCMP-bisSATE led to formation of intracellular L-FddCTP levels of 410.1± 46.2 and 242.1 ± 13.2 pmol/106 cells in unstimulated and PHAstimulated PBM cells, respectively; whereas, exposure of cells to the parent nucleoside, L-FddC, generated 5-10-fold less L-FddCTP. In Hep-G2 cells and EGF/HGF stimulated and unstimulated primary cultured hepatocytes, the active metabolite reached 113 ± 29, 23.9 ± 15.6, and 20.6 ± 10.5 pmol/106 cells. Three other metabolites, L-FddCMP-monoSATE, L-FddCMP-SH, and M I, were detected intracellularly and extracellularly in all cell types examined. Intravenous administered dose of 3 mg/kg L-FddCMP-bisSATE to rhesus monkeys resulted in plasma concentration levels of 2.06 ± 1.00 and 0.39 ± 0.15 & M of L-FddCMP-monoSATE and L-FddC, respectively, while the prodrug was completely cleared metabolically within 15 min. Following oral administration of an equivalent dose, the absolute oral bioavailability of L-FddC derived from L-FddCMP-bisSATE administration was 65%.