Synthesis of 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-substituted-benzene thymidine mimics, some related alpha-anomers, and their evaluation as antiviral and anticancer agents

Nucleoside analogues: N-glycosylation methodologies, synthesis of antiviral and antitumor drugs and potential against drug-resistant bacteria and Alzheimer's disease

Nucleosides have gained significant attention since the discovery of the structure of DNA. Nucleoside analogues may be synthesized through multiple synthetic pathways, however the N-glycosylation of a nucleobase is the most common method. Amongst the different classical N-glycosylation methodologies, the Vorbrüggen glycosylation is the most popular method. This review focuses on the synthesis and therapeutic applications of several FDA approved nucleoside analogues as antiviral and anticancer agents. Moreover, this review also focuses on the potential of these compounds as new antibacterial and anti-Alzheimer's disease agents, offering an overview of the most recent research in these fields.

Metabolism, Biochemical Actions, and Chemical Synthesis of Anticancer Nucleosides, Nucleotides, and Base Analogs

Nucleoside, nucleotide, and base analogs have been in the clinic for decades to treat both viral pathogens and neoplasms. More than 20% of patients on anticancer chemotherapy have been treated with one or more of these analogs. This review focuses on the chemical synthesis and biology of anticancer nucleoside, nucleotide, and base analogs that are FDA-approved and in clinical development since 2000. We highlight the cellular biology and clinical biology of analogs, drug resistance mechanisms, and compound specificity towards different cancer types. Furthermore, we explore analog syntheses as well as improved and scale-up syntheses. We conclude with a discussion on what might lie ahead for medicinal chemists, biologists, and physicians as they try to improve analog efficacy through prodrug strategies and drug combinations.

Luminescent iridium(III) complexes with N^C^N-coordinated terdentate ligands: dual tuning of the emission energy and application to organic light-emitting devices

A family of complexes (1a-3a and 1b-3b) was prepared, having the structure Ir(N^C^N)(N^C)Cl. Here, N^C(∧)N represents a terdentate, cyclometallating ligand derived from 1,3-di(2-pyridyl)benzene incorporating CH(3) (1a,b), F (2a,b), or CF(3) (3a,b) substituents at the 4 and 6 positions of the benzene ring, and N^C is 2-phenylpyridine (series a) or 2-(2,4-difluorophenyl)pyridine (series b). The complexes are formed using a stepwise procedure that relies on the initial introduction of the terdentate ligand to form a dichloro-bridged iridium dimer, followed by cleavage with the N^C ligand. (1)H NMR spectroscopy reveals that the isomer that is exclusively formed in each case is that in which the pyridyl ring of the N^C ligand is trans to the cyclometallating aryl ring of the N^C^N ligand. This conclusion is unequivocally confirmed by X-ray diffraction analysis for two of the complexes (1b and 3a). All of the complexes are highly luminescent in degassed solution at room temperature, emitting in the green (1a,b), blue-green (2a,b), and orange-red (3a,b) regions. The bidentate ligand offers independent fine-tuning of the emission energy: for each pair, the "b" complex is blue-shifted relative to the analogous "a" complex. These trends in the excited-state energies are rationalized in terms of the relative magnitudes of the effects of the substituents on the highest occupied and lowest unoccupied orbitals, convincingly supported by time-dependent density functional theory (TD-DFT) calculations. Luminescence quantum yields are high, up to 0.7 in solution and close to unity in a PMMA matrix for the green-emitting complexes. Organic light emitting devices (OLEDs) employing this family of complexes as phosphorescent emitters have been prepared. They display high efficiencies, at least comparable, and in some cases superior, to similar devices using the well-known tris-bidentate complexes such as fac-Ir(ppy)(3). The combination of terdentate and bidentate ligands is seen to offer a versatile approach to tuning of the photophysical properties of iridium-based emitters for such applications.

Inhibition of pyrimidine and purine nucleoside phosphorylases by a 3,5-dichlorobenzoyl-substituted 2-deoxy-D-ribose-1-phosphate derivative

The 3,5-dichlorobenzoyl-substituted 2-deoxy-D-ribose-1-phosphate derivative, designated Cf2891, was found to inhibit a variety of pyrimidine and purine nucleoside phosphorylases (NPs) with preference for uridine- and inosine-hydrolyzing enzymes [uridine phosphorylase (UP; EC 2.4.2.3), pyrimidine nucleoside phosphorylase (PyNP; EC 2.4.2.2) and purine nucleoside phosphorylase (PNP; EC 2.4.2.1)]. Kinetic analyses revealed that Cf2891 competes with inorganic phosphate (P(i)) for binding to the NPs and, depending on the nature of the enzyme, acts as a competitive or non-competitive inhibitor with regard to the nucleoside binding site. Also, the compound prevents breakdown of pyrimidine analogues used in the treatment of viral infections and cancer. Since NPs are abundantly present in tumor tissue and may be overexpressed due to secondary bacterial infections in immunocompromised patients suffering viral infections, Cf2891 may serve as a lead molecule for the development of inhibitors to be used in nucleoside-based combination therapy.

Biodistribution and imaging of 1-(2-deoxy-beta-d-ribofuranosyl)-2,4-difluoro-5-[123/125I]iodobenzene (dRF[(123/125)I]IB), a nonpolar thymidine-mimetic nucleoside, in rats and tumor-bearing mice

1-(2-Deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene (dRFIB) is a putative bioisostere of iododeoxyuridine (IUdR). The advantages of dRFIB over IUdR for in vivo studies include resistance to both phosphorolytic cleavage of the nucleoside bond and de-iodination. dRFIB was radioiodinated (dRF(123/125)IB) by copper-catalyzed exchange using commercial sodium [(123/125)I]iodide. The in vivo biodistribution of dRF[(125)I]IB in BALBc mice and imaging of dRF[(123)I]IB in Sprague-Dawley rats are reported. In vivo data for rats show rapid clearance of radioactivity from blood (>95%ID in 15 minutes), extensive excretion in urine (56%ID/24 hours), concentration in the hepatobiliary-small intestine system and very little fecal excretion (approximately 3%ID/24 hours). Pharmacokinetic data for dRF[(125)I]IB (i.v. 48.7 ug/kg) in rats (t(1/2)[h] = 0.51 +/- 0.14, AUC(inf)[microg.min/mL] = 3.7 +/- 0.4, Cl[L/kg/h] = 0.75 +/- 0.12, Vss[L/kg] = 0.96 +/- 0.18) confirm previously reported dose-dependent pharmacokinetics. Scintigraphic images of rats dosed with dRF[(123)I]I were compatible with rapid soft-tissue clearance and extensive accumulation of radioactivity in bladder/urine and liver/small intestine. In tumor-bearing mice, thyroid and stomach radioactivity was indicative of moderate deiodination. An unidentified polar radioactive metabolite was detected in serum.

Syntheses and phosphorescent properties of blue emissive iridium complexes with tridentate pyrazolyl ligands

Novel neutral mixed-ligand Ir(N=C=N)(N=C)X complexes (N=C=N = 1,3-bis(3-methylpyrazolyl)benzene (bpzb), 1,5-dimethyl-2,4-bis(3-methylpyrazolyl)benzene (dmbpzb), and 1,5-difluoro-2,4-bis(3-methylpyrazolyl)benzene (dfbpzb); N=C = 2-phenyl pyridine (ppy); and X = Cl or CN) have been synthesized and characterized. An X-ray single-crystal structure of the complex Ir(dmbpzb)(ppy)Cl shows that the nitrogen atom in the ppy ligand occupied the trans position to the carbon atom in the tridentate N=C=N ligand of dmbpzb with the Ir-C bond length of 1.94(1) A, whereas the coordinating carbon atom occupied the trans position of chlorine. Electrochemical data show that the complexes exhibit an oxidation Ir(III/IV) process in the potential range of +0.5 approximately 0.9 V and two irreversible reductions at approximately -2.6 and -3.0 V against Fc (0)/Fc (+), respectively. All of the Ir(III) complexes do not emit phosphorescence at room temperature, although strong phosphorescence is exhibited at 77 K with the 0-0 transition centered at around 450 nm and lifetimes of 3-14 mus. DFT calculations indicate that the HOMOs are mainly localized on iridium 5dpi and chlorine ppi*, whereas the LUMOs are mainly from the ppy ligand pi* orbitals. The phosphorescence originates from a (3)LC state mixed with the (3)MLCT and (3)XLCT ones. Temperature-dependent lifetime measurements of Ir(dfbpzb)(ppy)Cl reveal the existence of a thermal deactivation process with a low activation energy (1720 cm (-1)) and very high frequency factor (2.3 x 10 (13) s (-1)). An unrestricted density functional theory indicates that the dd state, in which both the Ir-N (pyrazolyl) bond lengths increase considerably, exists almost at the same energy as that for the phosphorescent state. A thorough analysis based on the potential energy surfaces for the T 1 and S 0 states allows us to determine the reaction pathway responsible for this thermal deactivation. The calculated activation energies of 1600 approximately 1800 cm (-1) are in excellent agreement with the observed values.

Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) oligonucleotide incorporating 7-deazaguanine bases

DNG nucleotides represent a positively charged DNA analog in which the negatively charged phosphodiester linkages of DNA are replaced by positively charged guanidinium linkages. We report herein the synthesis of 3'-end, middle, and 5'-end monomers required for the synthesis of a DNG sequence in which the natural guanine base is replaced by 7-deazaguanine (c(7)G). 7-Deazaguanine nucleobase was chosen because of their unique glycoside bond stability and their ability to prevent G-quartet formation. A facile and high yield two-step synthesis of xylo-7-deazaguanine 7, a key intermediate for introducing 3'-amino functionality, is carried out under Mitsunobu conditions. Subsequently, the 3'-Fmoc-protected thiourea monomers 13 and 19 were prepared from 7 via their corresponding 3'-amino-7-deazaguanines 11 and 18, respectively. The smooth coupling of these thiourea monomers with monomethoxytrityl (MMTr)-protected 3'-end monomer 25, prepared from 5, occurred on solid phase in 3'-->5' direction. The resultant trimeric HO-c(7)Ggc(7)Ggc(7)G-OH (1) has been designed to be included into DNA using standard DNA synthesis technology. The combination of C-c(7)G base pairing and electrostatic association of phosphodiester and guanidinium backbone allows the small synthesized DNG trimer 1 to form 1:1 complex with DNA-C pentamer.

Phosphorylation of isocarbostyril- and difluorophenyl-nucleoside thymidine mimics by the human deoxynucleoside kinases

The thymidine mimics isocarbostyril nucleosides and difluorophenyl nucleosides were tested as deoxynucleoside kinase substrates using recombinant human cytosolic thymidine kinase (TK1) and deoxycytidine kinase (dCK), and mitochondrial thymidine kinase (TK2) and deoxyguanosine kinase (dGK). The isocarbostyril nucleoside compound 1-(2-deoxy-beta-D-ribofuranosyl)-isocarbostyril (EN1) was a poor substrate with all the enzymes. The phosphorylation rates of EN1 with TK1 and TK2 were <1% relative to Thd, where as the phosphorylation rates for EN1 were 1.4% and 1.1% with dCK and dGK relative to dCyd and dGuo, respectively. The analogue 1-(2-deoxy-beta-D-ribofuranosyl)-7-iodoisocarbostyril (EN2) showed poor relative-phosphorylation efficiencies (kcat/Km) with both TK1 and dGK, but not with TK2. The kcat/Km value for EN2 with TK2 was 12.6% relative to that for Thd. Of the difluorophenyl nucleosides, 5-(1'-(2'-deoxy-beta-D-ribofuranosyl))-2,4-difluorotoluene (JW1) and 1-(1'-(2'-deoxy-beta-D-ribofuranosyl))-2,4-difluoro-5-iodobenzene (JW2) were substrates for TK1 with phosphorylation efficiencies of about 5% relative to that for Thd. Both analogues were considerably more efficient substrates for TK2, with kcat/Km values of 45% relative to that for Thd. 2,5-Difluoro-4-[1-(2-deoxy-beta-L-ribofuranosyl)]-aniline (JW5), a L-nucleoside mimic, was phosphorylated up to 15% as efficiently as deoxycytidine by dCK. These data provide a possible explanation for the previously reported lack of cytotoxicity of the isocarbostyril- and difluorophenyl nucleosides, but potential mitochondrial effects of EN2, JW1 and JW2 should be further investigated.

Cyclosaligenyl pronucleotides of 5-iodo and 5-trifluoromethyl-1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluorobenzene mimics of thymidine: synthesis and evaluation of this pronucleotide monophosphate delivery system for compounds with potential anticancer activity

A group of unnatural 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluorobenzenes possessing a 5-I or 5-CF3 substituent, that were originally designed as thymidine mimics, were coupled via their 5'-OH group to a cyclosaligenyl (cycloSal) ring system having a variety of C-3 substituents (Me, OMe, H). The 5'-O-cycloSal-pronucleotide concept was designed to effect a thymidine kinase-bypass, thereby providing a method for the intracellular delivery and generation of the 5'-O-monophosphate for nucleosides that are poorly phosphorylated. The 5'-O-cycloSal pronucleotide phosphotriesters synthesized in this study were obtained as a 1:1 mixture of two diastereomers that differ in configuration (S(P) or R(P)) at the asymmetric phosphorous center. The (S(P))- and (R(P))-diastereomers for the 5'-O-3-methylcycloSal- and 5'-O-3-methoxycycloSal derivatives of 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene were separated by silica gel flash column chromatography. This class of cycloSal pronucleotide compounds generally exhibited weak cytotoxic activities in a MTT assay (CC50 values in the 10(-3) to 10(-4) M range), against a number of cancer cell lines (143B, 143B-LTK, EMT-6, Hela, 293), except for cyclosaligenyl-5'-O-[1'-(2,4-difluoro-5-iodophenyl)-2'-deoxy-beta-D-ribofuranosyl]phosphate that was more potent (CC50 values in the 10(-5) to 10(-6) M range), than the reference drug 5-iodo-2'-deoxyuridine (IUDR) which showed CC50 values in the 10(-3) to 10(-5) M range.

Electrophysiological characterization of a recombinant human Na+-coupled nucleoside transporter (hCNT1) produced in Xenopus oocytes

Human concentrative nucleoside transporter 1 (hCNT1) mediates active transport of nucleosides and anticancer and antiviral nucleoside drugs across cell membranes by coupling influx to the movement of Na(+) down its electrochemical gradient. The two-microelectrode voltage-clamp technique was used to measure steady-state and presteady-state currents of recombinant hCNT1 produced in Xenopus oocytes. Transport was electrogenic, phloridzin sensitive and specific for pyrimidine nucleosides and adenosine. Nucleoside analogues that induced inwardly directed Na(+) currents included the anticancer drugs 5-fluorouridine, 5-fluoro-2'-deoxyuridine, cladribine and cytarabine, the antiviral drugs zidovudine and zalcitabine, and the novel thymidine mimics 1-(2-deoxy-beta-d-ribofuranosyl)-2,4-difluoro-5-methylbenzene and 1-(2-deoxy-beta-d-ribofuranosyl)-2,4-difluoro-5-iodobenzene. Apparent K(m) values for 5-fluorouridine, 5-fluoro-2'-deoxyuridine and zidovudine were 18, 15 and 450 microm, respectively. hCNT1 was Na(+) specific, and the kinetics of steady-state uridine-evoked Na(+) currents were consistent with an ordered simultaneous transport model in which Na(+) binds first followed by uridine. Membrane potential influenced both ion binding and carrier translocation. The Na(+)-nucleoside coupling stoichiometry, determined directly by comparing the uridine-induced inward charge movement to [(14)C]uridine uptake was 1: 1. hCNT1 presteady-state currents were used to determine the fraction of the membrane field sensed by Na(+) (61%), the valency of the movable charge (-0.81) and the average number of transporters present in the oocyte plasma membrane (6.8 x 10(10) per cell). The hCNT1 turnover rate at -50 mV was 9.6 molecules of uridine transported per second.

Biochemical and pharmacokinetic evaluation of a novel pyrimidine nucleoside nitric oxide donor as a potential anticancer/antiviral agent

The objective of this study was to determine the physiochemical, biochemical and pharmacokinetic properties of 5-iodo-3'-O-nitro-2'-deoxyuridine (INUdR), a novel prodrug releasing both nitric oxide (NO) and 5-iodo-2'-deoxyuridine. The INUdR partition coefficient (log P=1.12) was determined by both the shake-flask method and by calculation using Interactive Analysis Log P Program. In vitro binding of INUdR to bovine serum albumin (BSA) was estimated using an ultrafiltration method to be 65 to 77%, depending on the INUdR concentration. INUdR was stable in phosphate buffer (pH 7.4) and in water, at both ambient temperature and at 37 degrees C. INUdR was resistant to phosphorolysis when incubated with thymidine phosphorylase. Plasma, L-cysteine and glutathione catalyzed release of NO from INUdR, as determined using the Griess reaction. In all three systems, the release of NO by INUdR was equal to or greater than that of the reference drug isosorbide dinitrate. The pharmacokinetics of INUdR following single intravenous bolus and oral doses of INUdR (40 mg/kg) to male Sprague-Dawley rats were characterized by a short elimination half-life (T(1/2) 0.27 h), a large steady-state volume of distribution (V(ss) 0.89 l/kg) and high oral bioavailability (F=0.95). In conclusion, INUdR lipophilicity, shelf-stability, and resistance towards catabolic breakdown by thymidine phosphorylase, together with its non-spontaneous, yet considerable NO release, constitute favorable characteristics of a potential anticancer/antiviral agent.

Dose-dependent pharmacokinetics of 1-(2-Deoxy-?-D- ribofuranosyl)-2,4-difluoro-5-iodobenzene: A potential mimic of 5-iodo-2?-deoxyuridine

The dose-range pharmacokinetics of l-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene (5-IDFPdR), a C-aryl nucleoside mimic of IUdR, were studied in male Sprague-Dawley rats following single intravenous (i.v.) and oral doses. After i.v. administration, the blood clearance decreased from approximately 32 ml/min/kg at a dose of 15 mg/kg, to approximately 19 ml/min/kg when dosed at 54 mg/kg, and the elimination half-life increased from 8.4 min to 21.5 min, for the respective doses. While the dose-normalized area under the concentration-time curve (AUCnorm) remained practically unchanged (0.132 kg min ml(-1)) upon increasing the i.v. dose from 5 to 15 mg/kg, it increased by about 44% ( approximately 0.19 kg min ml(-1)) when the i.v. dose was increased from 15 to 54 mg/kg. Similarly, there was a dose-dependent increase in AUCnorm with increasing oral doses: AUCnorm increased by 49% as the oral dose increased from 20 to 40 mg/kg, and further by 55% as the oral dose was increased from 40 mg/kg to 54 mg/kg. For the respective oral doses, the elimination half-life increased from 24.5 min to 176 min, while blood clearance was reduced from approximately 37 ml/min/kg to approximately 17 ml/min/kg. The urinary recoveries of unchanged 5-IDFPdR and its glucuronides (as percent of the dose) were somewhat increased at higher doses. This increase was more pronounced following the highest oral dose. The total biliary recovery of 5-IDFPdR (as percent of the dose) was, however, decreased with increasing doses. The overall kinetic profile of 5-IDFPdR based on these data is suggestive of dose-dependent pharmacokinetics. Decreased elimination of 5-IDFPdR with increasing dose, as supported by longer elimination half-lives at higher doses, is one likely mechanism contributing to the dose-dependent behaviour of this compound. Saturable non-renal metabolism might explain the reduced total body clearance of 5-IDFPdR at higher doses, despite the unchanged or increased urinary clearance. For drugs exhibiting nonlinear kinetics, the dosage regimens may need to be carefully designed to avoid potential unpredictable toxicity and/or lack of pharmacological response associated with the disproportional changes in steady state drug concentrations on changing dose. Manifestation in the rat of nonlinear kinetics at doses of 5-IDFPdR, which may be of therapeutic relevance, warrants extended dose-range evaluations of this compound in future preclinical and clinical studies, to establish safe and efficacious dosage regimens.

First stereoselective synthesis of 2-deoxy-alpha-D-ribosyl-1-phosphate: novel application of crystallization-induced asymmetric transformation

A first stereoselective synthesis of bis(cyclohexylamine) 2-deoxy-alpha-D-ribosyl-1-phosphate has been achieved. The synthesis features a key crystallization-induced asymmetric transformation (AT) to generate a desired alpha-anomer in 99% yield at a 98.8:1.2 ratio of alpha/beta.

Pharmacokinetics and metabolism of the novel synthetic C-nucleoside, 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene: a potential mimic of 5-iodo-2'-deoxyuridine

1-(2-Deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-iodobenzene (5-IDFPdR) is one of the several unnatural 1-(2-deoxy-beta-D-ribofuranosyl)-2,4-difluoro-5-substituted-benzenes recently synthesized for evaluation as anticancer, antiviral and diagnostic imaging agents. This class of C-nucleosides was designed to exploit several potential advantages relative to classical 5-substituted-2'-deoxyuridines, including stability towards phosphorolysis by pyrimidine phosphorylase, increased lipophilicity that may alter their ability to cross the blood-brain-barrier, and a greater resistance towards catabolism and deiodination. The physiochemical evaluation of 5-IDFPdR showed high lipophilicity (log P = 2.8), moderately high protein binding (70-75%), stability towards phosphorolysis (e.g. no evidence of metabolic deglycosylation) by thymidine phosphorylase, and minimal microsomal metabolism in vitro. Pharmacokinetic studies of 5-IDFPdR in rat were characterized by a short elimination half-life (9-12 min), modest urinary elimination in pooled 0-24 h urine specimens (10-14%, including 2% as unconjugated drug) and high oral bioavailability (F = 0.96). Both glucuronide and sulfate metabolites were present in urine. Glucuronidation was the predominant conjugation pathway.

Synthesis of unnatural 7-substituted-1-(2-deoxy-beta-D-ribofuranosyl)isocarbostyrils: "thymine replacement" analogs of deoxythymidine for evaluation as antiviral and anticancer agents

A group of unnatural 1-(2-deoxy-beta-D-ribofuranosyl)isocarbostyrils having a variety of C-7 substituents [H, 4,7-(NO2)2, I, CF3, CN, (E)-CH=CH-I, -C triple bond CH, -C triple bond C-I, -C triple bond C-Br, -C=C-Me], designed as nucleoside mimics, were synthesized for evaluation as anticancer and antiviral agents. This class of compounds exhibited weak cytotoxicity in a MTT assay (CC50 = 10(-3) to 10(-5) M range) with the 4,7-dinitro derivative being the most cytotoxic, relative to thymidine (CC50 = 10(-3) to 10(-5) M range), against a variety of cancer cell lines. The 4,7-dinitro, 7-I and 7-C triple bond CH compounds exhibited similar cytotoxicity against non-transfected (KBALB, 143B), and HSV-1 TK+ gene transfected (KBALB-STK, 143B-LTK) cancer cell lines possessing the herpes simplex virus type 1 (HSV-1) thymidine kinase gene (TK+). This observation indicates that these compounds are not substrates for HSV type-1 TK, and are therefore unlikely to be useful in gene therapy based on the HSV gene therapy paradigm.