Fluorinated Nucleosides: Synthesis and Biological Implication

High-performance liquid chromatography purification of chemically modified RNA aptamers

2'-Fluoro modified RNAs are useful as potential therapeutics and as special substrates for studying RNA function. 2'-Fluoro modified RNAs generally need to be purified after they are prepared either enzymatically or by solid-phase synthesis. Here we introduce a protocol by which 2'-fluoro modified RNAs with 57 and 58 nucleotides can be resolved and purified using ion-pair, reverse-phase high-performance liquid chromatography (HPLC). Because the size of our RNA samples is in the range of many known RNA aptamers of therapeutic values, our protocol should be generally useful.

Raising the pKa limit of "soft" nucleophiles in palladium-catalyzed allylic substitutions: application of diarylmethane pronucleophiles

The Tsuji-Trost allylic substitution reaction provides a useful and efficient approach to construct C-C bonds between sp(3)-hybridized carbons. The widely accepted paradigm for classifying the mode of attack of nucleophiles on palladium π-allyl intermediates in the Tsuji-Trost reaction is based on the pKa of the pronucleophile: (1) stabilized or "soft" carbon nucleophiles and heteroatom nucleophiles (e.g., pronucleophiles with pKa's < 25), and (2) unstabilized or "hard" nucleophiles (those from pronucleophiles with pKa's > 25). One of the keys to the continuing development of allylic substitution processes remains broadening the scope of "soft" nucleophiles. Herein we report a general method for the room temperature Pd-catalyzed allylic substitution with diarylmethane derivatives (pKa's up to 32). The synthetic significance of the method is that it provides a rapid access to products containing allylated diarylmethyl motifs. The method is general for a wide range of nucleophiles derived from diarylmethanes and heterocyclic derivatives. A procedure for the Pd-catalyzed allylic substitutions to afford diallylation products with quaternary centers is also described. With triarylmethanes and alkylated diarylmethanes the corresponding allylated products are isolated. We anticipate that the described method will be a valuable complement to the existing arsenal of nucleophiles in Pd-catalyzed allylic substitutions. Mechanistic studies show that the nucleophile derived from diphenylmethane undergoes external attack on π-allyl palladium species under our reaction conditions. This unexpected observation indicates that diarylmethane derivatives behave as "soft" or stabilized nucleophiles. The results of this study indicate that the cutoff between "soft" and "hard" nucleophiles should be raised from a pronucleophile pKa of 25 to at least 32.

Metal-catalyzed benzylic fluorination as a synthetic equivalent to 1,4-conjugate addition of fluoride

We explore in detail the iron-catalyzed benzylic fluorination of substrates containing aromatic rings and electron-withdrawing groups positioned β to one another, thus providing direct access to β-fluorinated adducts. This operationally convenient process can be thought of not only as a contribution to the timely problem of benzylic fluorination but also as a functional equivalent to a conjugate addition of fluoride, furnishing products in moderate to good yields and in excellent selectivity.

GRL-04810 and GRL-05010, difluoride-containing nonpeptidic HIV-1 protease inhibitors (PIs) that inhibit the replication of multi-PI-resistant HIV-1 in vitro and possess favorable lipophilicity that may allow blood-brain barrier penetration

We designed, synthesized, and identified two novel nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs), GRL-04810 and GRL-05010, containing the structure-based designed privileged cyclic ether-derived nonpeptide P2 ligand, bis-tetrahydrofuranylurethane (bis-THF), and a difluoride moiety, both of which are active against the laboratory strain HIV-1LAI (50% effective concentrations [EC50s], 0.0008 and 0.003 μM, respectively) with minimal cytotoxicity (50% cytotoxic concentrations [CC50s], 17.5 and 37.0 μM, respectively, in CD4(+) MT-2 cells). The two compounds were active against multi-PI-resistant clinical HIV-1 variants isolated from patients who had no response to various antiviral regimens. GRL-04810 and GRL-05010 also blocked the infectivity and replication of each of the HIV-1NL4-3 variants selected by up to 5 μM lopinavir (EC50s, 0.03 and 0.03 μM, respectively) and atazanavir (EC50s, 0.02 and 0.04 μM, respectively). Moreover, they were active against darunavir (DRV)-resistant variants (EC50 in 0.03 to 0.034 μM range for GRL-04810 and 0.026 to 0.043 μM for GRL-05010), while DRV had EC50s between 0.02 and 0.174 μM. GRL-04810 had a favorable lipophilicity profile as determined with the partition (log P) and distribution (log D) coefficients of -0.14 and -0.29, respectively. The in vitro blood-brain barrier (BBB) permeability assay revealed that GRL-04810 and GRL-05010 may have a greater advantage in terms of crossing the BBB than the currently available PIs, with apparent penetration indexes of 47.8 × 10(-6) and 61.8 × 10(-6) cm/s, respectively. The present data demonstrate that GRL-04810 and GRL-05010 exert efficient activity against a wide spectrum of HIV-1 variants in vitro and suggest that two fluorine atoms added to their bis-THF moieties may well enhance their penetration across the BBB.

Iron(II)-catalyzed benzylic fluorination

Direct C-F functionalization of benzylic sp(3) C-H bonds is a synthetic challenge that has yet to be propitiously overcome. A mild, one-pot synthesis of monofluorinated benzylic substrates is reported with commercially available iron(II) acetylacetonate and Selectfluor in good to excellent yields and selectivity. A convenient route to β-fluorinated products of 3-aryl ketones is also highlighted, providing a synthetic equivalent to the difficult to accomplish conjugate addition of fluoride to α,β-unsaturated ketones.

Recombinant purine nucleoside phosphorylases from thermophiles: preparation, properties and activity towards purine and pyrimidine nucleosides

Thermostable nucleoside phosphorylases are attractive biocatalysts for the synthesis of modified nucleosides. Hence we report on the recombinant expression of three 'high molecular mass' purine nucleoside phosphorylases (PNPs) derived from the thermophilic bacteria Deinococcus geothermalis, Geobacillus thermoglucosidasius and from the hyperthermophilic archaeon Aeropyrum pernix (5'-methythioadenosine phosphorylase; ApMTAP). Thermostability studies, kinetic analysis and substrate specificities are reported. The PNPs were stable at their optimal temperatures (DgPNP, 55 °C; GtPNP, 70 °C; ApMTAP, activity rising to 99 °C). Substrate properties were investigated for natural purine nucleosides [adenosine, inosine and their C2'-deoxy counterparts (activity within 50-500 U·mg(-1))], analogues with 2'-amino modified 2'-deoxy-adenosine and -inosine (within 0.1-3 U·mg(-1)) as well as 2'-deoxy-2'-fluoroadenosine (9) and its C2'-arabino diastereomer (10, within 0.01-0.03 U·mg(-1)). Our results reveal that the structure of the heterocyclic base (e.g. adenine or hypoxanthine) can play a critical role in the phosphorolysis reaction. The implications of this finding may be helpful for reaction mechanism studies or optimization of reaction conditions. Unexpectedly, the diastereomeric 2'-deoxyfluoro adenine ribo- and arabino-nucleosides displayed similar substrate properties. Moreover, cytidine and 2'-deoxycytidine were found to be moderate substrates of the prepared PNPs, with substrate activities in a range similar to those determined for 2'-deoxyfluoro adenine nucleosides 9 and 10. C2'-modified nucleosides are accepted as substrates by all recombinant enzymes studied, making these enzymes promising biocatalysts for the synthesis of modified nucleosides. Indeed, the prepared PNPs performed well in preliminary transglycosylation reactions resulting in the synthesis of 2'-deoxyfluoro adenine ribo- and arabino- nucleosides in moderate yield (24%).

A facile synthesis of 5'-fluoro-5'-deoxyacadesine (5'-F-AICAR): a novel non-phosphorylable AICAR analogue

The substitution of a hydroxyl group by a fluorine atom in a potential drug is an efficient reaction that can, in principle, improve its pharmacological properties. Herein, the synthesis of the novel compound 5'-fluoro-5'-deoxyacadesine (5'-F-AICAR), a strict analogue of AICAR that cannot be 5'-phosphorylated to ZMP by cellular kinases, is reported.

Synthesis, evaluation of anti-HIV-1 and anti-HCV activity of novel 2',3'-dideoxy-2',2'-difluoro-4'-azanucleosides

A series of 2',3'-dideoxy-2',2'-difluoro-4'-azanucleosides of both pyrimidine and purine nucleobases were synthesized in an efficient manner starting from commercially available L-pyroglutamic acid via glycosylation of difluorinated pyrrolidine derivative 15. Several 4'-azanucleosides were prepared as a separable mixture of α- and β-anomers. The 6-chloropurine analogue was obtained as a mixture of N(7) and N(9) regioisomers and their structures were identified based on NOESY and HMBC spectral data. Among the 4'-azanucleosides tested as HIV-1 inhibitors in primary human lymphocytes, four compounds showed modest activity and the 5-fluorouracil analogue (18d) was found to be the most active compound (EC(50)=36.9μM) in this series. None of the compounds synthesized in this study demonstrated anti-HCV activity.

Synthesis and biological activity of the nucleoside analogs based on polyfluoroalkyl-substituted 1,2,3-triazoles

This paper offers the results of a synthesis and study of cytotoxicity and the anti-Epstein-Barr virus (EBV) activity of new 2-deoxy-2-chloro-pyranosyl derivatives of 4-tosyl-5-trifluoromethyl-1,2,3-triazole obtained via the addition reaction of the corresponding 2-N-chlorotriazole to the double bond of 3,4,6-tri-O-acetyl-D-glucal. Nucleoside mimetics, derivatives of 4-tosyl-5-polyfluoroalkyl-1,2,3-triazoles containing fragments of 3-chloro-tetrahydrofuran, 3-chloro-tetrahydropyran, tetrahydropyran, dihydrofuran, dihydropyran, or acyclic substituents, were also studied. Evaluation of cytotoxicity (trypan blue and MTT methods) and anti-EBV activity (polymerase chain reaction (PCR) method) showed high selectivity indices for the compounds 4a, 4b, 5b, 6, and 8. A total of 15 novel compounds were examined in this study.

Skeletal rearrangements resulting from reactions of 1,6:2,3- and 1,6:3,4-dianhydro-β-D-hexopyranoses with diethylaminosulphur trifluoride

A complete series of eight 1,6:2,3- and 1,6:3,4-dianhydro-β-D-hexopyranoses were subjected to fluorination with DAST. The 1,6:3,4-dianhydropyranoses yielded solely products of skeletal rearrangement resulting from migration of the tetrahydropyran oxygen (educts of D-altro and D-talo configuration) or of the 1,6-anhydro bridge oxygen (D-allo, D-galacto). The major products yielded by the 1,6:2,3-dianhydropyranoses were compounds arising from nucleophilic substitution, with configuration at C4 either retained (D-talo, D-gulo) or inverted (D-manno), or from C6 migration (D-allo). The minor products in the 1,6:2,3-series resulted from migration of the tetrahydropyran oxygen (D-gulo) or the oxirane oxygen (D-manno), or from nucleophilic substitution with retention of configuration (D-manno). The structure of most of the rearranged products was verified by X-ray crystallography.

From bifunctional to trifunctional (tricomponent nucleophile-transition metal-lewis acid) catalysis: the catalytic, enantioselective α-fluorination of acid chlorides

We report in full detail our studies on the catalytic, asymmetric α-fluorination of acid chlorides, a practical method that produces an array of α-fluorocarboxylic acid derivatives in which improved yield and virtually complete enantioselectivity are controlled through electrophilic fluorination of a ketene enolate intermediate. We discovered, for the first time, that a third catalyst, a Lewis acidic lithium salt, could be introduced into a dually activated system to amplify yields of aliphatic products, primarily through activation of the fluorinating agent. Through our mechanistic studies (based on kinetic data, isotopic labeling, spectroscopic measurements, and theoretical calculations) we were able to utilize our understanding of this "trifunctional" reaction to optimize the conditions and obtain new products in good yield and excellent enantioselectivity.

Combining asymmetric catalysis with natural product functionalization through enantioselective alpha-fluorination

An examination into the derivatization of various natural products using newly developed alpha-fluorination methodology is disclosed. An activated ketene enolate, generated from an acid chloride, is allowed to react with an electrophilic fluorine source (NFSi). Quenching the reaction with a nucleophilic natural product produces biologically relevant alpha-fluorinated carbonyl derivatives of select chemotherapeutics, antibiotics, and other pharmaceuticals.

New preparation and synthetic reactions of 3,3,3-trifluoropropynyllithium, -borate and -stannane: facile synthesis of trifluoromethylated allenes, arylacetylenes and enynes

Background: Since trifluoromethyl-containing compounds have found diverse applications in the fields of pharmaceuticals and agrochemicals, facile and selective synthetic methods for trifluoromethyl-substituted compounds are an essential tool for advanced medicinal chemistry. Now that diverse synthetic transformations of carbon–carbon triple bonds are available, 3,3,3-trifluoropropynyl-substituted compounds serve as versatile building blocks for target molecules containing trifluoromethyl groups. Thus, novel synthetic methods and reagents for incorporation of a 3,3,3-trifluoropropynyl group into an organic compound have been the major concern in exploration and modification of fluorine-based biologically active substances. Results & discussion: We report a preparative method of 3,3,3-trifluoropropynyllithium and its reaction with electrophiles including aldehydes, ketones, trimethoxyborane, chlorosilanes and chlorostannanes in detail. Palladium-catalyzed synthetic reactions of the carbonyl adducts and the trifluoromethyl-containing metalloid reagents are also demonstrated, which provide simple synthetic methods of trifluoromethylated allenes, arylacetylenes and enynes. The synthetic transformations presented here expand the repertoire of trifluoromethylated compounds available for medicinal scientists and contribute to the advance of future medicinal chemistry.

Dideoxy fluoro-ketopyranosyl nucleosides as potent antiviral agents: synthesis and biological evaluation of 2,3- and 3,4-dideoxy-3-fluoro-4- and -2-keto-beta-d-glucopyranosyl derivatives of N(4)-benzoyl cytosine

The synthesis of the dideoxy fluoro ketopyranonucleoside analogues, 1-(2,3-dideoxy-3-fluoro-6-O-trityl-beta-d-glycero-hexopyranosyl-4-ulose)-N(4)-benzoyl cytosine (7a), 1-(3,4-dideoxy-3-fluoro-6-O-trityl-beta-d-glycero-hexopyranosyl-2-ulose)-N(4)-benzoyl cytosine (13a) and their detritylated analogues 8a and 14a, respectively, is described. Condensation of peracetylated 3-deoxy-3-fluoro-D-glucopyranose (1) with silylated N(4)-benzoyl cytosine, followed by selective deprotection and isopropylidenation afforded compound 2. Routine deoxygenation at position 2', followed by a deprotection-selective reprotection sequence afforded the partially tritylated dideoxy nucleoside of cytosine 6, which upon oxidation of the free hydroxyl group at the 4'-position, furnished the desired tritylated 2,3-dideoxy-3-fluoro ketonucleoside 7a in equilibrium with its hydrated form 7b. Compound 2 was the starting material for the synthesis of the dideoxy fluoro ketopyranonucleoside 13a. Similarly, several subsequent protection and deprotection steps as well as routine deoxygenation at position 4', followed by oxidation of the free hydroxyl group at the 2'-position of the partially tritylated dideoxy nucleoside 12, yielded the desired carbonyl compound 13a in equilibrium with its hydrated form 13b. Finally, trityl removal from 7a/b and 13a/b provided the unprotected 2,3-dideoxy-3-fluoro-4-keto and 3,4-dideoxy-3-fluoro-2-ketopyranonucleoside analogues 8a and 14a, in equilibrium with their gem-diol forms 8b and 14b. None of the compounds showed inhibitory activity against a wide variety of DNA and RNA viruses at subtoxic concentrations, except 7a/b that was highly efficient against rotavirus infection. Nucleoside 7a/b also exhibited cytostatic activity against cells of various cancers. BrdU-cell cycle analysis revealed that the mechanism of cytostatic activity may be related to a delay in G1/S phase and initiation of programmed cell death.