Synthesis of tricarbonyl rhenium and technetium complexes of a 5′-carboxamide 5-ethyl-2′-deoxyuridine for selective inhibition of herpes simplex virus thymidine kinase 1

Herpes simplex virus thymidine kinase type 1 (HSV1-TK) is frequently used as reporter protein in gene therapy. Our aim is to produce single photon emitting reporter probe based on technetium-99m. The synthesis of organometallic technetium and rhenium complexes of a 5′-carboxamide 5-ethyl-2′-deoxyuridine derivative able to selectively inhibit HSV1-TK is presented. The 5-ethyl-2′-deoxyuridine functionalized with a suitable tridentate chelating system at position 5′ was synthesized from commercial 2′-deoxyuridine in seven steps. The 5-ethyl-2′-deoxyuridine derivative was labeled with the fac-M(CO)₃-core (M = Tc, Re). The resulting rhenium complex was found to be a selective competitive inhibitor of HSV1-TK (K_i = 4.56 μM). Inhibition of the human cytosolic thymidine kinase (hTK1) previously reported with organometallic rhenium and technetium complexes of 5′-carboxamide thymidine derivative was not observed. The uptake of the technetium-99m complex in transfected cells expressing HSV1-TK has been evaluated to assess its possible use as reporter.     

5-Alkynyl-2′-deoxyuridines, containing bulky aryl groups: evaluation of structure-anti-HSV-1 activity relationship

Four 5-alkynyl-2′-deoxyuridines containing different bulky substituents and flexible linkers between the triple bond and the aromatic residue have been prepared and tested against HSV-1 in Vero cells. Two nucleosides containing carbonyl groups, 5-(4-benzoylphenoxypropyn-1-yl)-2′-deoxyuridine (19a) and 5-(estron-3-yloxypropyn-1-yl)-2′-deoxyuridine (19c), showed low cytotoxicity and moderate antiviral activity. The flexible linker appears not to be favorable for antiviral properties of 5-alkynyl-2′deoxyuridines: 5-[(perylen-3-yl)methoxypropyn-1-yl]-2′-deoxyuridine (19d) showed considerable cytotoxicity and no antiviral activity in contrast to the active and nontoxic 5-(perylen-3-ylethynyl)-2′-deoxyuridine (9), a nucleoside with a rigid triple-bond-connection of the aromatic system to the nucleobase.     

Development and validation of an ion pair HPLC method for gemcitabine and 2′,2′-difluoro-2′-deoxyuridine determination

A reverse phase HPLC method based on ion-pair formation was set up for the simultaneous determination of gemcitabine and its metabolite 2′,2′-difluoro-2′-deoxyuridine (dFdU) in plasma samples obtained from cancer patients. The separation was performed on a μBondapack C₁₈ (300 mm × 3.9 mm i.d., 10 μm particle size) column at room temperature. The mobile phase, 5 mM pentane-1-sulfonic acid pH 3.1/methanol (96:4), was pumped at a flow rate of 1.5 mL min⁻¹. Gemcitabine and dFdU eluted in less than 16 min. Linearity, sensitivity, and reproducibility studies, which actual values met the demands for bioanalytical assays, validated the method. This assay provided pharmacokinetic data from patients treated with intravenous gemcitabine.     

Preparation of 5-Hydroxymethyl-pyrimidine Based Nucleosides: A Reinvestigation

5-Hydroxymethyl-pyrimidine-based nucleobases have attracted attention in the last years due to their important role in gene regulation. It prompted the development of efficient routes to the corresponding nucleoside building blocks for further incorporation into oligonucleotides. Several pathways have been employed in recent years to access properly protected 5-hydroxymethyl-pyrimidine based nucleosides, including hydroxymethylation of 2’-deoxyuridine, radical bromination of thymidine followed by bromine substitution, or carbonylative coupling through Stille conditions starting from 5-iodo-2’-deoxyuridine. In this study, we review the different approaches currently used to introduce the 5-hydroxymethyl moiety, we reinvestigate some of them, and finally, we propose an alternative route based on the oxidation of the methyl of thymidine followed by its reduction that allows access to protected 5-hydroxymethyl-2’-deoxyuridine in a simple way with good yields. Finally, we present some examples of application including the synthesis of base J and 5-azidomethyl-2’-deoxyuridine.     

Synthesis of hapten-phosphoramidites from 2′-deoxyuridine

A total of 11 novel phosphoramidites, 3a-d, 4a-d and 14a-c were prepared from 2′-deoxyuridine functionalized at 5 and 6-position of the pyrimidine ring with hapten reporter groups, e.g. adamantane, carbazole, dansyl and dabsyl, suitable for use in immunodetection nucleic acid testing assays.     

Uracil ring opening in the reaction of 5-formyl-2′-deoxyuridine with primary alkyl amines

Treatment of 5-formyl-2′-deoxyuridine (f⁵dU) with stoichiometric amounts of strongly nucleophilic, non-hindered primary alkyl amines led to fast and quantitative formation of the corresponding Schiff bases. In the presence of excess amines, novel nucleosides with ring opened pyrimidine bases were formed as a result of the Michael addition of a second amine to the pre-formed imines. In the reaction of f⁵dU with aromatic amines, the formation of Schiff base derivatives was slower and even under prolonged treatment with an excess of amine the uracil ring remained intact.     

Synthesis,cytotoxicity and antiviral activity studies of the conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives

A series of novel conjugates of cobalt bis(1,2-dicarbollide)(-I) with 5-ethynyl-2′-deoxyuridine and its cyclic derivatives were synthesized. Conjugates with 5-ethynyl-2-deoxyuridine were prepared by the direct Sonogashira coupling of a series of cobalt bis(1,2-dicarbollide)(-I) terminal alkynes and 5-iodo-2′-deoxyuridine. Their furo[2,3-d]pyrimidin-2(3H)-one isomers were obtained either by intermolecular cyclization of the above conjugates or by Sonogashira coupling using Pd/C as a catalyst. Action of ammonia on these furo[2,3-d]pyrimidin-2(3H)-one conjugates resulted in pyrrolo[2,3-d]pyrimidin-2(3H)-one conjugates. Most of the designed compounds have shown low cytotoxicity in several cell lines. Some 5-ethynyl-2-deoxyuridine and furo[2,3-d]pyrimidin-2(3H)-one conjugates have also presented antiviral activity.     

Novel and efficient syntheses of 3′,5′-diamino derivatives of 2′,3′,5′-trideoxycytidine and 2′,3′,5′-trideoxyadenosine. Protonation behavior of 3′,5′-diaminonucleosides

High yielding synthetic routes to 3′,5′-diamino-2′,3′,5′-trideoxycytidine and 3′,5′-diamino-2′,3′,5′-trideoxyadenosine are described. In addition, the protonation behavior of 3′,5′-diamino-2′,3′,5′-trideoxycytidine, 3′,5′-diamino-2′,3′,5′-trideoxyadenosine, 3′,5′-diamino-3′,5′-dideoxythymidine, and 3′,5′-diamino-2′,3′,5′-trideoxyuridine has been studied by means of pH-metric measurements and NMR spectroscopy. The ionization constants and the sequence of protonation sites have been determined.     

The effect of electron charge transfer in biological activity and vibrational wavenumbers of 2′-Deoxyuridine and 5-Fluoro-2′-Deoxyuridine: DFT approach

Vibrational analysis of the 2′-Deoxyuridine and 5-Fluoro-2′-deoxyuridine compounds has been performed using FT-Raman and FTIR spectroscopic techniques. The optimized geometry, various bonding features and harmonic vibrational wavenumbers have been computed with the help of B3LYP/6-31G (d, p) density functional theory method. The natural bond orbital analysis, Mulliken population analysis on atomic charges and the HOMO–LUMO energy have been calculated to explore the reasons for the change in biological activity and vibrational wavenumbers of the title compounds. Potential energy distribution analysis has been used to assign the normal modes of vibrations unambiguously.     

Syntheses of 5′-amino-2′,5′-dideoxy-2′,2′-difluorocytidine derivatives as novel anticancer nucleoside analogs

A novel class of 5′-amino-2′,5′-dideoxy-2′,2′-difluorocytidine derivatives has been synthesized in order to identify anticancer nucleoside analogs. Several synthetic routes were devised and implemented which relied upon either S_N2 displacement or reductive amination to provide the desired derivatives.     

Electrophile-promoted addition of hydroxymethylphosphonate to 4′,5′-didehydronucleosides: a way to novel isosteric analogues of 5′-nucleotides

An electrophile-promoted addition of dialkyl-hydroxymethylphosphonate to the protected 4′,5′-didehydronucleosides resulted in an epimeric mixture of 4′-dialkylphosphonomethoxy derivatives of 2′,5′-dideoxynucleosides, novel analogues of 2′-deoxynucleoside 5′-monophosphates. Several types of electrophiles (pyridinium tosylate, NIS, NBS, MCPBA and others) were evaluated in addition reactions with 4′,5′-didehydrothymidine. Out of them, pyridinium tosylate was found to have a practical usefulness in these transformations. Its use has led to the preparation of a series of 4′-phosphonomethoxy derivatives of common 2′-deoxynucleosides. On biological screening, these free phosphonic acids exerted no significant cytostatic or antiviral activity.     

Synthesis of new 6-substituted purinyl-5′-nor-1′-homocarbanucleosides based on indanol

A series of new 6-substituted purinyl-5′-nor-1′-homocarbanucleosides based on indanol were synthesized from (±)-cis-3-hydroxymethyl-1-indanol, an appropriately functionalized derivative of which was reacted with 6-chloropurine in the presence of NaH and 18-crown-6 ether to prepare a key intermediate that gave access to the target molecules, purinylcarbanucleosides in which position 6 is occupied by a chloro, hydroxy, methoxy, amino or substituted phenyl group.     

New and efficient synthesis of 5′-amino-5′-(S)-methyl-2′,5′-dideoxynucleosides

A short, efficient synthesis of 5′-amino-5′-(S)-methyl-2′,5′-dideoxynucleosides 1 has been developed through the diastereoselective addition of methylmagnesium bromide or methyllithium to an intermediate tert-butylsulfinimide.     

3′-Selective modification of a 4′,5′-didehydro-5′-deoxy-2′,3′-epoxyuridine using nucleophiles

1-(2,3-Anhydro-5-deoxy-4,5-didehydro-α-l-erythro-pent-4-enofuranosyl)uracil 4 was obtained by the treatment of 5′-iodo-2′,3′-epoxyuridine 5 with LiHMDS in excellent yield. The pyrimidine nucleoside 4 possesses quite unique vinyl epoxide moiety within the molecules. The reactions of 4 with a variety of nucleophiles gave 3′-substituted pyrimidine nucleosides without the formation of the corresponding 2′-substituted isomers. In the case of NaN₃ or PhSH, the corresponding 5′-adduct was obtained as a minor product together with the expected 3′-adduct.     

Concise synthesis of 5-methyl-, 5-formyl,and 5-carboxy analogues of 2′-deoxycytidine-5′-triphosphate

We describe a concise and efficient synthesis of 5-methyl-, 5-formyl-, and 5-carboxy-analogues of 2′-deoxycytidine-5′-triphosphate which are well known for their various biological applications. A protection-free one-pot synthesis was used to convert 5-methyl-2′-deoxycytidine into 5-methyl-2′-deoxycytidine-5′-triphosphate in high yield. 5-Formyl-2′-deoxycytidine-5′-triphosphate was obtained upon photosensitized oxidation (UV-A irradiation, λ ∼365 nm) of an aerated aqueous solution of 5-methyl-2′-deoxycytidine-5′-triphosphate with the use of menadione as the photosensitizer. 5-Formyl-2′-deoxycytidine-5′-triphosphate was converted into 5-carboxy-2′-deoxycytidine-5′-triphosphate by using biphasic TEMPO/BAIB oxidation method in high yield.     

An efficient synthesis of certain 5-substituted-2'-deoxyuridine 3',5'-cyclic monophosphate p-o-alkyl(aralkyl) esters. The crystal and molecular structure of 5-IODO-2'-deoxyuridine 3',5'-cyclic monophosphate p-o-methyl ester with axial methoxy group

Some 5-alkyl- and 5-halogeno-2'-deoxyuridine 3',5'-cyclic mono- phosphate P-O-alkyl(aralkyl) esters have been prepared from the silver salts of the parent cyclic monophosphates and alkyl(aralkyl) iodides. The diastereomeric phosphotriesters have been characterized by spectroscopic methods. The crystal and molecular structure of 5-iodo-2'-deoxyuridine 3',5'-cyclic monophosphate P-O-methyl ester with axial methoxy group has been determined. We failed to obtain the desired triesters from the reactions of the cAMP silver salt with alkyl iodides, contrary to previous claims in the literature.     

Unexpected formation of 2′-deoxy-N3-(3,3,3-trifluoro-1-propenyl)uridine via a Michael-type addition to 3,3,3-trifluoropropyne

Reaction of 3,3,3-trifluoropropyne with 2′-deoxy-5-iodouridine under conditions that have previously been used to prepare 5-alkynyl-2′-deoxyuridine derivatives gave 2′-deoxy-N3-(3,3,3-trifluoro-1-propenyl)uridine. This unexpected alkylation is a result of a Michael-type addition of N3 on the pyrimidine base to the electron deficient trifluoropropyne.     

Novel and efficient regioselective enzymatic approach to 3′-, 5′- and 3′,5′-di-O-crotonyl 2′-deoxynucleoside derivatives

Regioselective syntheses of several O-crotonyl 2′-deoxynucleoside derivatives have been efficiently achieved using a biocatalytic methodology. While Candida antarctica lipase B (CAL-B) afforded the 5′-O-acylated compounds, immobilized lipase from Pseudomonas cepacia (PSL-C) provided the 3′-O-crotonylated analogs. Since classical chemical approaches did not work appropriately due to side isomerization reactions, a mixture of both lipases was used to achieve a useful synthetic route toward diacylated nucleosides.     

Enantiospecific synthesis of 5′,5′,5′-trifluoro-5′-deoxyneplanocin A

(−)-(1S,4R)-4-Hydroxy-2-cyclopenten-1-yl acetate provided a convenient entry point for a 12-step chiral preparation of 5′,5′,5′-trifluoro-5′-deoxyneplanocin A.