Synthesis and Cytostatic and Antiviral Activities of 2′‐Deoxy‐2′,2′‐difluororibo‐ and 2′‐Deoxy‐2′‐fluororibonucleosides Derived from 7‐(Het)aryl‐7‐deazaadenines

A series of sugar‐modified derivatives of cytostatic 7‐heteroaryl‐7‐deazaadenosines (2′‐deoxy‐2′‐fluororibo‐ and 2′‐deoxy‐2′,2′‐difluororibonucleosides) bearing an aryl or heteroaryl group at position 7 was prepared and screened for biological activity. The difluororibonucleosides were prepared by non‐ stereoselective glycosidation of 6‐chloro‐7‐deazapurine with benzoyl‐protected 2‐deoxy‐2,2‐difluoro‐D ‐erythro‐pentofuranosyl‐1‐mesylate, followed by amination and aqueous Suzuki cross‐couplings with (het)arylboronic acids. The fluororibo derivatives were prepared by aqueous palladium‐catalyzed cross‐coupling reactions of the corresponding 7‐iodo‐7‐deazaadenine 2′‐deoxy‐2′‐fluororibonucleoside 20 with (het)arylboronic acids. The key intermediate 20 was prepared by a six‐step sequence from the corresponding arabinonucleoside by selective protection of 3′‐ and 5′‐hydroxy groups with acid‐labile groups, followed by stereoselective S_N2 fluorination and deprotection. Some of the title nucleosides and 7‐iodo‐7‐deazaadenine intermediates showed micromolar cytostatic or anti‐HCV activity. The most active were 7‐iodo and 7‐ethynyl derivatives. The corresponding 2′‐deoxy‐2′,2′‐difluororibonucleoside 5′‐O‐triphosphates were found to be good substrates for bacterial DNA polymerases, but are inhibitors of human polymerase α.     

Recognition and Excision Properties of 8‐Halogenated‐7‐Deaza‐2′‐Deoxyguanosine as 8‐Oxo‐2′‐Deoxyguanosine Analogues and Fpg and hOGG1 Inhibitors

Cellular DNA continuously suffers various types of damage, and unrepaired damage increases disease progression risk. 8‐Oxo‐2′‐deoxyguanine (8‐oxo‐dG) is excised by repair enzymes, and their analogues are of interest as inhibitors and as bioprobes for study of these enzymes. We have developed 8‐halogenated‐7‐deaza‐2′‐deoxyguanosine derivatives that resemble 8‐oxo‐dG in that they adopt the syn conformation. In this study, we investigated their effects on Fpg (formamidopyrimidine DNA glycosylase) and hOGG1 (human 8‐oxoguanine DNA N‐glycosylase 1). Relative to 8‐oxo‐dG, Cl‐ and Br‐deaza‐dG were good substrates for Fpg, whereas they were less efficient substrates for hOGG1. Kinetics and binding experiments indicated that, although hOGG1 effectively binds Cl‐ and Br‐deaza‐dG analogues with low K_m values, their lower k_cat values result in low glycosylase activities. The benefits of the high binding affinities and low reactivities of 8‐oxo‐dG analogues with hOGG1 have been successfully applied to the competitive inhibition of the excision of 8‐oxoguanine from duplex DNA by hOGG1.     

Synthesis of C8‐N‐Arylamine‐Modified 2′‐Deoxyguanosine‐5′‐Triphosphates and Their Effects on Primer Extension by DNA Polymerases

C8‐N‐arylamine adducts of 2′‐deoxyguanosine (2′‐dG) play an important role in the induction of the chemical carcinogenesis caused by aromatic amines. C8‐N‐acetyl‐N‐arylamine dG adducts that differ in their substitution pattern in the aniline moiety were converted by cycloSal technology into the corresponding C8‐N‐acetyl‐N‐arylamine‐2′‐deoxyguanosine‐5′‐triphosphates and C8‐NH‐arylamine‐2′‐deoxyguanosine‐5′‐triphosphates. Their conformation preference has been investigated by NOE spectroscopy and DFT calculations. The substrate properties of the C8‐dG adducts were studied in primer‐extension assays by using Klenow fragment exo^? of Escherichia coli DNA polymerase I and human DNA polymerase β. It was shown that the incorporation was independent of the substitution pattern in the aryl moiety and the N‐acetyl group. Although the triphosphates were poor substrates for the human polymerases, they were incorporated twice before the termination of the elongation process occurred; this might demonstrate the importance of C8‐N‐arylamine‐2′‐deoxyguanosine‐5′‐triphosphates in chemical carcinogenesis.     

6‐Substituted 2‐Aminopurine‐2′‐deoxyribonucleoside 5′‐Triphosphates that Trace Cytosine Methylation

Gene expression is extensively regulated by the occurrence and distribution of the epigenetic marker 2′‐deoxy 5‐methylcytosine (5mC) in genomic DNA. Because of its effects on tumorigenesis there is an important link to human health. In addition, detection of 5mC can serve as an outstanding biomarker for diagnostics as well as for disease therapy. Our previous studies have already shown that, by processing O⁶‐alkylated 2′‐deoxyguanosine triphosphate (dGTP) analogues, DNA polymerases are able to sense the presence of a single 5mC unit in a template. Here we present the synthesis and evaluation of an extended toolbox of 6‐substituted 2‐aminopurine‐2′‐deoxyribonucleoside 5′‐triphosphates modified at position 6 with various functionalities. We found that sensing of 5‐methylation by this class of nucleotides is more general, not being restricted to O⁶‐alkyl modification of dGTP but also applying to other functionalities.     

Synthesis and Antiviral Evaluation of TriPPPro‐AbacavirTP,TriPPPro‐CarbovirTP,and Their 1′,2′‐cis‐Disubstituted Analogues

Herein we describe the synthesis of lipophilic triphosphate prodrugs of abacavir, carbovir, and their 1′,2′‐cis‐substituted carbocyclic analogues. The 1′,2′‐cis‐carbocyclic nucleosides were prepared by starting from enantiomerically pure (1R,2S)‐2‐((benzyloxy)methyl)cyclopent‐3‐en‐1‐ol by a microwave‐assisted Mitsunobu‐type reaction with 2‐amino‐6‐chloropurine. All four nucleoside analogues were prepared from their 2‐amino‐6‐chloropurine precursors. The nucleosides were converted into their corresponding nucleoside triphosphate prodrugs (TriPPPro approach) by application of the H‐phosphonate route. The TriPPPro compounds were hydrolyzed in different media, in which the formation of nucleoside triphosphates was proven. While the TriPPPro compounds of abacavir and carbovir showed increased antiviral activity over their parent nucleoside, the TriPPPro compounds of the 1′,2′‐cis‐substituted analogues as well as their parent nucleosides proved to be inactive against HIV.     

Organosoluble polyimides derived from asymmetric 2‐substituted‐and 2,2′,6‐trisubstituted‐4,4′‐oxydianilines

We report a new method for the preparation of asymmetric diamines using 4,4′‐oxydianiline (4,4′‐ODA) as the starting material. By controlling the equivalents of bromination agent, N‐bromosuccinimide, we were able to attach bromide and phenyl substituents at the 2‐ or 2,2′,6‐positions of 4,4′‐ODA. Thus, four new asymmetric aromatic diamines, 2‐bromo‐4,4′‐oxydianiline (6), 2,2′,6‐tribromo‐4,4′‐oxydianiline (7), 2‐phenyl‐4,4′‐oxydianiline (8) and 2,2′,6‐triphenyl‐4,4′‐oxydianiline (9), were synthesized by this method. Their structural asymmetry was confirmed using ¹H NMR spectroscopy. Asymmetric polyimides (PI10–PI13) were prepared from these diamines and three different dianhydrides (pyromellitic dianhydride (PMDA), 3,3′,4,4′‐biphenyltetracarboxylic dianhydride and 2,2‐bis(3,4‐dicarboxyphenyl)hexafluoropropane dianhydride) in refluxing m‐cresol. The formed polyimides, except PI10a derived from 6 and PMDA, were all soluble in m‐cresol without premature precipitation during polymerization. These polyimides with inherent viscosity of 0.41–0.96 dL g^?1, measured at a concentration of 0.5 g dL^?1 in N‐methyl‐2‐pyrrolidone at 30 °C, can form tough and flexible films. Because of the structural asymmetry, they also exhibited enhanced solubility in organic solvents. Especially, polyimides PI11a and PI13a derived from 7 and 9 with rigid PMDA were soluble in various organic solvents at room temperature. The structural asymmetry of the prepared polyimides was also evidenced from ¹H NMR spectroscopy. In the ¹H NMR spectrum of PI11a, the protons of pyromellitic moiety appeared in an area ratio of 1:2:1 at three different chemical shifts, which were assigned to head‐to‐head, head‐to‐tail and tail‐to‐tail configurations, respectively. These polyimides also exhibited good thermal stability. Their glass transition temperatures ranged from 297 to 344 °C measured using thermal mechanical analysis. © 2013 Society of Chemical Industry     

Synthesis and Biological Evaluation of Purine 2′‐Fluoro‐2′‐deoxyriboside ProTides as Anti‐influenza Virus Agents

2′‐Fluoro‐2′‐deoxyguanosine has been reported to have potent anti‐influenza virus activity in vitro and in vivo. Herein we describe the synthesis and biological evaluation of 6‐modified 2′‐fluoro‐2′‐deoxyguanosine analogues and their corresponding phosphoramidate ProTides as potential anti‐influenza virus agents. Whereas the parent nucleosides were devoid of antiviral activity in two different cellular assays, the 5′‐O‐naphthyl(methoxy‐L ‐alaninyl) ProTide derivatives of 6‐O‐methyl‐2′‐fluoro‐2′‐deoxyguanosine, 6‐O‐ethyl‐2′‐fluoro‐2′‐deoxyguanosine, and 2′‐deoxy‐2′‐fluoro‐6‐chloroguanosine, and the 5′‐O‐naphthyl(ethoxy‐L ‐alaninyl) ProTide of 6‐O‐ethyl‐2′‐fluoro‐2′‐deoxyguanosine displayed antiviral EC₉₉ values of ～12 μM . The antiviral results are supported by metabolism studies. Rapid conversion into the L ‐alaninyl metabolite and then 6‐modified 2′‐fluoro‐2′‐deoxyguanosine 5′‐monophosphate was observed in enzymatic assays with yeast carboxypeptidase Y or crude cell lysate. Evidence for efficient removal of the 6‐substituent on the guanine part was provided by enzymatic studies with adenosine deaminase, and by molecular modeling of the nucleoside 5′‐monophosphates in the catalytic site of a model of ADAL1, thus indicating the utility of the double prodrug concept.     

siRNA Modified with 2′‐Deoxy‐2′‐C‐methylpyrimidine Nucleosides

(2′S)‐2′‐Deoxy‐2′‐C‐methyluridine and (2′R)‐2′‐deoxy‐2′‐C‐methyluridine were incorporated in the 3′‐overhang region of the sense and antisense strands and in positions 2 and 5 of the seed region of siRNA duplexes directed against Renilla luciferase, whereas (2′S)‐2′‐deoxy‐2′‐C‐methylcytidine was incorporated in the 6‐position of the seed region of the same constructions. A dual luciferase reporter assay in transfected HeLa cells was used as a model system to measure the IC₅₀ values of 24 different modified duplexes. The best results were obtained by the substitution of one thymidine unit in the antisense 3′‐overhang region by (2′S)‐ or (2′R)‐2′‐deoxy‐2′‐C‐methyluridine, reducing IC₅₀ to half of the value observed for the natural control. The selectivity of the modified siRNA was measured, it being found that modifications in positions 5 and 6 of the seed region had a positive effect on the ON/OFF activity.     

Structure‐Based Design,Synthesis, and Evaluation of 2′‐(2‐Hydroxyethyl)‐2′‐deoxyadenosine and the 5′‐Diphosphate Derivative as Ribonucleotide Reductase Inhibitors

Analysis of the recently solved X‐ray crystal structures of Saccharomyces cerevisiae ribonucleotide reductase I (ScRnr1) in complex with effectors and substrates led to the discovery of a conserved water molecule located at the active site that interacted with the 2′‐hydroxy group of the nucleoside ribose. In this study 2′‐(2‐hydroxyethyl)‐2′‐deoxyadenosine 1 and the 5′‐diphosphate derivative 2 were designed and synthesized to see if the conserved water molecule could be displaced by a hydroxymethylene group, to generate novel RNR inhibitors as potential antitumor agents. Herein we report the synthesis of analogues 1 and 2 , and the co‐crystal structure of adenosine diphosphate analogue 2 bound to ScRnr1, which shows the conserved water molecule is displaced as hypothesized.     

An Efficient Lanthanide‐Dependent DNAzyme Cleaving 2′–5′‐Linked RNA

RNA can form two types of linkage. In addition to the predominant 3′–5′ linkage, 2′–5′‐linked RNA is also important in biology, medicine, and prebiotic studies. Here, in vitro selection was used to isolate a DNAzyme that specifically cleaves 2′–5′ RNA by using Ce³⁺ as the metal cofactor, but leaves the 3′–5′ counterpart intact. This Ce5 DNAzyme requires trivalent light lanthanide ions and shows a rate of 0.16 min^?1 in the presence of 10 μm Ce³⁺; the activity decreases with heavier lanthanide ions. This is the fastest DNAzyme reported for this reaction, and it might enable applications in chemical biology. As a proof‐of‐concept, using this DNAzyme, the reactions between phosphorothioate‐modified RNA and strongly thiophilic metals (Hg²⁺ and Tl³⁺) were studied as a function of pH.     

Bacterial Alarmone,Guanosine 5′‐Diphosphate 3′‐Diphosphate (ppGpp), Predominantly Binds the β′ Subunit of Plastid‐Encoded Plastid RNA Polymerase in Chloroplasts

It's alarming : Bacterial alarmone guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp), which is a key regulatory molecule that controls the stringent response, also exists in chloroplasts of plant cells. Cross‐linking experiments with 6‐thioguanosine 5′‐diphosphate 3′‐diphosphate (6‐thioppGpp) and chloroplast RNA polymerase indicate that ppGpp binds the β′ subunit of plastid‐encoded plastid RNA polymerase that corresponds to the Escherichia coli β′ subunit.

     

Exploring the Potent Inhibition of CTP Synthase by Gemcitabine‐5′‐Triphosphate

CTP synthase (CTPS) catalyzes the conversion of UTP to CTP and is a target for the development of antiviral, anticancer, antiprotozoal, and immunosuppressive agents. Exposure of cell lines to the antineoplastic cytidine analogue gemcitabine causes depletion of intracellular CTP levels, but the direct inhibition of CTPS by its metabolite gemcitabine‐5′‐triphosphate (dF‐dCTP) has not been demonstrated. We show that dF‐dCTP is a potent competitive inhibitor of Escherichia coli CTPS with respect to UTP [K_i=(3.0±0.1) μm ], and that its binding affinity exceeds that of CTP ≈75‐fold. Site‐directed mutagenesis studies indicated that Glu149 is an important binding determinant for both CTP and dF‐dCTP. Comparison of the binding affinities of the 5′‐triphosphates of 2′‐fluoro‐2′‐deoxycytidine and 2′‐fluoro‐2′‐deoxyarabinocytidine revealed that the 2′‐F‐arabino group contributes markedly to the strong binding of dF‐dCTP. Geminal 2′‐F substitution on UTP (dF‐dUTP) did not result in an increase in binding affinity with CTPS. Remarkably, CTPS catalyzed the conversion of dF‐dUTP into dF‐dCTP, thus suggesting that dF‐dCTP might be regenerated in vivo from its catabolite dF‐dUTP.     

Highly Regio‐ and Stereoselective Iodohydroxylation of Non‐ Heteroatom‐Substituted Allenes: An Efficient Synthesis of 4‐[3′‐Hydroxy‐2′‐iodoalk‐1′(Z)‐enyl]‐2(5H)‐furanone Derivatives

An efficient protocol for the highly regio‐ and stereoselective synthesis of 4‐(3′‐hydroxy‐2′‐iodoalk‐1′(Z)‐enyl)furan‐2(5H)‐one derivatives via selective iodohydroxylation of non‐heteroatom‐substituted allenes, i.e., 4‐allenyl‐2(5H)furanones, has been developed. The regio‐ and stereoselectivity of this reaction may be controlled by the electronic and steric effects of the furanone ring.     

Antioxidant mechanism of a 3‐arylbenzofuranone containing a 2′‐hydroxyl group

5‐Methyl‐7‐tert‐butyl‐3‐(2′hydroxyl‐5′‐methylphenyl)3H‐benzofuran‐2‐one (PCRBF2), is a better scavenger of 2,2‐diphenyl‐1‐picrylhydrazyl radicals than benzofuranone analogs without the 2′‐substituent, which indicates that PCRBF2 will cause good stabilization in polymers. To prove this further, antioxidation by PCRBF2 and other benzofuranone analogs, namely, 5‐methyl‐7‐tert‐butyl‐3‐(3′,4′‐dimethylphenyl)3H‐benzofuran‐2‐one (OXBF2) and 5‐methyl‐7‐tert‐butyl‐3‐(2′,5′‐dimethylphenyl)3H‐benzofuran‐2‐one (PXBF2), was comparatively studied in polypropylene. The resulting antioxidant activity order of these benzofuranones was PCRBF2 > OXBF2 > PXBF2, an observation showing that the hydroxyl group in the 2′‐position does not weaken the antioxidant activity of benzofuranone, but, on the contrary, increases it. Analyses by FTIR revealed intramolecular hydrogen bonding between the 3‐position hydrogen and the oxygen of the 2′‐hydroxyl group, which makes the 2′‐hydroxyl hydrogen of PCRBF2 more reactive than the 3‐position reactive hydrogen. Thus the hydroxyl group reacts with radicals first. J. VINYL ADDIT. TECHNOL., 19:198‐202, 2013. © 2013 Society of Plastics Engineers     

Approaches to the Preparation of Enantiomerically Pure (2R,2′R)‐(+)‐threo‐Methylphenidate Hydrochloride

Various approaches to the preparation of enantiomerically pure (2R,2′R)‐(+)‐threo‐methylphenidate hydrochloride ( 1 ) are reviewed. These approaches include synthesis using enantiomerically pure precursors obtained by resolution, classical and enzyme‐based resolution approaches, enantioselective synthesis approaches, and approaches based on enantioselective synthesis of (2S,2′R)‐erythro‐methylphenidate followed by epimerization at the 2‐position. 1 Introduction 2 Methods for the Enhancement of Enantiomeric Purity of 1 3 Approaches Using Enantiomerically Pure Precursors Obtained by Resolution 4 Classical Resolution Approaches 4.1 Resolution of Amide and Acid Derivatives 4.2 Resolution of (±)‐threo‐Methylphenidate 5 Enzyme‐Based Resolution Approaches 6 Enantioselective Synthesis Approaches 7 Approaches Based on Enantioselective Synthesis of (2S,2′R)‐erythro‐Methylphenidate and Epimerization 8 Conclusions     

Synthesis and Biological Evaluation of Pyrrolo[2,1‐f][1,2,4]triazine C‐Nucleosides with a Ribose, 2′‐Deoxyribose,and 2′,3′‐Dideoxyribose Sugar Moiety

The synthesis of hitherto unknown pyrrolo[2,1‐f][1,2,4]triazine C‐nucleosides is described. Structural variations (chlorine, bromine, iodine, and cyano groups) were introduced at position 7 of 4‐aza‐7,9‐dideazaadenine. In addition, pyrrolo[2,1‐f][1,2,4]triazine C‐nucleosides bearing a 2′‐deoxy‐, 2′,3′‐dideoxy‐, and 2′,3′‐dehydrodideoxyribose moiety were also prepared. Among these analogues, the pyrrolo[2,1‐f][1,2,4]triazine C‐ribonucleosides with either a hydrogen atom or cyano group at position 7 of the nucleobase displayed potent cytotoxic activity in a panel of various cancer cell lines.     

2′‐Bispyrene‐Modified 2′‐O‐Methyl RNA Probes as Useful Tools for the Detection of RNA: Synthesis,Fluorescent Properties,and Duplex Stability

The synthesis and properties two series of new 2′‐O‐methyl RNA probes, each containing a single insertion of a 2′‐bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21‐fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5′‐side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3′‐side are important: CC, CG, and UC dinucleotide units on the 3′‐side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2′‐bispyrene‐labeled 2′‐O‐methyl RNA probes might be useful tools for detection of RNAs.     

Discovery of 5′′‐Chloro‐N‐[(5,6‐dimethoxypyridin‐2‐yl)methyl]‐2,2′:5′,3′′‐terpyridine‐3′‐carboxamide (MK‐1064): A Selective Orexin 2 Receptor Antagonist (2‐SORA) for the Treatment of Insomnia

The field of small‐molecule orexin antagonist research has evolved rapidly in the last 15 years from the discovery of the orexin peptides to clinical proof‐of‐concept for the treatment of insomnia. Clinical programs have focused on the development of antagonists that reversibly block the action of endogenous peptides at both the orexin 1 and orexin 2 receptors (OX₁R and OX₂R), termed dual orexin receptor antagonists (DORAs), affording late‐stage development candidates including Merck’s suvorexant (new drug application filed 2012). Full characterization of the pharmacology associated with antagonism of either OX₁R or OX₂R alone has been hampered by the dearth of suitable subtype‐selective, orally bioavailable ligands. Herein, we report the development of a selective orexin 2 antagonist (2‐SORA) series to afford a potent, orally bioavailable 2‐SORA ligand. Several challenging medicinal chemistry issues were identified and overcome during the development of these 2,5‐disubstituted nicotinamides, including reversible CYP inhibition, physiochemical properties, P‐glycoprotein efflux and bioactivation. This article highlights structural modifications the team utilized to drive compound design, as well as in vivo characterization of our 2‐SORA clinical candidate, 5′′‐chloro‐N‐[(5,6‐dimethoxypyridin‐2‐yl)methyl]‐2,2′:5′,3′′‐terpyridine‐3′‐carboxamide (MK‐1064), in mouse, rat, dog, and rhesus sleep models.     

Synthesis and properties of organosoluble polyimides derived from 2,2′‐dibromo‐ and 2,2′,6,6′‐tetrabromo‐4,4′‐oxydianilines

Two new aromatic diamines, 2,2′‐dibromo‐4,4′‐oxydianiline (DB‐ODA 4 ) and 2,2′,6,6′‐tetrabromo‐4,4′‐oxydianiline (TB‐ODA 5 ), have been synthesized by oxidation, bromination, and reduction of 4,4′‐oxydianiline (4,4′‐ODA). Novel polyimides 6a–f and 7a–f were prepared by reacting DB‐ODA ( 4 ) and TB‐ODA ( 5 ) with several dianhydrides by one‐step method, respectively. The inherent viscosities of these polyimides ranged from 0.31 to 0.99 dL/g (0.5 g/dL, in NMP at 30°C). These polyimides showed enhanced solubilities compared to those derived from 4,4′‐oxydianiline and corresponding dianhydrides. Especially, polyimides 7a , derived from rigid PMDA and TB‐ODA ( 5 ) can also be soluble in THF, DMF, DMAc, DMSO, and NMP. These polyimides also exhibited good thermal stability. Their glass transition temperatures measured by thermal mechanical analysis (TMA) ranged from 251 to 328°C. When the same dianhydrides were used, polyimides 7 containing four bromide substituents had higher glass transition temperatures than polyimides 6 containing two bromide substituents. The effects of incorporating more polarizable bromides on the refractive indices of polyimides were also investigated. The average refractive indices (n_av) measured at 633 nm were from 1.6088 to 1.7072, and the in‐plane/out‐of‐plane birefringences (Δn) were from 0.0098 to 0.0445. It was found that the refractive indices are slightly higher when polyimides contain more bromides. However, this effect is not very obvious. It might be due to loose chain packing resulted from bromide substituents at the 2,2′ and 2,2′,6,6′ positions of the oxydiphenylene moieties. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010