Acyclic Analogues Research Articles

Stereospecific cross-coupling reactions of aryl-substituted tetrahydrofurans, tetrahydropyrans, and lactones.

The stereospecific ring-opening of O-heterocycles to provide acyclic alcohols and carboxylic acids with controlled formation of a new C–C bond is reported. These reactions provide new methods for synthesis of acyclic polyketide analogs with complex stereochemical arrays. Stereoselective synthesis of the cyclic template is utilized to control relative configuration; subsequent stereospecific nickel-catalyzed ring-opening affords the acyclic product. Aryl-substituted tetrahydrofurans and tetrahydropyrans undergo nickel-catalyzed Kumada-type coupling with a range of Grignard reagents to furnish acyclic alcohols with high diastereoselectivity. Enantioenriched lactones undergo Negishi-type cross-coupling with dimethylzinc to afford enantioenriched carboxylic acids. Application in a two-step enantioselective synthesis of an anti-dyslipidemia agent is demonstrated.

Alteration in substrate specificity of horse liver alcohol dehydrogenase by an acyclic nicotinamide analog of NAD(+).

A new, acyclic NAD-analog, acycloNAD(+) has been synthesized where the nicotinamide ribosyl moiety has been replaced by the nicotinamide (2-hydroxyethoxy)methyl moiety. The chemical properties of this analog are comparable to those of β-NAD(+) with a redox potential of -324mV and a 341nm λmax for the reduced form. Both yeast alcohol dehydrogenase (YADH) and horse liver alcohol dehydrogenase (HLADH) catalyze the reduction of acycloNAD(+) by primary alcohols. With HLADH 1-butanol has the highest Vmax at 49% that of β-NAD(+). The primary deuterium kinetic isotope effect is greater than 3 indicating a significant contribution to the rate limiting step from cleavage of the carbon-hydrogen bond. The stereochemistry of the hydride transfer in the oxidation of stereospecifically deuterium labeled n-butanol is identical to that for the reaction with β-NAD(+). In contrast to the activity toward primary alcohols there is no detectable reduction of acycloNAD(+) by secondary alcohols with HLADH although these alcohols serve as competitive inhibitors. The net effect is that acycloNAD(+) has converted horse liver ADH from a broad spectrum alcohol dehydrogenase, capable of utilizing either primary or secondary alcohols, into an exclusively primary alcohol dehydrogenase. This is the first example of an NAD analog that alters the substrate specificity of a dehydrogenase and, like site-directed mutagenesis of proteins, establishes that modifications of the coenzyme distance from the active site can be used to alter enzyme function and substrate specificity. These and other results, including the activity with α-NADH, clearly demonstrate the promiscuity of the binding interactions between dehydrogenases and the riboside phosphate of the nicotinamide moiety, thus greatly expanding the possibilities for the design of analogs and inhibitors of specific dehydrogenases.

Beneficial response of cervical dystonia spasmodic torticollis to cidofovir, an acyclic phosphonate analog (s-1-3-hydroxy-2- phosphonylmethoxypropyl) of cytosine

Beneficial response of cervical dystonia spasmodic torticollis to cidofovir, an acyclic phosphonate analog (s-1-3-hydroxy-2- phosphonylmethoxypropyl) of cytosine

Simple molecular engineering of glycol nucleic acid: Progression from self-pairing to cross-pairing with cDNA and RNA

The acyclic chiral nucleic acid analogue, Glycol Nucleic Acid (GNA), displayed exceptional structural simplicity and atom economy while forming self-paired duplexes, using canonical Watson–Crick base pairing. We disclose here that the replacement of phosphodiester linker in GNA with somewhat rigid and shorter carbamate linker in Glycol Carbamate Nucleic Acid (GCNA) backbone allows unprecedented stability to the antiparallel self-paired duplexes. The R-GCNA oligomers were further found to form cross-paired antiparallel duplexes with cDNA and RNA following Watson–Crick base pairing. The stability of cross-paired GCNA:DNA and GCNA:RNA duplexes was higher than the corresponding DNA:DNA and DNA:RNA duplexes. The chiral (R) and (S) precursors were easily accessible from naturally occurring l-serine.

Activity of antifungal organobismuth(III) compounds derived from alkyl aryl ketones against S. cerevisiae: comparison with a heterocyclic bismuth scaffold consisting of a diphenyl sulfone.

A series of hypervalent organobismuth(III) compounds derived from alkyl aryl ketones [XBi(5-R'C6H3-2-COR)(Ar)] was synthesized to investigate the effect of the compounds’ structural features on their antifungal activity against the yeast Saccharomyces cerevisiae. In contrast to bismuth heterocycles [XBi(5-RC6H3-2-SO2C6H4-1'-)] derived from diphenyl sulfones, a systematic quantitative structure-activity relationship study was possible. The activity depended on the Ar group and increased for heavier X atoms, whereas lengthening the alkyl chain (R) or introducing a substituent (R') reduced the activity. IBi(C6H4-2-COCH3)(4-FC6H4) was the most active. Its activity was superior to that of the related acyclic analogues ClBi[C6H4-2-CH2N(CH3)2](Ar) and ClBi(C6H4-2-SO2 tert-Bu)(Ar) and also comparable to that of heterocyclic ClBi(C6H4-2-SO2C6H4-1'-), which was the most active compound in our previous studies. Density function theory calculations suggested that hypervalent bismuthanes undergo nucleophilic addition with a biomolecule at the bismuth atom to give an intermediate ate complex. For higher antifungal activity, adjusting the lipophilicity-hydrophilicity balance, modeling the three-dimensional molecular structure around the bismuth atom, and stabilizing the ate complex appear to be more important than tuning the Lewis acidity at the bismuth atom.

Acyclic tethers mimicking subunits of polysaccharide ligands: selectin antagonists.

We report on the design and synthesis of molecules having E- and P-selectins blocking activity both in vitro and in vivo. The GlcNAc component of the selectin ligand sialyl Lewis(X) was replaced by an acyclic tether that links two saccharide units. The minimization of intramolecular dipole-dipole interactions and the gauche effect would be at the origin of the conformational bias imposed by this acyclic tether. The stereoselective synthesis of these molecules, their biochemical and biological evaluations using surface plasmon resonance spectroscopy (SPR), and in vivo assays are described. Because the structure of our analogues differs from the most potent E-selectin antagonists reported, our acyclic analogues offer new opportunities for chemical diversity.

First enzymatic galactosylation of acyclic nucleoside drugs by β-galactosidase: Synthesis of water-soluble β-D-galactosidic prodrugs

Acyclic nucleoside analogs constitute an important group of antiviral agents. However, these nucleoside drugs suffer from poor water solubility and low oral bioavailability in the clinic use. In the present work, the enzymatic synthesis of the water-soluble galactosidic prodrugs of acyclic nucleosides by using bovine liver β-galactosidase was described. In the enzymatic transgalactosylation between acyclovir (ACV) and o-nitrophenyl β-galactopyranoside (oNPGal), the optimum enzyme dosage, buffer pH, temperature and molar ratio of ACV to oNPGal were 0.225 U/mL, 7.0, 40°C and 2.5, respectively, under which the initial reaction rate and the yield reached 0.40 mM/h and 29%, respectively. In addition, this enzyme could accept ganciclovir (GCV) and penciclovir (PCV) as substrates, affording the corresponding 4’-β-galactosylated derivatives with the yields of 26% and 71%, respectively.

Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides.

Molecular diversity plays a pivotal role in modern drug discovery against phenotypic or enzyme-based targets using high throughput screening technology. Under the auspices of the Pilot Scale Library Program of the NIH Roadmap Initiative, we produced and report herein a diverse library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues which were prepared in a parallel high throughput solution-phase reaction format. A set of assorted amines were reacted with several nucleic acid N-acetic acids utilizing HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide analogues. These reactions were performed using 24 well reaction blocks and an automatic reagent-dispensing platform under inert atmosphere. The targeted compounds were purified on an automated purification system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS, and were analyzed for purity by HPLC before submission to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH. Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) program, indicates that several analogues showed diverse and interesting biological activities.

Synthesis, Antioxidant, Anticancer and Antiviral Activities of Novel Quinoxaline Hydrazone Derivatives and their Acyclic C-Nucleosides

The present investigation describes the synthesis of a new series of aldehydo-sugar-N-(3-phenylquinoxalin-2- yl)hydrazones 3a-d and their acyclic C-nucleoside analogs, 1-(4-phenyl-[1,2,4]triazolo[4,3-a]quinoxalin-1-yl)alditols 7ad by using 2-hydrazino-3-phenylquinoxaline 1 as key intermediate. The synthesized compounds were screened for their antioxidant activities by 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical cation scavenging method. Compounds 3d and 7a, showed potent scavenging activities against ABTS(+) radicals and were found to be the most potent antioxidants described in this study. Out of the synthesized compounds, compounds 3d and 7a were selected by the National Cancer Institute for evaluation of their in vitro anticancer activity. Results revealed that compounds 3d and 7a exhibited non-selective broad spectrum activity against all cancer cell lines between 10(-6) to 10(-5) molar concentrations. Compound 3d showed the highest sensitivity against leukemia cell line HL-60 (TB) with GI50 of 5.15 µM, while compound 7a showed the highest sensitivity against ovarian cancer cell lines IGROV1 and OVCAR-4 with GI50 of 14.5 and 16.0 μM, respectively. In addition, compounds 3d and 7a showed TGI values of 72.2 and 96.3 µM, respectively against ovarian cancer cell line OVCAR-4. Furthermore, the target compounds were tested for antiviral activity against Herpes Simplex virus type-1 (HSV-1) using plaque reduction infectivity assay. The results indicated that compounds 3a-d and 7a exhibited very weak antiviral activity in comparison to Aphidicolin as a positive control.

Design, synthesis, antiviral and cytostatic activity of ω-(1H-1,2,3-triazol-1-yl)(polyhydroxy)alkylphosphonates as acyclic nucleotide analogues

The efficient synthesis of a new series of polyhydroxylated dibenzyl ω-(1H-1,2,3-triazol-1-yl)alkylphosphonates as acyclic nucleotide analogues is described starting from dibenzyl ω-azido(polyhydroxy)alkylphosphonates and selected alkynes under microwave irradiation. Selected O,O-dibenzylphosphonate acyclonucleotides were transformed into the respective phosphonic acids. All compounds were evaluated in vitro for activity against a broad variety of DNA and RNA viruses and for cytostatic activity against murine leukemia L1210, human T-lymphocyte CEM and human cervix carcinoma HeLa cells. Compound (1S,2S)-16b exhibited antiviral activity against Influenza A H3N2 subtype (EC50=20μM—visual CPE score; EC50=18μM—MTS method; MCC >100μM, CC50 >100μM) in Madin Darby canine kidney cell cultures (MDCK), and (1S,2S)-16k was active against vesicular stomatitis virus and respiratory syncytial virus in HeLa cells (EC50=9 and 12μM, respectively). Moreover, compound (1R,2S)-16l showed activity against both herpes simplex viruses (HSV-1, HSV-2) in HEL cell cultures (EC50=2.9 and 4μM, respectively) and feline herpes virus in CRFK cells (EC50=4μM) but at the same time it exhibited cytotoxicity toward uninfected cell (MCC⩾4μM). Several other compounds have been found to inhibit proliferation of L1210, CEM as well as HeLa cells with IC50 in the 4–50μM range. Among them compounds (1S,2S)- and (1R,2S)-16l were the most active (IC50 in the 4–7μM range).

A Theoretical Investigation of the Relative Stability of Isomeric Dihydropyridines

The molecular structure and relative stability of isomeric dihydropyridines have been calculated using the density functional theory and the Moller–Plesset second order perturbation theory. The results of the calculations demonstrate that 3,4- and 2,3-dihydropyridines are the most stable species despite the presence of a 4π-electron conjugated system within the ring. A comparison of the relative energy of acyclic analogs of dihydropyridines indicates that this is caused by the internal properties of the conjugated system. The remaining dihydropyridines are strongly destabilized by the formation of antiaromatic conjugated (or quasi-conjugated) systems due to the interaction of pz atomic orbitals of the carbon and nitrogen atoms with the pseudo-π fragment orbital of the methylene group. Application of the more accurate CCSD(T)/CBS method results in considerable stabilization of 1,4-dihydropyridine. However, the order of stability of other isomers remains the same as it was found at the MP2 level of theory. How to Cite Shishkin, O. V.; Zubatyuk, R. I.; Desenko, S. M.; Leszczynski, J. Chem. Heterocycl. Compd. 2014 , 50 , 327. [ Khim. Geterotsikl. Soedin. 2014 , 357.] For this article in the English edition see DOI 10.1007/s10593-014-1480-9

Selective coordination of multidentate ligands in manganese(II) complexes: Syntheses, structures and phenoxazinone synthase mimicking activity

The present report describes the syntheses, structures and catalytic activity mimicking the function of phenoxazinone synthase of four new mononuclear manganese(II) complexes, [Mn(L1)Cl2] (1), [Mn(L2)Cl2] (2), [Mn(L3)Cl2] (3) and [Mn(L4)Cl2]·H2O (4), derived from the multidentate ligands L1–L4, which are the 1:2 condensation products of triamines (or tetraamine) and 2-pyridinecarboxaldehyde (or 6-methyl-2-pyridinecarboxaldehyde). X-ray crystallography reveals the preferential coordination ability of all the ligands (cyclic isomers over the acyclic analogues) to a common metal center (Mn2+) and in one case (2) methanol addition across the –CN– bond. All the complexes show moderate phenoxazinone synthase activity and the experimental data suggest that a correlation can be drawn between E1/2 and Vmax of the complexes, namely the lower the E1/2 value the higher the catalytic activity. The effect of methyl substitution on the pyridine ring (in 3) on the matrix parameters and on the phenoxazinone synthase activity is also noticeable. The ESI-MS positive spectrum of a mixture of a representative complex (1 or 4) and o-aminophenol shows a peak corresponding to [Mn(L)(OAP)]+ (OAPH=o-aminophenol), suggesting that the catalytic activity proceeds through the formation of a stable complex–substrate intermediate.

Rational design, synthesis, and evaluation of tetrahydroxamic acid chelators for stable complexation of zirconium(IV).

Metals of interest for biomedical applications often need to be complexed and associated in a stable manner with a targeting agent before use. Whereas the fundamentals of most transition-metal complexation processes have been thoroughly studied, the complexation of Zr(IV) has been somewhat neglected. This metal has received growing attention in recent years, especially in nuclear medicine, with the use of (89) Zr, which a β(+) -emitter with near ideal characteristics for cancer imaging. However, the best chelating agent known for this radionuclide is the trishydroxamate desferrioxamine B (DFB), the Zr(IV) complex of which exhibits suboptimal stability, resulting in the progressive release of (89) Zr in vivo. Based on a recent report demonstrating the higher thermodynamic stability of the tetrahydroxamate complexes of Zr(IV) compared with the trishydroxamate complexes analogues to DFB, we designed a series of tetrahydroxamic acids of varying geometries for improved complexation of this metal. Three macrocycles differing in their cavity size (28 to 36-membered rings) were synthesized by using a ring-closing metathesis strategy, as well as their acyclic analogues. A solution study with (89) Zr showed the complexation to be more effective with increasing cavity size. Evaluation of the kinetic inertness of these new complexes in ethylenediaminetetraacetic acid (EDTA) solution showed significantly improved stabilities of the larger chelates compared with (89) Zr-DFB, whereas the smaller complexes suffered from insufficient stabilities. These results were rationalized by a quantum chemical study. The lower stability of the smaller chelates was attributed to ring strain, whereas the better stability of the larger cyclic complexes was explained by the macrocyclic effect and by the structural rigidity. Overall, these new chelating agents open new perspectives for the safe and efficient use of (89) Zr in nuclear imaging, with the best chelators providing dramatically improved stabilities compared with the reference DFB.

1‐Amino‐3‐(1H‐1,2,3‐triazol‐1‐yl)propylphosphonates as Acyclic Analogs of Nucleotides

A new series of 1-amino-3-(1H-1,2,3-triazol-1-yl)propylphosphonates (R)- and (S)-16 were obtained from enantiomerically pure (R)- and (S)-1-tert-butoxycarbonyl (Boc)-amino-3-azidopropylphosphonates and N-propargylated nucleobases in good yields. All 1,2,3-triazolylphosphonates (R)- and (S)-16 were evaluated for their activities against a broad range of DNA and RNA viruses. Compound (R)-16g (B = 3-acetylindole) was moderately active against vesicular stomatitis virus in HeLa cell cultures (EC50 = 45 µM). In addition, (S)-16c (B = adenine), (R)-16f (B = N(3)-Bz-benzuracil), (R)-16g (B = 3-acetylindole), and (R)-16h (B = 5,6-dimethylbenzimidazole) were cytotoxic toward Crandell-Rees feline kidney (CRFK) cells (CC50 = 2.9, 45, 72, and 96 µM, respectively). Compounds (R)-16g, (S)-16g, and (S)-16h were slightly cytostatic to different tumor cell lines.

Novel Acyclic Phosphonylated 1,2,3‐Triazolonucleosides with an Acetamidomethyl Linker: Synthesis and Biological Activity

A new series of 4-substituted [(1,2,3-triazol-1-yl)acetamido]methylphosphonates as acyclic nucleotide analogs were synthesized from diethyl (2-chloroacetamido)methylphosphonate via azidation followed by 1,3-dipolar cycloaddition with selected alkynes derived from natural nucleobases or their mimetics. All compounds were tested for their antiviral activities against DNA and RNA viruses as well as for cytostatic activity or cytotoxicity. Among all tested compounds, [(1,2,3-triazol-1-yl)acetamido]methylphosphonate 6e substituted with the N(3)-Bz-benzuracil moiety showed activity against the vesicular stomatitis virus (EC50 = 45 µM) in HeLa cell cultures.

Comparative Studies of Thermally Induced Homolytic CarbonCarbon Bond Cleavage Reactions of Strained Dicarba[2]ferrocenophanes and Their Ring-Opened Oligomers and Polymers

Reactivity studies of dicarba[2]ferrocenophanes and also their corresponding ring-opened oligomers and polymers have been conducted in order to provide mechanistic insight into the processes that occur under the conditions of their thermal ring-opening polymerisation (ROP) (300 °C). Thermolysis of dicarba[2]ferrocenophane rac-[Fe(η(5)-C5H4)2(CHPh)2] (rac-14; 300 °C, 1 h) does not lead to thermal ROP. To investigate this system further, rac-14 was heated in the presence of an excess of cyclopentadienyl anion, to mimic the postulated propagating sites for thermally polymerisable analogues. This afforded acyclic [(η(5)-C5H5)Fe(η(5)-C5H4)-CH2Ph] (17) through cleavage of both a Fe-Cp bond and also the C-C bond derived from the dicarba bridge. Evidence supporting a potential homolytic C-C bond cleavage pathway that occurs in the absence of ring-strain was provided through thermolysis of an acyclic analogue of rac-14, namely [(η(5)-C5H5)Fe(η(5)-C5H4)(CHPh)2-C5H5] (15; 300 °C, 1 h), which also afforded ferrocene derivative 17. This reactivity pathway appears general for post-ROP species bearing phenyl substituents on adjacent carbons, and consequently was also observed during the thermolysis of linear polyferrocenylethylene [Fe(η(5)-C5H4)2(CHPh)2]n (16; 300 °C, 1 h), which was prepared by photocontrolled ROP of rac-14 at 5 °C. This afforded ferrocene derivative [Fe(η(5)-C5H4CH2Ph)2] (23) through selective cleavage of the -H(Ph)C-C(Ph)H- bonds in the dicarba linkers. These processes appear to be facilitated by the presence of bulky, radical-stabilising phenyl substituents on each carbon of the linker, as demonstrated through the contrasting thermal properties of unsubstituted linear trimer [(η(5)-C5H5)Fe(η(5)-C5H4)(CH2)2(η(5)-C5H4)Fe(η(5)-C5H4)(CH2)2(η(5)-C5H4)Fe(η(5)-C5H5)] (29) with a -H2 C-CH2- spacer, which proved significantly more stable under analogous conditions. Evidence for the radical intermediates formed through C-C bond cleavage was detected through high-resolution mass spectrometric analysis of co-thermolysis reactions involving rac-14 and 15 (300 °C, 1 h), which indicated the presence of higher molecular weight species, postulated to be formed through cross-coupling of these intermediates.

Design, synthesis, antiviral and cytotoxic evaluation of novel acyclic phosphonate nucleotide analogues with a 5,6-dihydro-1H-[1,2,3]triazolo[4,5-d]pyridazine-4,7-dione system.

A series of diethyl 2-(4,5-dimethoxycarbonyl-1H-1,2,3-triazol-1-yl)alkylphosphonates was synthesised from ω-azidoalkylphosphonates and dimethyl acetylenedicarboxylate and was further transformed into the respective diamides, dihydrazides, and 5,6-dihydro-1H-[1,2,3]triazolo[4,5-d]pyridazine-4,7-diones as phosphonate analogues of acyclic nucleosides having nucleobases replaced with substituted 1,2,3-triazoles. All compounds containing P–C–C–triazole or P–C–C–CH2–triazole moieties exist in single conformations in which the diethoxyphosphoryl and substituted 1,2,3-triazolyl or substituted (1,2,3-triazolyl)methyl groups are oriented anti. All phosphonates were evaluated in vitro for activity against a variety of DNA and RNA viruses. None of the compounds were endowed with antiviral activity. They were not cytostatic at 100 μM.Graphical abstract Electronic supplementary materialThe online version of this article (doi:10.1007/s00706-013-1137-x) contains supplementary material, which is available to authorized users.

Probing the substrate specificity of Trypanosoma brucei GlcNAc-PI de-N-acetylase with synthetic substrate analogues.

A series of synthetic analogues of 1-D-(2-amino-2-deoxy-α-D-glucopyranosyl)-myo-inositol 1-(1,2-di-O-hexadecanoyl-sn-glycerol 3-phosphate), consisting of 7 variants of either the D-myo-inositol, D-GlcpN or the phospholipid components, were prepared and tested as substrates and inhibitors of GlcNAc-PI de-N-acetylase, a genetically validated drug target enzyme responsible for the second step in the glycosylphosphatidylinositol (GPI) biosynthetic pathway of Trypanosoma brucei. The D-myo-inositol in the physiological substrate was successfully replaced by cyclohexanediol and is still a substrate for T. brucei GlcNAc-PI de-N-acetylase. However, this compound became sensitive to the stereochemistry of the glycoside linkage (the β-anomer was neither substrate or inhibitor) and the structure of the lipid moiety (the hexadecyl derivatives were inhibitors). Chemistry was successfully developed to replace the phosphate with a sulphonamide, but the compound was neither a substrate or an inhibitor, confirming the importance of the phosphate for molecular recognition. We also replaced the glucosamine by an acyclic analogue, but this also was inactive, both as a substrate and inhibitor. These findings add significantly to our understanding of substrate and inhibitor binding to the GlcNAc-PI de-N-acetylase enzyme and will have a bearing on the design of future inhibitors.

Carbene complexes of phosphorus(v) fluorides substituted with perfluoroalkyl-groups synthesized by oxidative addition. Cleavage of the complexes reveals a new synthetic protocol for ionic liquids

The crystal structures of the previously reported 2,2-difluoro-1,3-dimethylimidazolidine and its acyclic analog were determined by in situ crystallization. Both liquid fluorinating agents have recently been introduced as potent precursors for the synthesis of p-block element carbene complexes. These fluorine compounds were compared with chloro-amidinium chlorides, which are already established carbene precursors. The chlorides were characterized as ion pairs and contrasted to the previous interpretation as charge-transfer complexes between carbene and dichlorine. Furthermore, the two precursors are used for the synthesis of a series of new carbene complexes of phosphorus(v) fluorides substituted with perfluoroalkyl-groups. These unusually stable hexacoordinate phosphorus(v) complexes were treated with anhydrous hydrogen fluoride to yield imidazolium phosphates. This procedure allows the synthesis of salts used as ionic liquids in high yield and high purity.

Outstanding effects on antithrombin activity of modified TBA diastereomers containing an optically pure acyclic nucleotide analogue.

Herein, we report optically pure modified acyclic nucleosides as ideal probes for aptamer modification. These new monomers offer unique advantages in exploring the role played in thrombin inhibition by a single residue modification at key positions of the TBA structure.