Nucleotides part LXXX: Synthesis of 3'-O fluorescence labeled thymidine derivatives and their 5'-O-triphosphates.

A new labeling technique attaching a fluorescent pteridine derivative (3, 5) via a linker onto the 3'-OH group of 5'-O-dimethoxytritylthymidine (7) was developed to lead to the conjugates 8 and 11. After detritylation to give 9 and 12, the final conversion into the corresponding 5'-triphosphates (13, 14), which were isolated as sodium salts, was performed by known methods.

Synthesis and in vitro evaluation of 2-amino-4-N-piperazinyl-6-(3,4-dimethoxyphenyl)-pteridines as dual immunosuppressive and anti-inflammatory agents.

Screening of a pteridine-based compound library led to the identification of compounds exhibiting immunosuppressive as well as anti-inflammatory activity. Optimization afforded a series of 2-amino-4-N-piperazinyl-6-(3,4-dimethoxyphenyl)pteridine analogues. The most potent congeners in this series displayed low nM IC(50) values in the Mixed Lymphocyte Reaction (MLR) assay. In addition, these compounds also have potent anti-inflammatory activity as measured in the Tumor Necrosis Factor (TNF) assay.

Nitrosation of N-methyl derivatives of uric acid and their transnitrosation ability to N-acetylcysteine.

When 1,3-dimethyluric acid was treated with a nitric oxide donor, diethylamine NONOate, in an aerobic neutral solution and the reaction was analyzed by HPLC, 1,3-dimethyluric acid was consumed to yield a nitrosated derivative, which decomposed with a half-life of 17.9 min at pH 7.4 and 37 degrees C. When 1,3,7-trimethyluric acid was treated with diethylamine NONOate, no consumption of 1,3,7-trimethyluric acid was observed. However, in the reaction of N-acetylcysteine with diethylamine NONOate, the yield of N-acetyl-S-nitrosocysteine increased by the addition of 1,3,7-trimethyluric acid as well as 1,3-dimethyluric acid. For 1,3,7,9-tetramethyluric acid, no consumption in the reaction with diethylamine NONOate and no effect on the S-nitrosation were observed. These results suggest that 1,3-dimethyluric and 1,3,7-trimethyluric acids are both nitrosated by diethylamine NONOate on the nitrogen atom of their oxoimidazole ring, although the half-life of the nitrosated 1,3,7-trimethyluric acid is too short to detect by HPLC. Consequently, these two acids can act as vehicles of nitric oxide.

Plasma cytokine concentration changes induced by the antitumor agents dipterinyl calcium pentahydrate (DCP) and related calcium pterins.

Analysis of plasma cytokine concentration changes determined that oral dosing with the antitumor agent (1:4 mol:mol) calcium pterin (CaPterin) increased plasma IL-10, decreased plasma IL-6, and decreased plasma IFN-gamma concentrations in nude mice with MDA-MB-231 xenograph tumors [Moheno, P., Pfleiderer, W., Dipasquale, A.G., Rheingold, A.L., Fuchs, D., 2008. Cytokine and IDO metabolite changes effected by calcium pterin during inhibition of MDA-MB-231 xenograph tumors in nude mice. Int. J. Pharm. 355, 238-248]. A further analysis, reported here, of plasma cytokine concentration changes in nude mice with the same tumor xenographs treated with dipterinyl calcium pentahydrate (DCP), (1:2 mol:mol) calcium pterin, and CaCl(2).2H(2)O has been carried out. The measured cytokines included: IL-1beta, IL-2, IL-4, IL-6, IL-10, IL-12, IFN-gamma, and TNF-alpha. The major preliminary findings from the analyses of these data are that (1) the overall relative tumor volumes for the treatments correlated significantly with a full study antitumor plasma cytokine pattern (fsAPCP), a composite measure consisting of decreased plasma IL-6 and increased IL-4 concentrations, and (2) DCP induces a significant threshold antitumor response strongly correlated to a derived DCP antitumor plasma cytokine pattern (DCP/APCP) consisting of plasma IL-12, IL-6, and IL-4 concentration changes. This DCP/APCP composite measure identifies plasma IL-12 concentration increases, plasma IL-6 concentration decreases, and plasma IL-4 concentration increases correlated to relative tumor volume decreases caused by DCP dosing. The finding that the novel calcium pterins and CaCl(2).2H(2)O treatments decrease plasma IL-6 concentrations corroborates the previous finding that CaPterin dosing decreases plasma IL-6 concentrations in this mouse/tumor system [Moheno, P., Pfleiderer, W., Dipasquale, A.G., Rheingold, A.L., Fuchs, D., 2008. Cytokine and IDO metabolite changes effected by calcium pterin during inhibition of MDA-MB-231 xenograph tumors in nude mice. Int. J. Pharm. 355, 238-248].

Nucleosides part LXVI I: synthesis of 4-amino-7(8H)pteridinone-N8-nucleosides-structural analogs of adenosine.

Various 4-amino-7(8H)pteridones (6, 12, 14, 15, 20, 22) have been glycosylated with 1-chloro-2'-deoxy-D-ribofuranose derivatives (25, 26) applying the new DBU-salt method to form the N(8)-2'-deoxy-D-ribofuranosides (27-36) which can be regarded as 2'-deoxyadenosine analogs. Analogously reacted the 2-N,N-dimethyl-amino-methyleneimino-7(8H)pteridones (43-48) to give preferentially the corresponding N(8)-beta-D-anomers (49-55). Ribosylation with 1-bromo-2,3,5-tri-O-benzoyl-a-D-ribofuranose (56) proceeded as well with 6, 12, 15, 45, and 46 to yield to N(8)-beta-D-ribofuranosides 57-61. Sugar deprotection led to the free N(8)-2'-deoxy-beta-D-ribofuranosides 37-42 and N(8)-beta-D-ribofurano-sides 62-65, respectively. Glycosylations via the silyl-method under Vorbruggen conditions led with 6, 12 and 15 to the same results, however, 4-amino-6-phenyl-7(8H)pteridone (14) reacted differently forming the N(1)-beta-D-ribofuranosides (71, 79) and the N(1)-2'-deoxy-alpha-and ss-D-ribofuranosides 73, 74, 77, 78. The assignments of the structures have been achieved by (1)H-NMR- and UV-spectra. C,H,N-elemental analyses account for the composition.

Intramolecular sensitization of photocleavage of the photolabile 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group: photoproducts and photokinetics of the release of nucleosides.

Novel photolabile protecting groups based on the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group with a covalently linked thioxanthone as an intramolecular triplet sensitizer exhibit significantly enhanced light sensitivity under continuous illumination. Herein we present a detailed study of the photokinetics and photoproducts of nucleosides caged with these new protecting groups. Relative to the parent NPPOC group, the light sensitivity of the new photolabile protecting groups is enhanced by up to a factor of 21 at 366 nm and is still quite high at 405 nm, the wavelength at which the sensitivity of the parent compound is practically zero. A new pathway for deprotection of the NPPOC group proceeding through a nitroso benzylalcohol intermediate has been discovered to complement the main mechanism, which involves beta elimination. Under standard conditions of lithographic DNA-chip synthesis, some of the new compounds, while maintaining the same chip quality, react ten times faster than the unmodified NPPOC-protected nucleosides.

Cytokine and IDO metabolite changes effected by calcium pterin during inhibition of MDA-MB-231 xenograph tumors in nude mice.

UNLABELLED: In vivo studies of the effectiveness of various forms of calcium pterin reveal significant antitumor activity associated with (1:4, mol/mol) calcium pterin (CaPterin), (1:2, mol/mol) calcium pterin, dipterinyl calcium pentahydrate (DCP), as well as unexpectedly for a calcium chloride dihydrate solution in nude mice with MDA-MB-231 xenographs. Stepwise regression analysis of nine plasma cytokine and indoleamine 2,3-dioxygenase (IDO) metabolite levels identified four effects correlated to (1:4, mol/mol) calcium pterin administration: (1) decreased IL-6, (2) increased IL-10, (3) decreased IFN-gamma, and (4) increased kynurenine. CONCLUSION: (1:4, mol/mol) CaPterin exerts significant (by Spearman rank order correlation) dose-response antitumor activity in nude mice with MDA-MB-231 xenographs, and sustains both inflammatory and anti-inflammatory changes in the levels of certain plasma factors.

On the mechanism of intramolecular sensitization of photocleavage of the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group.

A spectroscopic study of a variety of covalently linked thioxanthone(TX)-linker-2-(2-nitrophenyl)propoxycarbonyl(NPPOC)-substrate conjugates is presented. Herein, the TX chromophore functions as an intramolecular sensitizer to the NPPOC moiety, a photolabile protecting group used in photolithographic DNA chip synthesis. The rate of electronic energy transfer between TX and NPPOC was quantified by means of stationary fluorescence as well as nanosecond and femtosecond time-resolved laser spectroscopy. A dual mechanism of triplet-triplet energy transfer has been observed comprising a slower mechanism involving the T1(pipi*) state of TX with linker-length-dependent time constants longer than 20 ns and a fast mechanism with linker-length-dependent time constants shorter than 3 ns. Evidence is provided that the latter mechanism is due to energy transfer from the T2(npi*) state which is in fast equilibrium with the fluorescent S1(pipi*) state. In the case of direct linkage between the aromatic rings of TX and NPPOC, the spectroscopic properties are indicative of one united chromophore which, however, still shows the typical NPPOC cleavage reaction triggered by intramolecular hydrogen atom transfer to the nitro group.

Inhibition of HIV type 1 replication in CD4+ and CD14+ cells purified from HIV type 1-infected individuals by the 2-5A agonist immunomodulator, 2-5A(N6B).

Two major interferon (IFN)-mediated antiviral defense enzymes are double-stranded (ds)RNA-dependent 2',5'-oligoadenylate (2-5A) synthetase (2-5OAS) and p68 kinase (PKR). When activated by dsRNA, 2-5OAS synthesizes 2-5A, which binds to and activates RNase L. Activated RNase L hydrolyzes single-stranded viral RNA, thereby inhibiting viral protein synthesis. HIV-1 inhibits the IFN-mediated intracellular antiviral pathways. We have reported the synthesis and characterization of a nuclease-resistant 2-5A agonist (2-5A(N6B)) that overcomes the HIV-1 induced blockades by restoring the 2-5OAS/RNase L antiviral pathway (Homan JW, et al., J Acquir Immune Defic Syndr 2002;30:9-20). The objective of this study was to test the effect of 2-5A(N6B) on chronically infected CD4(+) T lymphocytes and CD14(+) monocytes derived from HIV-1-seropositive individuals. Wild-type HIV-1 replication was effectively inhibited by 2-5A(N6B) in CD4(+) T lymphocytes and CD14(+) monocytes purified from HIV-1 seropositive individuals (n = 18) compared to untreated cells. We also assessed the cytotoxicity of 2-5A(N6B) and report that 2-5A(N6B) exerts its anti-HIV-1 activity with no evidence of cytotoxicity (IC(90) > 100,000 nM). Furthermore, 2-5A(N6B) did not alter the cellular RNA profile, affect CCR5 or CXCR4 coreceptor expression, or activate caspase-dependent apoptosis. Evidence is also provided to show that 2-5A(N6B), and naturally occurring 2-5A(4), act as ligands to activate human Toll-like receptor 4. These results indicate that the 2-5A agonist 2-5A(N6B) has the potential to enhance host cell innate and acquired immune defense mechanisms against HIV-1 infection.

Universal 2-(4-nitrophenyl)ethyl and 2-(4-nitrophenyl)ethoxycarbonyl protecting groups for nucleosides and nucleotides.

A universal blocking group strategy for nucleobases is described, using the 2-(4-nitrophenyl)ethyl (NPE) group for O4-T-, O4-U-, O6-dG-, and O6-G-protection as well as the 2-(4-nitrophenyl)ethoxycarbonyl (NPEOC) group for amino protection in dC, C, dA, A, dG, and G. Conversion into the corresponding 5'-O-dimethoxytrityl derivatives and subsequent phosphitylation to form the fully protected 3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidites) and 3'-O-(2-(4-nitrophenyl)ethyl-N,N-diisopropylphosphoramidites) produces a new class of interesting building blocks for oligonucleotide synthesis.

Specific interaction of the diastereomers 7(R)- and 7(S)-tetrahydrobiopterin with phenylalanine hydroxylase: implications for understanding primapterinuria and vitiligo.

Pterin-4a-carbinolamine dehydratase (PCD) is an essential component of the phenylalanine hydroxylase (PAH) system, catalyzing the regeneration of the essential cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin [6(R)BH4]. Mutations in PCD or its deactivation by hydrogen peroxide result in the generation of 7(R,S)BH4, which is a potent inhibitor of PAH that has been implicated in primapterinuria, a variant form of phenylketonuria, and in the skin depigmentation disorder vitiligo. We have synthesized and separated the 7(R) and 7(S) diastereomers confirming their structure by NMR. Both 7(R)- and 7(S)BH4 function as poor cofactors for PAH, whereas only 7(S)BH4 acts as a potent competitive inhibitor vs. 6(R)BH4 (Ki=2.3-4.9 microM). Kinetic and binding studies, as well as characterization of the pterin-enzyme complexes by fluorescence spectroscopy, revealed that the inhibitory effects of 7(R,S)BH4 on PAH are in fact specifically based on 7(S)BH4 binding. The molecular dynamics simulated structures of the pterin-PAH complexes indicate that 7(S)BH4 inhibition is due to its interaction with the polar region at the pterin binding site close to Ser-251, whereas its low efficiency as cofactor is related to a suboptimal positioning toward the catalytic iron. 7(S)BH4 is not an inhibitor for tyrosine hydroxylase (TH) in the physiological range, presumably due to the replacement of Ser-251 by the corresponding Ala297. Taken together, our results identified structural determinants for the specific regulation of PAH and TH by 7(S)BH4, which in turn aid in the understanding of primapterinuria and acute vitiligo.

Recent highlights on photolithic oligonucleotide array in situ synthesis.

Light directed synthesis of high-density oligonucleotide microarrays is currently performed using either ortho-nitro-benzyl-type [MeNPOC] (Pease, A.C.; Solas, D.; Sullivan, E.J.; Cronin, T.M.; Holmes, C.P.; Fodor, S.P.A. Proc. Natl. Acad Sci U.SA. 1994, 91, 6333.) or ortho-nitrophenylethyl-type [NPPOC] (Hasan, A.; Stengele, K.P.; Giegrich, H.; Cornwell, P.; Isham, K.R.; Sachleben, R.A.; Pfleiderer, W.; Foote, R.S. Tetrahedron 1997, 53, 424Z) protecting groups as the 5'-O-carbonate ester of the phosphoramidite building block. The synthesis cycle uses a combinatorial approach attaching one specific base per cycle, thus as many as 100 cycles need to be run to make an array of 25-mers. Time needed for deprotection/activation of the growing oligo chain determines overall manufacturing time and consequently also cost. In this report we demonstrate the development of photoprotected posphoramidite monomers for light directed array synthesis with increasing sensitivity to the UV light used. If combined with maskless array synthesis, this technology allows for synthesis of arrays with >780,000 different 25-mer oligonucleotides in about one hour and allows for high flexibility in array design and reiterative redesign. The arrays synthesized show high quality and reproducibility in our standard hybridization based assay.

Structural analysis of isoform-specific inhibitors targeting the tetrahydrobiopterin binding site of human nitric oxide synthases.

Nitric oxide synthesized from l-arginine by nitric oxide synthase isoforms (NOS-I-III) is physiologically important but also can be deleterious when overproduced. Selective NOS inhibitors are of clinical interest, given their differing pathophysiological roles. Here we describe our approach to target the unique NOS (6R,1'R,2'S)-5,6,7,8-tetrahydrobiopterin (H(4)Bip) binding site. By a combination of ligand- and structure-based design, the structure-activity relationship (SAR) for a focused set of 41 pteridine analogues on four scaffolds was developed, revealing selective NOS-I inhibitors. The X-ray crystal structure of rat NOS-I dimeric-oxygenase domain with H(4)Bip and l-arginine was determined and used for human isoform homology modeling. All available NOS structural information was subjected to comparative analysis of favorable protein-ligand interactions using the GRID/concensus principal component analysis (CPCA) approach to identify the isoform-specific interaction site. Our interpretation, based on protein structures, is in good agreement with the ligand SAR and thus permits the rational design of next-generation inhibitors targeting the H(4)Bip binding site with enhanced isoform selectivity for therapeutics in pathology with NO overproduction.

1,3-Dimethyllumazine derivatives from Limnatis nilotica.

Two previously unknown lumazine derivatives, 1 and 2, have been isolated from the parasitic freshwater leech Limnatis nilotica. The structures of the compounds have been elucidated by NMR and unambiguously corroborated by chemical synthesis.

Nucleotides. LXXIV synthesis of alpha-D-arabino-oligonucleotides.

The 5 alpha-D-arabinofuranosylnucleosides alpha-araU (15), alpha-araT (18), alpha-araC (22), alpha-araA (25), and alpha-araG (28) have been synthesized by the modified silyl-method. The amino groups at the nucleobases and the 2'-hydroxy group at the sugar moiety were protected by the 2-(4-nitro-phenyl)ethoxycarbonyl (npeoc) group (37-40) and the amide function in alpha-araG was additionally blocked by the 2-(4-nitrophenyl)ethyl group (63) to improve solubility in organic solvents. Mono-and dimethoxytritylation of the 5'-OH group was performed in the usual manner to give 41-48, 64, and 65 in high yields and further substitution of the 3'-OH group led to the monomeric building blocks 66-75 as well as the 3'-O-succinoyl derivatives 76-85 functioning as starting units in solid-support oligonucleotide synthesis. A large number of oligo-alpha-arabinonucleotides have been prepared on modified CPG-material applying the npeoc/npe strategy as a very efficient synthetic tool for highly purified, homogenous oligomers. Hybridizations between alpha-arabinonucleotide strands revealed in analogy to earlier findings an antiparallel orientation whereas the combination of an oligo-alpha-D-arabinonucleotide with a complementary oligo-2'-deoxy-beta-D-ribofuranosylnucleotide showed base-pairing only if a parallel polarity was present. The advantages in oligo-alpha-arabinonucleotide synthesis were furthermore demonstrated by the synthesis of the talpha-ANA(his) structural analog of the natural tRNA(his) of the phage T5.

Nucleosides. LXV. Synthesis of new pteridine-N8-nucleosides.

A general synthetic approach to various isoxanthopterin-nucleosides starting from 6-methyl-2-methylthio-4(3H),7(8H)-pterdinedione (1) has been developed. Ribosylation with 1-O-acetyl-2,3,5-tri-O-benzoyl-beta-D-ribofuranose via the silyl-method led to 2 and reaction with 1-chloro-2-deoxy-3,5-di-O-p-toluoyl-alpha-D-ribofuranose using the DBU-method afforded 28. Protection of the amide function at O4 by benzylation to 5 and by a Mitsunobu reaction with 2-(4-nitrophenyl)ethanol to 29 gave soluble intermediates which can be oxidized to the corresponding 2-methylsulfonyl derivatives 8 and 30, respectively. Nucleophilic displacement reactions of the highly reactive 2-methylsulfonyl functions by various amines proceeded under mild conditions to isoxanthopterin-N8-ribo- (11-17) and 2'-deoxyribomucleosides (31-33). Debenzylation can be achieve by Pd-catalyzed hydrogenation (9 to 19) and cleavage of the npe-protecting group (31, 32 to 34, 35) works well with DBU by beta-elimination.

Synthesis and some reactions of 3-chloro-2-(cyanomethylene)-1,2-dihydroquinoxalines.

2,3-Dichloroquinoxaline and some of its derivatives have been reacted with malononitrile and ethyl cyanoacetate to yield a variety of 3-chloro-2-(cyanomethylene)- 1,2-dihydroquinoxaline derivatives. The reaction of 3-chloro-2-(dicyanomethylene)-1,2- dihydroquinoxaline (2e) with pyridine and its methyl derivatives led to the zwitterionic structures 6a-6c. The structures of the newly synthesized compounds were assigned by spectroscopic data and elemental analyses.

Phytoene desaturase inhibition by O-(2-phenoxy)ethyl-N-aralkylcarbamates.

O-[1-Ethyl-2-(3-trifluoromethylphenoxy)]ethyl-N-benzylcarbamate exhibits a marked inhibition of carotenoid biosynthesis. Forty-one analogues were synthesized and assayed for plant-type phytoene desaturase (PDS) and zeta-carotene desaturase (ZDS) inhibition in a cell-free system using recombinant enzymes obtained from Escherichia coli transformants. The target enzyme of all carbamates synthesized in this study is PDS and not ZDS; no inhibition of ZDS was observed using a 10(-4) M inhibitor concentration. Four compounds, O-[1-ethyl-2-(3-trifluoromethylphenoxy)]ethyl-N-(2-phenylethyl)carbamate (23), O-[1-ethyl-2-(3-trifluoromethylphenoxy)]ethyl-N-(2-chlorobenzyl)carbamate (25), O-[1-ethyl-2-(3-trifluoromethylphenoxy)]ethyl-N-(2-chlorobenzyl)carbamate (26), and O-[1-methyl-2-(3-trifluoromethylphenoxy)]ethyl-N-benzylcarbamate (30), were the most potent PDS inhibitors. Their pI(50) values, the negative logarithms of the molar concentration that produces a 50% inhibition, were 7.5, representing the same inhibitory activity as norflurazon. With respect to a structure-activity relationship the oxygen atom of the phenoxy group and a carbamate structure in O-(1-ethyl-2-phenoxy)ethyl-N-aralkylcarbamates studied were found to be essential for strong PDS inhibitors. Also, introduction of an ethyl group at the alpha-position of the ethylene bridge between the phenoxy group and the carbamate was important for a strong PDS inhibitor. Substituents at the 2- and/or 3-position of the phenoxybenzene ring were found to be favorable to a strong PDS inhibition of the analogues.

Inhibition of morphine-potentiated HIV-1 replication in peripheral blood mononuclear cells with the nuclease-resistant 2-5A agonist analog, 2-5A(N6B).

Opioids potentiate HIV-1 infection in vitro at least partly by suppressing immunoresponsive processes in human lymphocytes and monocytes. For example, it appears that morphine inhibits the interferon (IFN)-alpha, -beta, and -gamma-mediated natural antiviral defense pathways in human peripheral blood mononuclear cells (PBMC). In this study, we show that restoration of a key component of the antiviral pathway reverses morphine-potentiated HIV-1 infection of human PBMC. The data show that HIV-1 replication is potentiated and RNase L activity is inhibited after morphine administration. Because HIV-1 inhibits the antiviral pathway at the level of 2',5'-oligoadenylate (2-5A) synthetase and p68 kinase, antiviral enzymes that require double-stranded RNA, we overcame this blockade by the addition of the nuclease-resistant, nontoxic 2-5A agonist, 2-5A(N6B), to PBMC in culture. Addition of 2-5A(N6B), but not zidovudine or saquinavir, to morphine-treated PBMC completely reversed the morphine-induced potentiation of HIV-1 infection. Further, 2-5A(N6B) significantly enhanced expression of both IFN-alpha and IFN-gamma. Also, increased expression of IFN-gamma was associated with a significant increase in expression of RANTES and monocyte chemotactic protein (MCP)-1, chemokines that may inhibit HIV-1 infection by blocking viral attachment to CCR2 and CCR5 co-receptors. Our results suggest that reactivation of the antiviral pathway by 2-5A agonists may be useful to inhibit opioid-potentiated HIV-1 replication.