Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2-deoxycytidine for the study of oligonucleotides

Pyrrolo-dC (1a, 6-methyl-3-(2-deoxy-β-d-ribofuranosyl)-3H-pyrrolo[2,3-d]pyrimidin-2-one) and its cyanoethyl phosphoramidite 2a were synthesized. The latter was incorporated into oligodeoxyribonucleotides by standard automated synthesis techniques, where pyrrolo-dC was found to serve as a fluorescent analog of deoxycytidine. The cyanoethylphosphoramidite (2b) of pyrrolo-C (2a, 6-methyl-3-(β-d-ribofuranosyl)-3H-pyrrolo[2,3-d]pyrimidin-2-one) was also synthesized and may find use for the site-specific incorporation of a fluorescent cytidine analog into oligoribonucleotides.     

A fluorescence-quencher pair for DNA hybridization studies based on hydrophobic base surrogates

The synthesis of the novel, fluorescent 3-aminobiphenyl-C-nucleoside M as well as the corresponding building block for oligodeoxynucleotide synthesis is described. M was incorporated into oligodeoxynucleotides via standard phosphoramidite chemistry and the thermal stabilities of duplexes with one and three consecutive M-M, M-P, and M-O pairs, where P denotes an unmodified biphenyl C-nucleoside and O a 3,5-dinitrobiphenyl-C-nucleoside, were determined. It was found that duplexes containing three consecutive M-O pairs were the most stable in the series, notably more stable than a duplex with one additional natural G-C pair instead of the modified residues. Furthermore it was found that the fluorescence of M is efficiently quenched in a duplex when placed opposite to the dinitrophenyl unit O. Thus M and O constitute a novel fluorophore/quencher pair that is orthogonal to natural base pairs in its recognition properties enabling its use as highly specific tags with reporting properties.     

Synthesis of poly-substituted pyrroles starting from the Baylis-Hillman adducts

We synthesized poly-substituted pyrrole derivatives 4a-e, 7a-c and 10a-d from the reaction of phenacyl bromide and the aza-Baylis-Hillman adducts 1a-d or their rearranged derivatives 5a-e. The pyrroles were synthesized via the successive N-alkylation, Michael addition, elimination of p-toluenesulfinic acid and oxidative aromatization processes.     

An efficient microwave assisted synthesis of novel class of Rhodanine derivatives as potential HIV-1 and JSP-1 inhibitors

(Z)-5-(2-(1H-Indol-3-yl)-2-oxoethylidene)-3-phenyl-2-thioxothiazolidin-4-one (7a-q) derivatives have been synthesized by the condensation reaction of 3-phenyl-2-thioxothiazolidin-4-ones (3a-h) with suitably substituted 2-(1H-indol-3-yl)-2-oxoacetaldehyde (6a-d) under microwave condition. The thioxothiazolidine-4-ones were prepared from the corresponding aromatic amines (1a-e) and di-(carboxymethyl)-trithiocarbonyl (2). The aldehydes (6a-h) were synthesized from the corresponding acid chlorides (5a-d) using HSnBu₃.     

Synthesis of ‘thianthrene dimer’ by the coupling reaction of stannylthianthrenes in the presence of copper catalysts

The coupling reaction of 1-tributylstannylthianthrene (5) and 2-tributylstannylthianthrene (7) in the presence of copper catalysts at rt afforded the thianthrene dimer 1,1′-bithianthrene (3), 2,2′-bithianthrene (8), and 1,2′-dithianthrene (9) in high yields. Also we obtained thianthrene oxide dimer (R,R) (S,S)-1-(10-S-monoxythianthrene-1-yl)thianthrene-10-S-monoxide (12) and (R,S) (S,R)-1-(10-S-monoxythianthrene-1-yl)thianthrene-10-S-monoxide (13) from 1-tributylstannyl-10-S-monoxythianthrene (10) under the same reaction condition. The final structural conformation of 3, 8, 9, and 12 was performed by X-ray crystallographic analysis. Further, the solvent effects in the coupling reactions were also examined.     

Highly fluorinated C18 fatty acids: synthesis and interfacial properties

A fluorinated oleic acid 1-Z containing a perfluorooctyl group and its analogues (E-isomer 1-E, alkyne type 2 and saturated type 3) were synthesized in good yields. In these syntheses, it was found that a key compound 5 could be converted to each of 1-Z, 1-E and 2. Furthermore, equilibrium spreading pressures of their monolayers at the air-water interface were measured in order to demonstrate how the degree of unsaturation in the hydrophobic chain, the geometric isomerization, and the presence of F-atoms influence the monolayer stability. Irrespective of the structural alteration in the hydrophobic chains, the fluorinated fatty acids formed more stable monolayers with high spreading pressures as compared to their hydrocarbon counterparts.     

Highly enantioselective copper-catalyzed conjugate addition of diethylzinc to cyclic enones with spirocyclic phosphoramidite ligands

A series of spirocyclic phosphoramidite ligands 6-9 with different substituents on the amine moiety were synthesized from the chiral spirocyclic diol (R)-5. These monodentate ligands have been applied in copper-catalyzed conjugate addition of diethylzinc to cyclic enones. Excellent enantioselectivities (up to 99% ee) can be achieved by the use of ligand (R,S,S)-9 bearing stereochemically matched structure derived from the C₂-symmetric (S,S)-bis(α-methylbenzyl)amine.     

Syntheses, optical and electrochemical properties of 4,4′-bis-[2-(3,4-dibutyl-2-thienylethynyl)]biphenyl and its oligomers

New π-conjugated oligomers (1-3) combined of thiophene rings, CC units, and phenylene rings were synthesized. The monomer (1) was synthesized by Sonogashira cross-coupling reaction. Lithiation and oxidation of the monomer led to the formation of dimer (2) and trimer (3). Optical and electrochemical properties of compounds 1-3 were studied. The oligomers with thioacetyl moieties were synthesized for self-assembly.     

Syntheses and bioactivities of tricyclic pyrones

In search of compounds that ameliorate the toxicity of amyloid-β (Aβ) peptides, new derivatives of tricyclic pyrones (1-7) were synthesized and their biological activities evaluated. The carboxylic ester and amide derivatives 1-4 were synthesized from a selective carboxylation of C3 methyl of (5aS,7S)-{7-Isopropenyl-3-methyl-1H,7H-5a,6,8,9-tetrahydro-1-oxopyrano[4,3-b][1]benzopyran (8) with LDA followed by benzyl chloroformate or carbon dioxide to provide ester 1 and carboxylic acid 9, respectively. Three isomeric tricyclic pyrone, 5-7, containing adenine moiety at C7 side chain were synthesized from the alkylation of mesylate 13 with adenine, and displacement of chloropurine 15 with amine 14. Although C3-benzyloxycarbonylmethyl analogs 1-3 have marginal ACAT and CETP activities, their modified aspartate analog 4 and C3-methyl-C7-(N3-adeninyl)-2-propyl analog 6 show a significant effect in protecting against neuron-cell death from the toxicity of intracellular accumulation of Aβ or Aβ-containing C-terminal fragments (CTF) of amyloid β precursor protein (APP). N9-Adenine analog 5 is 20-fold less effective than N3-adenine derivative 6 in the protection of neuron-cell death induced by Aβ, while N10-adenine analog 7 was inactive. As a result of this study, compounds 4 and 6 will well serve as lead compounds for further studies of the mechanism of action of Aβ-and CTF-induced neuron-cell death, studies which should enhance the future development of new drugs for the prevention and treatment of AD.     

Synthesis and hybridization affinity of oligodeoxyribonucleotides incorporating 4-N-(N-arylcarbamoyl)deoxycytidine derivatives

Modified oligodeoxynucleotides incorporating 4-N-(N-arylcarbamoyl)-dC derivatives 1a-c were synthesized. The ¹H NMR spectra of 1a-c suggest that the carbamoyl group forms an intramolecular hydrogen bond with the cytosine ring nitrogen atom so that formation of a Watson-Crick base pair with the complementary guanine base is inhibited. The hybridization properties of oligodeoxynucleotides containing 1a-c were investigated by use of T_m analysis. The hybridization properties of 4-N-(N-phenylcarbamoyl)-dC (1a) were similar to those of 4-N-(N-alkylcarbamoyl)-dC derivatives reported previously. In sharp contrast to 1a, it turned out that 4-N-(N-napht-1-yl) and (N-quionol-5-yl)-dC (1b,c) have a unique property as a universal base.     

Microwave assisted synthesis of novel imidazo [2,1-b]thiazole derivative attached to quinoxalinones

3-(6-Phenylimidazo[2,1-b]thiazol-5-yl)quinoxalin-2(1H)-ones (qunoxalinone) (6a-q) have been synthesized by the reaction of ethyl 2-oxo-2-(6-phenylimidazo[2,1-b]thiazol-5-yl)acetates (4a-e) with suitably substituted o-phenylenediamines (5a-f) under microwave heating. The ethyl 2-oxo-2-(6-phenylimidazo[2,1-b]thiazol-5-yl)acetates (4a-e) were prepared by the reaction of 6-phenylimidazo[2,1-b]thiazoles (3a-e) with ethyl chlorooxoacetate in refluxing 1,4-dioxane whereas the thiazoles (3a-e) were synthesized by the reaction of 2-bromo-1-phenylethanones (2a-e) with thiazol-2-amine in refluxing acetone.     

Synthesis and transformations of sulfur-substituted indolizidines and quinolizidines

3-Sulfolenes 1a-b underwent [4+2] cycloaddition reactions with p-toluenesulfonyl isocyanate to give tetrahydropyridinones 3a-b. Through N-detosylation of 3a-b and subsequent intramolecular cyclization, indolizidine 5a and quinolizidine 5b were synthesized. Useful functional group transformations of compounds 5a-b were also investigated.     

Asymmetric syntheses of 6-deoxyfagomin, d-deoxyrhamnojirimycin, and d-rhamnono-1,5-lactam

N-Allyl protected 3-O-benzyloxglutarimide 11 was synthesized as a useful variant of the chiral building block 10. This modification allowed a high-yielding deprotection of the allyl group from the lactam intermediate 14. Starting from this building block, the asymmetric syntheses of aza-sugars 6-deoxyfagomine (2), d-rhamnono-1,5-lactam (6), as well as d-deoxyrhamnojirimycin (5) have been achieved in high regio- and/or diastereo-controlled manner.     

Diterpenoids from Isodon pharicus

A phytochemical investigation of Isodon pharicus led to the isolation of a novel asymmetric ent-kauranoid dimer, bispseurata F (1), and three new diterpenoids, pharicinins A-C (2-4). Their structures were elucidated by extensive spectroscopic analysis. Compound 1 features a unique linkage pattern of C-17 with C-11′ to connect the two monomers. A possible biogenetic pathway of 1 was also proposed. Compounds 3 and 4 exhibited moderate inhibitory activity against NB4 and SH-SY5Y cell lines.     

Synthesis of new tetracyclic 7-oxo-pyrido[3,2,1-de]acridine derivatives

A series of (±)3-hydroxyl- and 2,3-dihydroxy-2,3-dihydro-7-oxopyrido[3,2,1-de]acridines were synthesized for antitumor evaluation. These agents can be considered as analogues of glyfoline or (±)1,2-dihydroxyacronycine derivatives. The key intermediates, 3,7-dioxopyrido[3,2,1-de]acridines (15a,b or 24a,b), for constructing the target compounds were synthesized either from 3-(N,N-diphenylamino)propionic acid (14a,b) by treating with Eaton’s reagent (P₂O₅/MsOH) (Method 1) or from (9-oxo-9H-acridin-10-yl)propionic acid (23a-c) via ring cyclization under the same reaction conditions (Method 2). Compounds 15a,b and 24a,b were converted into (±)3-hydroxy derivatives (25a-d), which were then further transformed into pyrido[3,2,1-de]acridin-7-one (28a-d) by treating with methanesulfonic anhydride in pyridine via dehydration. 1,2-Dihydroxylation of 28a-d afforded (±)cis-2,3-dihydroxy-7-oxopyrido[3,2,1-de]acridine (29a-d). Derivatives of (±)3-hydroxy (25a,b) and (±)cis-2,3-dihydroxy (29a-d) were further converted into their O-acetyl congeners 26a,b and 30a-d, respectively. We also synthesized 2,3-cyclic carbonate (31, 32, and 33) from 29a-c. The anti-proliferative study revealed that these agents exhibited low cytotoxicity in inhibiting human lymphoblastic leukemia CCRF-CEM cell growth in culture.     

Synthesis and ‘double click’ density functionalization of 8-aza-7-deazaguanine DNA bearing branched side chains with terminal triple bonds

The 7-[di(prop-2-ynl)amino]prop-1-ynyl derivative of 8-aza-7-deaza-2′-deoxyguanosine (1) was synthesized from 7-iodo-8-aza-7-deaza-2′-deoxyguanosine (7) by Sonogashira cross-coupling and converted into the phosphoramidite building block 10. Oligonucleotides bearing branched side chains with terminal triple bonds were prepared by solid-phase synthesis containing single or multiple residues of 1 as 2′-deoxyguanosine surrogates. T_m measurements demonstrate that compound 1 has a positive effect on duplex stability, which is comparable to the stabilizing effect of the octa-1,7-diynylated non-branched nucleoside 2. Nucleoside 1 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition ‘double click’ reaction with diverse ligands (AZT 3, benzyl azide 4, 11-azidoundecanol 5 and m-dPEG™₄-azide 6). The conjugation reactions were carried out in solution and on solid support. Nucleoside 1 allowed ‘double’ functionalization of a single residue with two reporter groups. The ‘double click’ reaction proceeded smoothly even when two residues of nucleoside 1 were arranged in proximal positions. Hybridization with complementary strands led to a stable oligonucleotide duplex. Molecular modeling indicates that inspite of the crowded steric situation with four AZT ligands within closest proximal positions, all ligands are well accommodated in the major groove not disturbing the DNA helix.     

Highly stable and fluorescent switching spirooxazines

Two novel photochromic spirooxazines, SO-NA1 and SO-NA2, containing a naphthalimide unit were synthesized. The imide group of naphthalimide unit is incorporated at the naphthoxazine fragment, thus giving strong electron-withdrawing effect favoring the long-lived merocyanine (MC) in the dark giving good colorability in solution. Remarkably, their open merocyanine (MC) forms exhibit significantly long lifetimes, almost three magnitudes longer than that of unsubstituted spironaphthoxazine (1). Moreover, the fluorescence of naphthalimide unit can be switched on and off by photoinduced conversion between the open and closed forms.     

Asymmetric addition of phenylboronic acid to cycloalkanones mediated by a Rh/phosphoramidite complex: a comparison between tropos versus nontropos behavior

Herein we report the asymmetric addition of phenylboronic acid to different cycloalkenones, mediated by a Rh(I) complex with the tropos phosphoramidite (S)-L₁ or the nontropos phosphoramidite (S)-L₂ ligand. Different values of enantiomeric purity of the 3-phenylcycloalkanone products have been obtained, mainly depending on the ring size of the substrates, with (S)-L₁ affording higher ee values than (S)-L₂. These results could be explained by reasoning that for the tropos phosphoramidite, a ‘chiral pocket’ is formed when the ligand links to the metal atom. By fitting in this pocket, the substrate can stereoselectively coordinate to the Rh(I) atom, undergoing attack of the phenyl ring from the phenylboronic acid to a preferred enantioface. This causes the high (up to 96%) values of enantioselectivity observed with some of the substrates. A ‘chiral pocket’ cannot be formed with the nontropos ligand (S)-L₂ and, as a consequence, the stereoselectivity is greatly reduced.     

Synthesis and photochemistry of pH-sensitive GFP chromophore analogs

GFP chromophore analogs (7a-e, 8, and 10a,b) containing 2-thienyl-, 5-methyl-2-furyl-, 2-pyrryl, and 6-methyl-2-pyridyl-groups were synthesized and their fluorescence spectra recorded in the pH range 1-7. NMR studies showed that protonation of 8 (2-thienyl system) inhibited photoisomerization (Z-E) about the exocyclic double bond but that protonation of 7c (E + Z) (2-pyrryl system) gave only 7cE. Fluorescence studies revealed enhancement of fluorescence intensity of 7c and 7b,e (furyl system) below pH 2.5 and gave a similar result for 10a (pyridyl system) below pH 6. Quantum yields at pH 1 were low, probably due to excited state proton transfer (ESPT).     

Novel nucleotide-calixarene conjugates via phosphoester linkage

Calix[4]arenes bearing thymine, adenine, cytosine, guanine 2′-deoxynucleotide residues have been synthesized following the phosphoramidite chemistry. Hybrid compounds 2a-d and 3a-d represent the first example of nucleotides linked to the calixarene lower rim by a phosphoester bond. Preliminary studies about their assembling in apolar solvent and host properties toward biologically interesting guests are also reported.