Synthesis and nucleic acids binding properties of diastereomeric aminoethylprolyl peptide nucleic acids (aepPNA)

A general synthetic method for Fmoc-protected monomers of all four diastereomeric aminoethyl peptide nucleic acid (aepPNA) has been developed. The key reaction is the coupling of nucleobase-modified proline derivatives and Fmoc-protected aminoacetaldehyde by reductive alkylation. Oligomerization of the aepPNAs up to 10mer was achieved by Fmoc-solid phase peptide synthesis methodology. Preliminary binding studies of these aepPNA oligomers with nucleic acids suggested that the "cis-" homothymine aepPNA decamers with (2'R,4'R) and (2'S,4'S) configurations can bind, albeit with slow kinetics, to their complementary RNA [poly(adenylic acid)] but not to the complementary DNA [poly(deoxyadenylic acid)]. On the other hand, the trans homothymine aepPNA decamers with (2'R,4'S) and (2'S,4'R) configurations failed to form stable hybrid with poly(adenylic acid) and poly(deoxyadenylic acid). No hybrid formation could be observed between a mixed-base (2'R,4'R)-aepPNA decamer with DNA and RNA in both antiparallel and parallel orientations.     

6-Thioguanine in Peptide Nucleic Acids. Synthesis and Hybridization Properties

Abstract

The synthesis of N-((2-amino-6-benzylthiopurine-9-yl)acetyl)-N-(2-tBoc-aminoethyl)glycine 4 and its incorporation into a peptide nucleic acid (PNA) oligomer are described. Introduction of a single 6-thioguanine residue (6sG) in the PNA of a 10-mer PNA:DNA heteroduplex resulted in a decrease in Tm of 8.5°C. Furthermore, we observed a hypochromic and a bathochromic shift of 6 nm above 346 nm when the 6sG containing PNA was hybridized to its complementary DNA strand.     

Effect of Amino Acids on Lysosomal Proteolytic Activities in Rat Livers

(R)-2-(4′-Isobutylphenyl)propanoic acid (ibuprofen), (S)-3(4′-isobutylphenyl)butanoic acid and (S)-4-(4′-isobutylphenyl)pentanoic acid were obtained using microbial oxidation of (±)-l-isobutyl-4-(1′ -methyloctyl)benzene by Rhodococcus sp. BPM 1613.     

Benzopyran Derivatives and an Aliphatic Compound from a Mangrove Endophytic Fungus Penicillium citrinum QJF‐22

Two new benzopyran derivatives, (2R,4S)‐5‐methoxy‐2‐methyl‐3,4‐dihydro‐2H‐1‐benzopyran‐4‐ol and (2S,4R,2′S,4′R)‐4,4′‐oxybis(5‐methoxy‐2‐methyl‐3,4‐dihydro‐2H‐1‐benzopyran), and a new aliphatic compound, (3E,5Z,8S,10E)‐8‐hydroxytrideca‐3,5,10,12‐tetraen‐2‐one, together with three known benzopyran derivatives, were obtained from a mangrove endophytic fungus Penicillium citrinum QJF‐22 collected in Hainan island. Their structures were determined by analysis of spectroscopic data and the relative configuration of (2R,4S)‐5‐methoxy‐2‐methyl‐3,4‐dihydro‐2H‐1‐benzopyran‐4‐ol was also confirmed by single‐crystal X‐ray diffraction. The absolute configurations of four compounds were established by comparison of ECD spectra to calculations. The configuration of (3E,5Z,8S,10E)‐8‐hydroxytrideca‐3,5,10,12‐tetraen‐2‐one was confirmed by comparison of optical value to the similar compound. The configurations of the compounds (2S,4S)‐5‐methoxy‐2‐methyl‐3,4‐dihydro‐2H‐1‐benzopyran‐4‐ol and (2R,4R)‐5‐methoxy‐2‐methyl‐3,4‐dihydro‐2H‐1‐benzopyran‐4‐ol were first determined. (3R,4S)‐3,4,8‐Trihydroxy‐3,4‐dihydronaphthalen‐1(2H)‐one exhibited moderate inhibitory effects on LPS‐induced NO production in RAW264.7 cells with IC₅₀ of 44.7 μM, and without cytotoxicity to RAW264.7 cells within 50 μM.     

Disrupting Protein Expression with Peptide Nucleic Acids Reduces Infection by Obligate Intracellular Rickettsia

Peptide Nucleic Acids (PNAs) are single-stranded synthetic nucleic acids with a pseudopeptide backbone in lieu of the phosphodiester linked sugar and phosphate found in traditional oligos. PNA designed complementary to the bacterial Shine-Dalgarno or start codon regions of mRNA disrupts translation resulting in the transient reduction in protein expression. This study examines the use of PNA technology to interrupt protein expression in obligate intracellular Rickettsia sp. Their historically intractable genetic system limits characterization of protein function. We designed PNA targeting mRNA for rOmpB from Rickettsia typhi and rickA from Rickettsia montanensis, ubiquitous factors important for infection. Using an in vitro translation system and competitive binding assays, we determined that our PNAs bind target regions. Electroporation of R. typhi and R. montanensis with PNA specific to rOmpB and rickA, respectively, reduced the bacteria’s ability to infect host cells. These studies open the possibility of using PNA to suppress protein synthesis in obligate intracellular bacteria.     

Rapid PaperMicrobial Oxygenation of Organo-metallic Bissulfides Leading to Formation of Planar Chirality and C2 Symmetry

1,2-Bis(methylthiomethyl)ferrocene (3) was oxidized by Corynebacterium equi IFO 3730 to give monosulfoxide 4 in two diastereomeric forms with (1S,2R,S_S) and (1S,2R,R_S) configurations in a ratio of 4:1, while 1,1′-bis(methylthiomethyl)ferrocene (5) was oxidized by Penicillium frequentans IFO 5692 to (R)-monosulfoxide 6 and then preferentially to (R,R)-bissulfoxide 7. Thus, the bacterial monooxygenase generated specific planar chirality in the metallocenic monosulfoxide, and the fungal enzyme formed C₂ symmetry in the bissulfoxide.     

Effect of LNA Modifications on Small Molecule Binding to Nucleic Acids

Abstract

Locked nucleic acid (LNA) is a conformationally constrained DNA analogue that exhibits exceptionally high affinity for complementary DNA and RNA strands. The deoxyribose sugar is modified by a 2′-O, 4′-C oxymethylene bridge, which projects into the minor groove. In addition to changing the distribution of functional groups in the groove and the overall helical geometry relative to unmodified DNA, the bridge likely alters the hydration of the groove. Each of these factors will impact the ability of small molecules, proteins and other nucleic acids to recognize LNA-containing hybrids. This report describes the ability of several DNA-intercalating ligands and one minor groove binder to recognize LNA-DNA and LNA-RNA hybrid duplexes. Using UV-vis, fluorescence and circular dichroism spectroscopies, we find that the minor groove binder as well as the intercalators exhibit significantly lower affinity for LNA-containing duplexes. The lone exception is the alkaloid ellipticine, which intercalates into LNA-DNA and LNA-RNA duplexes with affinities comparable to unmodified DNA-DNA and RNA-DNA duplexes.     

Discovery of Four New Compounds from Macropanax membranifolius and Their Cytotoxic Activity

A phytochemical investigation of the methanolic extract of the Macropanax membranifolius C.B. Shang leaves led to the isolation of three new flavans, (2R,3R)-4′-O-methylcatechin 5-O-β-D-glucopyranoside ( 1 ), (2S,3S)-4′-O-methylcatechin 5-O-β-D-glucopyranoside ( 2 ), (2S,3R)-4′-O-methylcatechin 5-O-β-D-glucopyranoside ( 3 ), one new triterpene glycoside 3-O-β-D-xylopyranosyl-(1→6)-[β-D-xylopyranosyl-(1→2)]-β-D-glucopyranosyl-oleanolic acid 28-O-β-D-glucopyranoside ( 4 ), together with nine known compounds ( 5 - 13 ). Their chemical structures were elucidated based on HR-ESI-MS, NMR spectroscopic data. The absolute configurations of compounds 1 – 3 were established by electronic circular dichroism (ECD) spectra. At concentration of 20 μM, compounds 1 – 13 showed the percentages of dead cell in the range of 2.14 % to 33.61 % against KB, HepG2, HL60, P388, HT29, and MCF7 cancerous cell lines by SRB assay.     

CD correlation of C-2′substituted monocyclic carotenoids

The scope and limitation of circular dichroism (CD) correlations of several C-2′ substituted monocyclic monochiral, homodichiral and heterodichiral carotenoids have been investigated, aiming at the assignment of absolute configuration at C-2′ by using the diester and 2′-β-d-tetraacetylglucosyl derivative of (2′R)-plectaniaxanthin and a synthetic chiral C₄₅-carotene as key references. The correlations are based on the additivity hypothesis, the conformational rule and a comparison of CD spectra, preferably conservative ones. Quantitative aspects of the conformational rule are considered. Substituent effects at C-2′ and C-1′ have been studied. Absolute configurations are suggested for (2′)-phleixanthophyll (3S,2′S)-2′-hydroxyflexixanthin, (3R,2′S)-myxoxanthophyll, (3S,2′S-4-ketomyxoxanthophyll (3R,2′S)-myxol-2′-O-methyl methylpentoside and (2R,2′S)-Cp. 473 from relevant CD correlations. The chiralities of (2′S)-4-ketophleixanthophyll and (2R,6R,2′S)-A.g. 471 are suggested from biogenetic considerations. A chemosystematic consideration of chirality and source is included.     

Synthesis of Both the Enantiomers of 3-Octanol,the Pheromone of Various Species of Ants

(2S,3R,1′S,2′S)-Serricorole (1) and (2S,3R,1′R)-serricorone (2), sex pheromone components of the cigarette beetle (Lasioderma serricorne F.), were synthesized, starting from the enantiomers of methyl 3-hydroxypentanoate. The stereochemistry of the naturally occurring 1 was determined to be 2S,3R,1′S,2′S, and that of 2 to be 2S,3R,1′RS by comparing between the CD spectra of the natural and synthetic samples.     

Occurrence of Stereoisomers of 1-(2′-Pyrrolidinethione-3′-yl)-1,2,3,4- tetrahydro-β-carboline-3-carboxylic Acid in Fermented Radish Roots and Their Different Mutagenic Properties

Stereoisomers of the tetrahydro-β-carboline derivative, 1-(2′-pyrrolidinethione-3′-yl)-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (PTCC), were formed from L-tryptophan with 4-methylthio-3-butenyl isothiocyanate, and their mutagenic properties and contents in different types of the radish products were studied. The isomers were identified as (1S ^*, 3S ^*, 3′R ^*)- and (1R ^*, 3S ^*, 3′R ^*)-PTCCs; the former was found as the major compound but had no mutagenic activity, while the latter was mutagenic toward Salmonella typhimurium TA 98 in the presence of a rat microsomal fraction. Both (1S ^*, 3S ^*, 3′R ^*)- and (1R ^*, 3S ^*, 3′R ^*)-PTCC were detected in a ratio of about 4:1 in a product fermented for 8 months, but only a trace was apparent in products manufactured within a few weeks.     

Effect of Cycloheximide on Protein Breakdown in Germinating Rice Seeds

1′-Epi-stegobinone [(2S,3R,1′S)-2,3-dihydro-2,3,5-trimethyl-6-(1′-methyl-2′-oxobutyl)-4H-pyran-4-one], an inhibitor of stegobinone, which is the sex pheromone of drugstore beetle (Stegobium paniceum L.), was synthesized by stereocontrol at C-2 and C-1′ starting from ethyl (R)-3-hydroxybutanoate and methyl (R)-3-hydroxypentanoate.     

Absolute configurations and CD spectra of axially chiral biphenyls prepared in a facile manner by crystallization‐induced configuration transformation

Axially chiral biphenyls such as (M,S)‐ 3k have been conveniently obtained by crystallization of their diastereomeric mixtures, which were synthesized from racemic 4,4′‐dimethoxy‐5,6,5′,6′‐bis(methylenedioxy)‐2‐carboxylester‐2′‐carboxyl‐biphenyls 4 and chiral amino alcohols (R)‐alaninol, (S)‐alaninol, (S)‐valinol, and (S)‐phenylalaninol. A crystallization‐induced configuration transformation of the biphenyls was thus achieved. It was found that amide formation of an (S)‐valinol or (S)‐phenylalaninol at the 2′‐position of the biphenyl usually induced the deposition of crystals with the (M)‐configuration from ethanol in yields higher than 50%. The absolute configurations (ACs) of two crystalline biphenyls have been determined by X‐ray crystallographic analysis. The ACs of nine biphenyls have been assigned based on their CD spectra. Further, stability investigation of these axially chiral biphenyls revealed that the ACs could revert upon redissolution. The energy barrier to epimerization between (P,R)‐ 3b and (M,R)‐ 3b was measured as ΔG^# = 21.45 kcal/mol and the half‐life in ethanol at 301 K was 17.1 h. Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Synthesis and Absolute Configuration of Pyriculol

A total synthesis of optically active pyriculol is described. The Wittig reaction between an aldehyde 19 and a triphenylphosphonium ylide 12 gave an intermediate 20. Successive treatment of 20 with p-toluenesulfonic acid, active manganese dioxide, and potassium carbonate gave (3′R,4′S)-pyriculol (23), which was identical with natural pyriculol (1) in all respects. From this synthesis, the absolute stereochemistry of pyriculol (1) was determined to be 2-[(3′R,4′S)-3′,4′-dihydroxy- (1′E,5′E)-1′,5′-heptadienyl]-6-hydroxybenzaldehyde     

Hybridization Studies with Chiral Peptide Nucleic Acids

A novel class of chiral peptide nucleic acids has been synthesized in which the sugar-phosphate backbone of DNA has been replaced with the glycyl-proline backbone of both the - and the -configurations, nucleobases being attached through the 4-position of proline withcis- andtrans-stereochemistry. TheT₁₀homopolymers withcis-stereochemistry in the - and -series bind strongly to poly(dA) withT_mvalues of 69 and 70°C, respectively. They bind more strongly to poly(rA) withT_mvalues of 73 and 72°C, respectively, and with apparent 1:1 stoichiometry. Using a mixed sequence decamer it was found that the thermal stability of the chiral peptide nucleic acid/oligonucleotide complex was comparable to that formed by Nielsen's polyamide nucleic acid.     

Utilization of Bacterial Xanthine Oxidase for Inorganic Phosphorus Determination

Two host-specific phytotoxic metabolites, AK-toxin I and II, were isolated from a culture broth of Alternaria alternata Japanese pear pathotype, the fungus causing black spot disease of susceptible Japanese pear cultivars. From chemical, spectral and X-ray crystallographic data, AK-toxin I was characterized as 8-(2′S, 3′S)-2′-acetylamino-3′-methyl-3′-phenyl-propionyloxy]-(8R,9S)-9,10-epoxy-9-methyl-deca-(2E,4Z,6E)-trienoic acid. The structure of AK-toxin II was also assigned to be 3′-demethyl derivative of AK-toxin I by comparing the spectral data with those of AK-toxin I.     

Iridoids from Pedicularis verticillata and Their Anti‐Complementary Activity

Three new iridoids named as pediverticilatasin A – C ( 1 – 3 , resp.), together with five known iridoids ( 4 – 8 , resp.) were isolated from the whole plants of Pedicularis verticillata. The structures of three new compounds were identified as (1S,7R)‐1‐ethoxy‐1,5,6,7‐tetrahydro‐7‐hydroxy‐7‐methylcyclopenta[c]pyran‐4(3H)‐one ( 1 ), (1S,4aS,7R,7aS)‐1‐ethoxy‐1,4a,5,6,7,7a‐hexahydro‐7‐hydroxy‐7‐methylcyclopenta[c]pyran‐4‐carboxylic acid ( 2 ), (1S,4aS,7R,7aS)‐1‐ethoxy‐1,4a,5,6,7,7a‐hexahydro‐7‐hydroxy‐7‐methylcyclopenta[c]pyran‐4‐carbaldehyde ( 3 ). Their structures were elucidated on the basis of spectroscopic methods and compared with the NMR spectra data in the literature. All compounds were evaluated for their anti‐complementary activity on the classical pathway of the complement system in vitro. Among which, compounds 1 , 3 , and 6 exhibited anti‐complementary effects with CH₅₀ values ranging from 0.43 to 1.72 mm , which are plausible candidates for developing potent anti‐complementary agents.     

Characterization of (2S,2'R,3'R)-2-(2',3'-[3H]-Dicarboxycyclopropyl)glycine Binding in Rat Brain

Abstract: [(2S,2′R,3′R)-2-(2′,3′-[³H]Dicarboxycyclopropyl)glycine ([³H]DCG IV) binding was characterized in vitro in rat brain cortex homogenates and rat brain sections. In cortex homogenates, the binding was saturable and the saturation isotherm indicated the presence of a single binding site with a K_D value of 180 ± 33 nM and a B_max of 780 ± 70 fmol/mg of protein. The nonspecific binding, measured using 100 µM LY354740, was <30%. NMDA, AMPA, kainate, l (?)-threo-3-hydroxyaspartic acid, and (S)-3,5-dihydroxyphenylglycine were all inactive in [³H]DCG IV binding up to 1 mM. However, several compounds inhibited [³H]DCG IV binding in a concentration-dependent manner with the following rank order of potency: LY341495 = LY354740 > DCG IV = (2S,1′S,2′S)-2-(2-carboxycyclopropyl)glycine > (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid > (2S,1′S,2′S)-2-methyl-2-(2-carboxycyclopropyl)glycine > l -glutamate = ibotenate > quisqualate > (RS)-α-methyl-4-phosphonophenylglycine = l (+)-2-amino-3-phosphonopropionic acid > (S)-α-methyl-4-carboxyphenylglycine > (2S)-α-ethylglutamic acid > l (+)-2-amino-4-phosphonobutyric acid. N-Acetyl-l -aspartyl-l -glutamic acid inhibited the binding in a biphasic manner with an IC₅₀ of 0.2 µM for the high-affinity component. The binding was also affected by GTPγS, reducing agents, and CdCl₂. In parasagittal sections of rat brain, a high density of specific binding was observed in the accessory olfactory bulb, cortical regions (layers 1, 3, and 4 > 2, 5, and 6), caudate putamen, molecular layers of the hippocampus and dentate gyrus, subiculum, presubiculum, retrosplenial cortex, anteroventral thalamic nuclei, and cerebellar granular layer, reflecting its preferential (perhaps not exclusive) affinity for pre- and postsynaptic metabotropic glutamate mGlu2 receptors. Thus, the pharmacology, tissue distribution, and sensitivity to GTPγS show that [³H]DCG IV binding is probably to group II metabotropic glutamate receptors in rat brain.     

Two new dihydrobenzofuran-type neolignans from Breynia fruticosa

(7S,8R,7′S)-9,7′,9′-Trihydroxy-3,4-methylenedioxy-3′-methoxy [7-O-4′,8-5′] neolignan (1) and (7S,8R,7′S)-9,9′-dihydroxy-3,4-methylenedioxy-3′,7′-dimethoxy [7-O-4′,8-5′] neolignan (2), two new natural dihydrobenzofuran-type neolignans, along with 9,9′-dihydroxy-3,4-methylenedioxy-3′-methoxy [7-O-4′,8-5′] neolignan (3) and (-)-machicendiol (4), were isolated from the whole plants of Breynia fruticosa. The structures of 1 and 2, including the absolute configurations, were determined by spectroscopic methods and circular dichroism (CD) techniques. The absolute configuration of 4 was confirmed by calculations of the OR spectrum, together with OR and ECD spectra of its p-bromobenzoate ester (4a).     

Compounds with neuroprotective activity from the medicinal plant Machilus thunbergii

The dichloromethane fraction of the bark of Machilus thunbergii Sieb. et Zucc. (Lauraceae) significantly protected primary cultures of rat cortical cells exposed to the excitotoxic amino acid, L-glutamate. Through the activity-guided isolation from the CH₂Cl₂ fraction, (+)-9′-hydroxygalbelgin (1), isogalcatin B (2), (7S,8S,8′R)-3′,4′-dimethoxy-3,4,-methylenedioxylignan-7-ol (3), 1-hydroxy-7-hydroxymethyl-6-methoxyxanthone (4), 5,7-dimethoxy-3′,4′-methylenedioxyflavan-3-ol (5), (+)-(3S,4S,6R)-3,6-dihydroxypiperitone (6), protocatechuic acid methyl ester (7) and tyrosol (8) were obtained. All of them had significant neuroprotective activities against glutamate-induced neurotoxicity in primary cultures of rat cortical cells at concentrations ranging from 0.1 μM to 10.0 μM and were comparable to MK-801, a well-known inhibitor of glutamate receptor.