Distant Neighbor Base Sequence Context Effects in Human Nucleotide Excision Repair of a Benzo[a]pyrene-derived DNA Lesion

The effects of non-nearest base sequences, beyond the nucleotides flanking a DNA lesion on either side, on nucleotide excision repair (NER) in extracts from human cells were investigated. We constructed two duplexes containing the same minor groove-aligned 10S (+)-trans-anti-B[a]P-N²-dG (G?) DNA adduct, derived from the environmental carcinogen benzo[a]pyrene (B[a]P): 5′-C-C-A-T-C-G?-C-T-A-C-C-3′ (CG?C-I), and 5′-C-A-C3-A4-C5-G?-C-A-C-A-C-3′ (CG?C-II). We used polyacrylamide gel electrophoresis to compare the extent of DNA bending, and molecular dynamics simulations to analyze the structural characteristics of these two DNA duplexes. The NER efficiencies are 1.6(± 0.2)-fold greater in the case of the CG?C-II than the CG?C-I sequence context in 135-mer duplexes. Gel electrophoresis and self-ligation circularization experiments revealed that the CG?C-II duplex is more bent than the CG?C-I duplex, while molecular dynamics simulations showed that the unique -C3-A4-C5- segment in the CG?C-II duplex plays a key role. The presence of a minor groove-positioned guanine amino group, the Watson-Crick partner to C3, acts as a wedge; facilitated by a highly deformable local -C3-A4- base step, this amino group allows the B[a]P ring system to produce a more enlarged minor groove in CG?C-II than in CG?C-I, as well as a local untwisting and enlarged and flexible Roll only in the CG?C-II sequence. These structural properties fit well with our earlier findings that in the case of the family of minor groove 10S (+)-trans-anti-B[a]P-N²-dG lesions, flexible bends and enlarged minor groove widths constitute NER recognition signals, and extend our understanding of sequence context effects on NER to the neighbors that are distant to the lesion.     

β-Diiminatolanthanoid(III) halides revisited

The crystalline compounds [LnCl₂(L)(thf)₂] [Ln = Ce (1), Tb (2), Yb (3)], [NdI₂(L)(thf)₂] (4), [LnCl(L′)₂] [Ln = Tb (5), Yb (6) (a known compound)] and [YbCl(L′′)(μ-Cl)₂Li(OEt₂)₂] (7) have been prepared [L = {N(C₆H₃Prⁱ₂-2,6)C(H)}₂CPh, L′ = {N(SiMe₃)C(Ph)}₂CH, L′′ = {N(SiMe₃)C(C₆H₄Ph-4)}₂CH]. The X-ray molecular structures of 2-7 have been established; in each, the monoanionic ligand L, L′ or L′′ is N,N′-chelating and essentially π-delocalised. Each of 1-7 was prepared from the appropriate LnCl₃, or for 4 [NdI₃(thf)₂], and an equivalent portion of the appropriate alkali metal [Li for 7, Na for 2, 3 and 5, or K for 1, 4 and 6] β-diiminate in thf; the isolation of exclusively 5 and 6 (rather than the L′ analogues of 2 or 3) is noteworthy, as is the structure of 7 which has no precedent in Group 3 or 4f metal β-diiminato chemistry.     

Chemical constituents of Picea neoveitchii

Four flavonoids, 5,7,4′-trihydroxy-3,8,-dimethoxy-6-C-methylflavone (1), 5,8,4′-trihydroxy-3,7-dimethoxy-6-C-methylflavone (2), 7-methoxy-6-C-methylkaempferol (3) and kaempferol-7-O-(2″-E-p-coumaroyl)-α-l-arabinofuranoside (4), together with 15 known compounds, were isolated from the twigs and leaves of Picea neoveitchii Mast. Their structures were elucidated on the basis of analyses of spectroscopic data. Compound 4 showed strong anti-fungal activity against Fusarium oxysporum whereas compounds 1-4 were all active against Rhizoctonia solani.     

Synthesis and characterization of oligodeoxynucleotides containing a novel tetraazabenzo[cd]azulene:naphthyridine base pair

The synthesis and thermal stability of oligodeoxynucleotides (ODNs) containing 4-amino-2,3,5,6-tetraazabenzo[cd]azulen-7-one nucleosides 5 (BaO^N) with the aim of developing new base pairing motif is described. The tricyclic nucleoside 5 was prepared starting with the 7-deaza-7-iodopurine derivative 1 via a palladium catalyzed cross-coupling reaction with methyl acrylate, followed by an intramolecular cyclization. The resulting nucleoside was incorporated into ODNs, and the base pairing property of the BaO^N:NaN^O (2-amino-7-hydroxy-1,8-naphthyridine nucleoside) pair in the duplex was evaluated by a thermal denaturation study. The melting temperature (T_m) of the duplex containing the BaO^N:NaN^O pair showed a higher value than that of the duplexes containing the adenine:thymine (A:T) and the guanine:cytosine (G:C) pairs, however it was lower than that of the ImO^N:NaN^O (ImO^N = 7-amino-imidazo[5′,4′:4,5]pyrido[2,3-d]pyrimidin-4(5H)-one nucleoside) pair. A temperature-dependent ¹H NMR study revealed that the H-bonding ability of BaO^N was lower than that of ImO^N, which would explain why the BaO^N:NaN^O pair was less thermally stable than the ImO^N:NaN^O pair.     

Iridoids from Gentiana loureirii

Iridoid glycosides, 2′,3′,6′-tri-O-acetyl-4′-O-trans-p-(O-β-d-glucopyranosyl)coumaroyl-7-ketologanin (1), 2′-O-caffeoylloganic acid (2), 2′-O-p-hydroxybenzoylloganic acid (3), 2′-O-trans-p-coumaroylloganic acid (4), and 2′-O-cis-p-coumaroylloganic acid (5), were isolated from whole plants of Gentiana loureirii along with six known iridoids, 7-ketologanin (6), loganin (7), loganic acid (8), sweroside, boonein, and isoboonein, and three other known compounds. Their structures were elucidated by spectroscopic means and chemical correlations. The isolated iridoids were evaluated for antibacterial and antioxidant activities, but were either inactive or very weakly active.     

Influence of cis-protecting groups toward ligand exchange reactions in polynuclear Pd(II)-based coordination cages

Polynuclear self-assembly molecules of general formula [{Pd(en)}_x(ligand)_y](NO₃)_2x (A) undergo ligand exchange reaction when heated in DMSO. A mixture of [Pd_m(ligand)_n](NO₃)_2m (B) and [Pd(en)₂](NO₃)₂ (C) is generated in this process. The binuclear compound (A) containing a bidentate, non-chelating ligand 1,4-bis(4′-pyridylmethyl)-2,3,5,6-tetrafluorobenzene, is subjected to ligand exchange where upon the compound (A) remains in a dynamic equilibrium with the mixture of ensuing (B) and (C). Combination of separately prepared (B) and (C) also generates (A), thus equilibrium of (A) with (B) and (C) is again observed. We predict [{Pd(bpy)}_x(ligand)_y](NO₃)_2x (A′) where 2,2′-bipyridyl (bpy) is the cis-protecting group would not probably undergo ligand exchange. The idea was conceived from the fact that (bpy) is more rigid compared to (en) moreover one of the expected products in the event of ligand exchange [Pd(bpy)₂](NO₃)₂ (C′) is not really very stable unlike (C). In fact, when (A′) is heated in DMSO no ligand exchange is observed at all. More interestingly combination of (B) and (C′) generated (A′) smoothly. Mononuclear complexes obtained from the ligand 4-phenylpyridine are also used for similar study for comparison. It is suggested that (bpy) could serve as a better cis-protecting group for Pd(II)-based self-assembly coordination cage compounds particularly when dissolution of the assemblies in polar solvents and heating of the resultant solution is required.     

Aromatic N-oxide bridged copper(II) coordination polymers: Synthesis, characterization and magnetic properties

The complexes [Cu₂(o-NO₂-C₆H₄COO)₄(PNO)₂] (1), [Cu₂(C₆H₅COO)₄(2,2′-BPNO)]_n (2), [Cu₂(C₆H₅COO)₄(4,4′-BPNO)]_n (3), [Cu(p-OH-C₆H₄COO)₂(4,4′-BPNO)₂·H₂O]_n (4), (where PNO = pyridine N-oxide, 2,2′-BPNO = 2,2′-bipyridyl-N,N′-dioxide, 4,4′-BPNO = 4,4′-bipyridyl-N,N′-dioxide) are prepared and characterized and their magnetic properties are studied as a function of temperature. Complex 1 is a discrete dinuclear complex while complexes 2-4 are polymeric of which 2 and 3 have paddle wheel repeating units. Magnetic susceptibility measurements from polycrystalline samples of 1-4 revealed strong antiferromagnetic interactions within the {Cu₂}⁴⁺ paddle wheel units and no discernible interactions between the units. The complex 5, [Cu(NicoNO)₂·2H₂O]_n·4nH₂O, in which the bridging ligand to the adjacent copper(II) ions is nicotinate N-oxide (NicoNO) the transmitted interaction is very weakly antiferromagnetic.     

Anti-inflammatory activity of constituents from Glechoma hederacea var. longituba

Rosmarinic acid, its analogues, and a phenolic compound were obtained from G. hederacea var. longituba. There were two new compounds, methyl isoferuloyl-7-(3,4-dihydroxyphenyl) lactate (1) and benzyl-4′-hydroxy-benzoyl-3′-O-β-d-glucopyranoside (4), and four known compounds (2, 3, 5 and 6). The structures of these compounds were determined on the basis of spectroscopic methods. Each compound was tested by NF-κB luciferase assay and three rosmarinic acid analogues inhibited NF-κB production and the induction of COX-2 and iNOS mRNA in HepG2 cells.     

Inhibition of nitric oxide production in lipopolysaccharide-stimulated RAW264.7 macrophage cells by lignans isolated from Euonymus alatus leaves and twigs

The 80% methanolic extract of Euonymus alatus leaves and twigs afforded three new lignans, (−)-threo-4,9,4′,9′-tetrahydroxy-3,7,3′,5′-tetramethoxy-8-O-8′-neolignan (1), (−)-threo-4,9,4′,9′-tetrahydroxy-3,5,7,3′-tetramethoxy-8-O-8′-neolignan (2), (7R,8R,7′R)-(+)-lyoniresinol (3), together with seventeen known lignans (4-20). The structures of 1-20 were elucidated by extensive 1D and 2D spectroscopic methods including ¹H NMR, ¹³C NMR, ¹H-¹H COSY, HMQC, HMBC and NOESY. All the isolated compounds except for dilignans (19 and 20) significantly inhibited nitric oxide production in lipopolysaccharide-stimulated RAW264.7 cells.     

New class of acetylcholinesterase inhibitors from the stem bark of Knema laurina and their structural insights

Bioassay-guided extraction of the stem bark of Knema laurina showed the acetylcholinesterase (AChE) inhibitory activity of DCM and hexane fractions. Further repeated column chromatography of hexane and DCM fractions resulted in the isolation and purification of five alkenyl phenol and salicylic acid derivatives. New compounds, (+)-2-hydroxy-6-(10′-hydroxypentadec-8′(E)-enyl)benzoic acid (1) and 3-pentadec-10′(Z)-enylphenol (2), along with known 3-heptadec-10′(Z)-enylphenol (3), 2-hydroxy-6-(pentadec-10′(Z)-enyl)benzoic acid (4), and 2-hydroxy-6-(10′(Z)-heptadecenyl)benzoic acid (5) were isolated from the stem bark of this plant. Compounds (1-5) were tested for their acetylcholinesterase inhibitory activity. The structures of these compounds were elucidated by the 1D and 2D NMR spectroscopy, mass spectrometry and chemical derivatizations. Compound 5 showed strong acetylcholinesterase inhibitory activity with IC₅₀ of 0.573 ± 0.0260 μM. Docking studies of compound 5 indicated that the phenolic compound with an elongated side chain could possibly penetrate deep into the active site of the enzyme and arrange itself through π-π interaction, H-bonding, and hydrophobic contacts with some critical residues along the complex geometry of the active gorge.     

Flavones and flavone glycosides from Halophila johnsonii

Halophila johnsonii Eiseman is a shallow-water marine angiosperm which contains UV-absorbing metabolites. Studies on methanol extracts of H. johnsonii by means of HPLC-UV, NMR, HPLC-MS resulted in isolation and identification of seven previously unknown flavone glycosides: 5,6,7,3′,4′,5′-hexahydroxyflavone-7-O-β-glucopyranoside (1), 5,6,7,3′,4′,5′-hexahydroxyflavone-7-O-(6″-O-acetyl)-β-glucopyranoside (2), 6-hydroxyluteolin-7-O-(6″-O-acetyl)-β-glucopyranoside (3), 6-hydroxyapigenin-7-O-(6″-O-acetyl)-β-glucopyranoside (4), 6-hydroxyapigenin-7-O-(6″-O-[E]-coumaroyl)-β-glucopyranoside (5), 6-hydroxyapigenin-7-O-(6″-O-[E]-caffeoyl)-β-glucopyranoside (6) and 6-hydroxyluteolin-7-O-(6″-O-[E]-coumaroyl)-β-glucopyranoside (7). Also isolated were three known flavone glycosides, 6-hydroxyluteolin 7-O-β-glucopyranoside (8), scutellarein-7-O-β-glucopyranoside (9), and spicoside (10), and five known flavones, pedalitin (11), ladanetin (12), luteolin (13), apegenin (14) and myricetin (15). Qualitative comparison of the flavonoid distribution in the leaf and rhizome-root portions of the plant was also investigated, with the aim of establishing the UV-protecting roles that flavonoids played in the sea grass.     

Biological evaluation of 3'-O-alkylated analogs of salacinol, the role of hydrophobic alkyl group at 3' position in the side chain on the α-glucosidase inhibitory activity

Four analogs with 3′-O-alkyl groups (9a: CH₃, 9b: C₂H₅, 9c: C₁₃H₂₇ or 9d: CH₂Ph) instead of the 3′-O-sulfate anion in salacinol (1), a naturally occurring potent α-glucosidase inhibitor, were synthesized by the coupling reaction of 1,4-dideoxy-1,4-epithio-d-arabinitols (18a and 18b) with appropriate epoxides (10a-10d). These analogs showed equal or considerably higher inhibitory activity against rat small intestinal α-glucosidases than the original sulfate (1), and one of them (9d) was found more potent than currently used α-glucosidase inhibitors as antidiabetics. Thus, introduction of a hydrophobic moiety at the C3′ position of this new class of inhibitor was found beneficial for onset of stronger inhibition against these enzymes.     

Sterically crowded triazenides as novel ancillary ligands in copper chemistry

We have synthesized copper salts MN₃RR′ derived from the biphenyl- or m-terphenyl-substituted triazenes Tph₂N₃H (1a) and Dmp(Tph)N₃H (1b) (Dmp = 2,6-Mes₂C₆H₃ with Mes = 2,4,6-Me₃C₆H₂; Tph = 2-TripC₆H₄ with Trip = 2,4,6-i-Pr₃C₆H₂). The homoleptic copper triazenide [CuN₃Tph₂] (2a) was obtained in high yield from the metallation of 1a with mesityl copper in n-heptane, while the complex [CuN₃(Dmp)Tph] (2b) was generated by the same method in situ only. Reaction of 2a with triphenylphosphane gave the 2:1 adduct [CuN₃Tph₂(PPh₃)₂] (3a), regardless of the used complex/donor ratio, while reaction of 2a or 2b with a stochiometric amount of t-butylisonitrile afforded the 1:1 adducts [Tph₂N₃CuCNtBu] (4a) and [Dmp(Tph)N₃CuCNtBu] (4b). All new compounds (except 2b) have been characterized by ¹H NMR, ¹³C NMR and IR spectroscopy, elemental analysis, melting point (not 2a), and X-ray crystallography. The IR spectroscopic examination of the ν(CN) stretch in the isonitrile adducts 4a and 4b revealed the weaker donor character of the supporting triazenido ligands compared to related β-diketiminato ligands.     

Natural Product Antifoulants from the octocorals of Indian waters

Natural Product Antifoulants (NPAs) have been proposed as one of the best alternatives for the globally banned toxic biocide -TBT-in antifouling coatings. In search of NPAs from Indian waters twenty nine species of Octocorals, collected from Gulf of Mannar and Lakshadweep islands, were screened for their antifouling potential against the cyprids of the cosmopolitan biofouler, Balanus amphitrite. The crude extracts of 8 species of these corals (Cladiella krempfi, Lobophytum irregulare, Lobophytum sarcophytoides, Sarcophyton ehrenbergi, Sarcophyton glaucum, Sinularia kavarattiensis, Melitodes sp. and Subergorgia reticulata) exhibited relatively high settlement inhibition properties. The bioassay-guided purification of the crude extracts of 3 active and abundant species-Cladiella krempfi, Sinularia kavarattiensis and Subergorgia reticulata-yielded five NPAs, (l’E,5′E)-2-(2′,6′-dimethylocta-l’,5′,7′-trienyl)-4-furoic acid 1, (−)-6-??-hydroxy polyanthellin A 2, (+)-(7R,10S)-2-methoxy calamenene 3, (+)-(7R,10S)-2,5-dimethoxy calamenene 4 and (+)-(7R,10S)-2-methoxy,5-acetoxy calamenene 5). Among these, 5 exhibited high future prospects on account of its low EC₅₀ value (0.0335 ??g/ml) and high therapeutic ratio (799).     

Regioselectivity in the glycosylation of 5-(3-chlorobenzo[b]thien-2-yl)-4H-1,2,4-triazole-3-thiol

The glycosylation of 5-(3-chlorobenzo[b]thien-2-yl)-4H-1,2,4-triazole-3-thiol (1) and its 3-benzylsulfanyl and 3-methylsulfanyl derivatives with different glycosyl halides 2-4 has been studied in presence of base. The S-glycosides 5-7 were obtained in the presence of triethylamine, whereas the respective S,N⁴-bis(glycosyl) derivatives 8-10 were synthesized in the presence of potassium carbonate; the S,N²-bis(glycosyl) isomer 11 could also be isolated in the case of the galactosyl analog. Similarly, after protecting 1 as 3-benzyl(methyl)sulfanyl derivatives 12 or 13, the N⁴-glycosyl analogs 14-19 as well as minor amounts of S,N²-bis(galactosyl) isomers 20 and 21 were formed. The theoretical calculations using AM1 semiempirical methods agreed with the experimental results. Microwave irradiation (MWI) led to higher yields in much less time than the conventional methods, and no change in regioselectivity has been noticed.     

Synthesis, characterization of [{(N-methyl-N-benzyl)amino}methyl]ferrocenes and their cyclopalladated complexes: Crystal structure of σ-Pd[(η-C5H5)Fe(η-C5H3CH2N(CH3)CH2C6H4NO2-4)]Cl(PPh3)

Condensation of aminomethylferrocene (1) and substituted benzaldehydes resulted in aldimines 2a-c which followed by reduction with sodium borohydride to give 3a-c. N-methylation of 3a-c with HCHO/NaCNBH₃/HOAc led to 4a-c. Treatment of 4a-c with sodium palladium tetrachloride in the presence of sodium acetate afforded cleanly cyclopalladated 5a-c in which configurations consisted of the R_NR_C, S_NS_C. The preferable activation of C_Ferrocenyl-H bond over C_Phenyl-H bond was also observed. All compounds 2-5 were characterized by elemental analysis, IR and ¹H NMR. In addition, the molecular structure of 5c was confirmed by single crystal X-ray diffraction. The possible mechanism for the formation of 5 was also discussed.     

Absolute configuration of podophyllotoxin related lignans from Bursera fagaroides using vibrational circular dichroism

The ethanol extract from the dried exudate of Bursera fagaroides (Burseraceae) showed significant cytotoxic activity in the HT-29 (human colon adenocarcinoma) test system. The extract provided four podophyllotoxin related lignans, identified as (7′R,8R,8′R)-(−)-deoxypodophyllotoxin (3), (7′R,8R,8′R)-(−)-morelensin (4), (8R,8′R)-(−)-yatein (5), and (8R,8′R)-(−)-5′-desmethoxyyatein (6), whose spectroscopic and chiroptical properties were compared with those of (7R,7′R,8R,8′R)-(−)-podophyllotoxin (1) and its acetyl derivative (2). Their absolute configurations were assigned by comparison of the vibrational circular dichroism spectra of 1 and 3 with those obtained by density functional theory calculations.     

Structural comparison of alkylated derivatives of (bmmp-dmed)Ni and (bmmp-dmed)Zn

The sulfur-alkylation of the nickel (1) and zinc (2) complexes of the dithiolate N₂S₂ ligand N,N′-bis-2-methyl-mercaptopropyl-N,N′-dimethylethylenediamine, H₂(bmmp-dmed), have been investigated. Reactions with iodomethane yield [(Me-bmmp-dmed)Ni]PF₆ (3), [(Me₂-bmmp-dmed)NiI₂] (4), and [(Me₂-bmmp-dmed)ZnI]₂[ZnI₄] (5). Addition of iodoacetamide yields [(AA₂-bmmp-dmed)Ni]I₂ (6) and [(AA₂-bmmp-dmed)Zn]I₂ (7). Each of the metal-thioether products (3-7) have been characterized spectroscopically and by X-ray crystallography. Structural data is compared with that of the previously reported thiolato precursors 1 and 2. Sulfur-alkylation of 1 results in small relative changes in the nickel-sulfur bond distance, whereas for 2, the zinc-sulfur bond distance increases significantly, but is not cleaved. The difference between nickel and zinc is attributed to the release of a π*-bonding interaction between the metal and sulfur upon alkylation that compensates for the decreased σ-donor ability of the thioether in the case of nickel, but not for zinc.     

Osteogenic constituents from Pterospermum acerifolium Willd. flowers

Phytochemical investigation of ethanol extracts of the Pterospermumacerifolium flowers led to the isolation and identification of two new flavones, 4′-(2-methoxy-4-(1,2,3-trihydroxypropyl) phenoxy luteolin (1) and 5,7,3′-trihydroxy-6-O-β-d-glucopyranosyl flavone (2), and one new lactone, 3,5-dihydroxyfuran-2(5H)-one (3) along with 14 known compounds (4-17). The structure of compounds 1-17 was established based on MS, 1D and 2D NMR, spectroscopic analysis. Eight of these compounds (1-6, 8 and 9) were assessed for osteogenic activity by using primary cultures of rat osteoblast. The compounds 1, 3 and 4 significantly stimulated osteoblast differentiation and mineralization as evident from a marked increase in expression of alkaline phosphatase and alizarin red-S staining of osteoblasts.     

Syntheses and characterization of titanium malonato and amino acid complexes: [Ti(cp)2(OOCCH2NMe2)] - The first structurally characterized α-amino acid titanium(III) complex

The reaction of [Ti(cp^∗)₂(BTMSA)] (1) (cp^∗ = η⁵-C₅Me₅, BTMSA = bis(trimethylsilyl)acetylene) with malonic acids ((HOOC)₂CR₂, R = H, Me) and N,N-dimethylglycine resulted in the formation of titanium(IV) dicarboxylato complexes [Ti(cp^∗)₂{(OOC)₂CR₂}] (R = H, 2; R = Me, 3) and an α-amino acid titanium(III) complex [Ti(cp^∗)₂(OOCCH₂NMe₂)] (4). The identities of complexes 2-4 were confirmed by microanalysis, ¹H and ¹³C NMR spectroscopy (2, 3), ESI-MS and CID experiments (2, 3) as well as by ESR and magnetic measurements (μ_eff = 1.81, 298 K) for 4. Single X-ray diffraction analyses of 2 and 4 exhibited monomolecular complexes in which the titanium atom is distorted tetrahedrally coordinated by two η⁵-C₅Me₅ rings and by the chelating bound malonato-κ²O,O′ (2) and N,N-dimethylglycinato-κ²O,O′ ligand (4).