Biomedical subjects

Y In

Publications and source records attributed to Y In.

At least 19 recordsLinked to original sources

PubMed2005

Orally active antioxidative copper(II) aspirinate: synthesis, structure characterization, superoxide scavenging activity, and in vitro and in vivo antioxidative evaluations.

Ever since it was proposed that reactive oxygen species (ROS) are involved in the pathogeneses of various diseases, superoxide dismutase (SOD)-mimetic complexes have been intensively studied. We prepared copper(II) aspirinate [Cu2(asp)4] from Cu(II) and aspirin, which has been in use for many years as an antipyretic, an analgesic, and an anti-inflammatory agent. However, Cu2(asp)4 has been found to have additional activities, including anti-inflammatory, antiulcer, anti-ischemic/reperfusion agent, anticancer, antimutagenic, and antimicrobial activities. The activity of copper salicylate [Cu(sal)2] was also compared with that of Cu2(asp)4. The structure of the Cu2(asp)4 was determined using X-ray structure analysis. Its SOD-mimetic activity was determined using cytochrome c, electron spin resonance (ESR) spectroscopy, and ESR spin trap methods. The activity of Cu2(asp)4 was slightly greater than CuSO4 and copper acetate [Cu(ace)2] and slightly less than that of Cu(sal)2. The in vitro antioxidant activity, evaluated in human epithelial or transformed neoplastic keratinocyte cells, HaCaT, and normal dermal fibroblasts in terms of cell survival following ultraviolet B (UVB) irradiation, was significantly increased in the presence of Cu2(asp)4, Cu(sal)2, and CuSO4. Further, ROS generation following UVA irradiation in the skin of hairless mice following oral treatment with Cu2(asp)4 for three consecutive days was significantly suppressed compared to the vehicle- or Cu(ace)2-treated mice. On the basis of these results, Cu2(asp)4 was observed to be a potent antioxidative compound possessing antioxidative activity in biological systems. In conclusion, Cu2(asp)4 is a potent antioxidative agent that may be useful for future treatment of diseases resulting from ROS.

Administration, Oral↗

PubMed2001

Structure and stereochemistry of epoxyserratanes from the cuticle of Piceajezoensis var. jezoensis.

Three new epoxytriterpenes, 14 beta,15 beta-epoxy-21 beta-hydroxyserratan-3-one (1), 13 alpha,14 alpha-epoxy-21 alpha-methoxyserratan-3-one (2), and 13 alpha,14 alpha-epoxy-3 beta-methoxyserratan-21 beta-ol (3), were isolated together with two known triterpenoids, 21 alpha-methoxyserrat-13-en-3-one (4) and 21 beta-hydroxyserrat-14-en-3-one (5), from the cuticle of Picea jezoensis var. jezoensis. The structures of these new compounds were established on the basis of spectral data (NMR, MS) and single-crystal X-ray analyses (1 and 2) and partial synthesis (2 and 3).

Chromatography, Thin Layer↗

PubMed2001

Conformational comparison of mu-selective endomorphin-2 with its C-terminal free acid in DMSO solution, by 1H NMR spectroscopy and molecular modeling calculation.

In order to make clear the structural role of the C-terminal amide group of endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH2), an endogenous mu-receptor ligand, in the biological function, the solution conformations of endomorphin-2 and its C-terminal free acid (EM2OH, H-Tyr-Pro-Phe-Phe-OH), studied using two-dimensional 1H NMR measurements and molecular modeling calculations, were compared. Both peptides were in equilibrium between the cis and trans isomers around the Tyr-Pro omega bond in a population ratio of approximately/= 1:2. The lack of significant temperature and concentration dependence of NH protons suggested that the NMR spectra reflected the conformational features of the respective molecules themselves. Fifty possible 3D structures for the each isomer were generated by the dynamical simulated annealing method under the proton-proton distance constraints derived from the ROE cross-peaks. These energy-minimized conformers, which were all in the phi torsion angles estimated from J(NHCalphaH) coupling constants within +/- 30 degrees, were then classified in groups one or two according to the folding backbone structures. All trans and cis EM2 conformers adopt an open conformation in which their extended backbone structures are twisted at the Pro2-Phe3 moiety. In contrast, the trans and cis conformers of EM2OH show conformational variation between the 'bow'-shaped extended and folded backbone structures, although the cis conformers of its zwitterionic form are refined into the folded structure of the close disposition of C- and N-terminal groups. These results indicate clearly that the substitution of carboxyl group for C-terminal amide group makes the peptide flexible. The conformational requirement for mu-receptor activation has been discussed based on the active form proposed for endomorphin-1 and by comparing conformational features of EM2 and EM2OH.

Algorithms↗

PubMed2001

Abietane diterpenoids from the cones of Larix kaempferi and their inhibitory effects on Epstein-Barr virus activation.

Four known (1-3, 8) and four new abietane diterpenes, 15-hydroxy-8alpha,14alpha,12alpha,13alpha-diepoxyabietan-18-oic acid (4), 7alpha,8alpha,13beta,14beta-diepoxyabietan-18-oic acid (5), 18-nor-abieta-8,11,13-triene-4alpha,7alpha,15-triol (6), and abieta-8,11,13-triene-7alpha,15,18-triol (7) were isolated from the CHCl3 extract of the cones of Larix koempferi. A known compound, 13,14-seco-13,14-dioxoabiet-13-en-18-oic acid (8) was isolated from natural sources for the first time. Their structures were determined by chemical and spectroscopic methods including 1D and 2D NMR techniques. The absolute stereostructure of 5 was determined by X-ray crystallographic analysis. The inhibitory effects of these compounds on Epstein-Barr virus early antigen (EBV-EA) activation induced by the tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA), were examined as a primary screening for antitumor promotors.

Abietanes↗

PubMed2001

Structural studies on C-amidated amino acids and peptides: structures of hydrochloride salts of C-amidated Ile, Val, Thr, Ser, Met, Trp, Gln and Arg, and comparison with their C-unamidated counterparts.

To elucidate the structural features of amino acids caused by the C-terminal alpha-amidation, the crystal structures of HCl salts of C-terminal amidated Ile, Val, Thr, Ser, Met, Trp, Gln and Arg were analysed and compared with those of their C-terminal free acids. The bonding parameter of the amide group was little affected by the different chemical properties of the side chains. As for the molecular packing patterns, some structural differences were observed by the C-amidation. The Calpha-H...O hydrogen bonds and carbonyl-carbonyl interactions were more strengthened by the salt formation with HCl in C-amides than C-acids. Furthermore, there is a clear difference between the interaction patterns with Cl ions. In most C-amide crystals, Cl ions are bifurcately hydrogen-bonded to two neighbouring amide NH(2) groups and the parallel layers of the C-amides and Cl ions are alternatively formed. In the case of the carboxyl OH in C-acid crystals, however, the direct hydrogen bond with the Cl ion is not always observed and is largely dependent on the crystal packing environment. This suggests the superior hydrogen-bonding ability of NH...Cl(-) compared with OH...Cl(-). The difference in hydrogen-bonding ability between the amide and carboxyl groups is considered, based on the spatial dispositions of the hydrogen-bonding polar atoms/groups.

Amides↗

PubMed2000

Structural studies of C-amidated amino acids and peptides: crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2.

As part of the series investigating the structural features of C-terminal amidated amino acids and peptides, three crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2 were analyzed by the X-ray diffraction method, and their molecular conformations and intermolecular interactions were investigated. Although the respective dipeptides exhibited an energetically allowable torsion angle concerning each backbone or side chain, the observed extended (Z-Gly-Phe-NH2, Asp-Phe-NH2) and folded (Tyr-Lys-NH2) conformations were considerably different from those of the corresponding unamidated peptides, due to the conformational flexibility of the respective dipeptides. The comparison between the crystal packings of the amidated and unamidated dipeptides indicated that the C-terminal amides tend to associate with the same neighboring group through hydrogen bonds, in which both the amide NH and O=C groups participate, while the unamidated peptides prefer a linear molecular connection, where both or either of the two carboxyl oxygens participate in the hydrogen bond formation. The difference in hydrogen bonding ability between the C-terminal amide and carboxyl groups has been considered to be based on the structural data of the related peptides analyzed so far.

Amides↗

PubMed1999

Conformational change of ascidiacyclamide caused by asymmetric modification for an isoleucine residue: structural analyses of [Gly], [Leu], and [Phe]ascidiacyclamides by x-ray diffraction and NMR spectroscopy.

Ascidiacyclamide, a cytotoxic cyclic peptide from tunicate, is composed of unusual amino acids and has a repeated sequence, c[-thiazole-D-Val-oxazoline-L-Ile-]2 ([Ile]ASC). The symmetric chemical structure has been assumed to be correlated with the cytotoxicity, and it is reasonable to consider that the disturbance of its structure from the C2 symmetry results in the changes of conformation and activity. In order to quantitatively estimate the molecular conformation-activity relationship, an isoleucine residue was substituted by Gly, Leu, or Phe to disturb the C2 symmetry. The conformations of three derivatives were examined by nmr spectroscopy and the crystal structure of [Leu]ASC was also analyzed by x-ray diffraction method. The 1H-nmr experiments and the constrained molecular dynamics simulations showed the twisted "figure 8" conformers for [Gly] and [Phe]ASCs and the "square" conformer for [Leu]ASC in the DMSO solution. The x-ray crystal analysis of [Leu]ASC also revealed the square form similar to the solution structure. On the other hand, their cytotoxic activities were measured using L1210 leukemia cells and were related with the bulkiness and/or hydrophobicity of the side chain of the substituted amino acid; [Phe] > or = [Ile] > [Leu] >> [Gly]ASCs. As an attempt to consider the correlation between the activity and conformer, the accessible surface area (ASA) was calculated for each derivative to estimate the size or bulkiness of its conformation. Although the ASAs of nmr structures were not directly related to the type of conformer (figure 8 or square form), it was an important probe to consider the cytotoxicity of each derivative.

Amino Acid Substitution↗

PubMed1999

Unique molecular conformation of aureobasidin A, a highly amide N-methylated cyclic depsipeptide with potent antifungal activity: X-ray crystal structure and molecular modeling studies.

A structural feature of aureobasidins, cyclic depsipeptide antibiotics produced by Aureobasidium pullulans R106, is the N-methylation of four out of seven amide bonds. In order to investigate possible relationship between the molecular conformation and the amide N-methylation, aureobasidin A (AbA), which exhibits the potent antifungal activity, was subjected to X-ray crystal analysis. The crystal, recrystallized from ether (orthorhombic, space group P2(1)2(1)2(1), a = 21.643 (3) A, b = 49.865(10) A, c = 12.427 (1) A, z= 8), contained two independent conformers per asymmetric unit and they took on a similar arrowhead-like conformation. The conformation consisted of three secondary structures of antiparallel beta-sheet, and beta- and gamma-turns, and was stabilized by three intramolecular and transannular N-H O=C hydrogen bonds. The beta-hydroxy-N-methyl-l-valine residue, which is indispensable for its bioactivity, was located at the tip of the corner. Since a nearly identical conformation has been observed for aureobasidin E, a related cyclic depsipeptide, this arrowhead-like conformation may be energetically stable and important for biological activity. The contribution of the amide N-methylation to the conformation was investigated by model building and energy calculations. The energy-minimizations of AbA analogs, in which some (one to four) of four N-methylated amide bonds were replaced with usual amide bond, led to some conformers which are fairly different from the arrowhead form of AbA, although they are stabilized by three intramolecular N-H...O=C hydrogen bonds. This result explains the reason why four out of the seven amide bonds have to be methylated to manifest biological activity, i.e. the high N-methylation of aureobasidin is necessary to form only one well-defined conformation.

Antifungal Agents↗

PubMed1999

Characterization of estrogen receptor-beta (ERbeta) messenger ribonucleic acid and protein expression in rat granulosa cells.

We have examined estrogen-responsiveness of ovarian granulosa cells by focusing on estrogen receptor (ER) expression. Estrogen responsiveness was determined by examining the effect of 17beta-estradiol (1-10 nM) on luciferase reporter activity in rat granulosa cells transfected with an ERE-luciferase construct. The results demonstrate an estrogen-induced (approximately 3-fold) increase in luciferase reporter activity, indicating that granulosa cells contain functional estrogen response element (ERE)-binding transcriptional activators. Gel mobility shift assays in combination with ER antibodies show that ERbeta is the predominant ERE-binding protein in granulosa cells. Western blotting results show that granulosa cells contain ERbeta-immunoreactive protein(s) migrating at a size substantially larger than the recombinant protein generated from the originally proposed 485 amino acid open-reading frame. This size discrepancy is not due to granulosa cell expression of ERbeta isoforms with insertions within the coding region because RT-PCR assays revealed products with sizes expected for ERbeta, ERbetaB, and delta3 isoforms. This size discrepancy appears to be due to usage of a well-conserved, upstream in-frame translation initiation codon (ATG436) leading to a 530 amino acid open reading frame. ERbeta messenger RNA (mRNA) characterization using 5'-rapid amplification of complementary DNA ends (5'-RACE) show the presence of two different (P1- and P2-) 5'-ends of rat ERbeta mRNA encoding the full-length ERbeta protein. The generation of the P2-specific exon is likely due to initiation of transcription from an alternative promoter. Both P1- and P2-specific exon-containing ERbeta mRNAs are expressed in granulosa cells, and they are rapidly down-regulated by the cAMP-mediated intracellular signaling pathway in cultured granulosa cells. Taken together, our results show that rat granulosa cells produce two different 3',5'-cAMP-regulated ERbeta mRNA species and that these mRNA species are capable of encoding the full-length ERbeta protein.

Animals↗

PubMed1998

Effect of mRNA cap structure on eIF-4E phosphorylation and cap binding analyses using Ser209-mutated eIF-4Es.

The in vitro phosphorylation of human recombinant eIF-4E by protein kinase C was most effective in the absence of m7GTP, supporting a 'performed complex model' as the mRNA binding step of initiation, i. e., eIF-4E first forms an initiation complex eIF-4F and is phosphorylated before interacting with mRNA. On the other hand, the comparison of m7GTP-binding ability of wild-type eIF-4E with those of four Ser209-mutated ones (S209A, S209D, S209E and S209K) showed that the addition of anionic charge on Ser209 increases the cap affinity of eIF-4E by repressing the release of the cap from the complex, not by increasing the complex formation, suggesting the importance of a retractable ionic bridge between Ser209 and Lys159 in controlling the cap binding by eIF-4E phosphorylation.

Binding Sites↗

PubMed1997

Synthesis, structure and quantitative structure-activity relationships of sigma receptor ligands, 1-[2-(3,4-dimethoxyphenyl)ethyl]-4-(3-phenylpropyl) piperazines.

A set of the title compounds having different substituents (R1, R2) on their phenyl groups was synthesized to find sigma receptor binding affinity. Among the compounds, 2b (R1 = R2 = Cl) has the most potent sigma 1-binding activity, while 2a (R1 = R2 = H, SA4503) was most selective to sigma 1 over sigma 2 receptor. The crystal structures of 2a and 2b were shown, by X-ray crystallography, to be similar except for the one torsional angle of their propylene parts. Quantitative structure-activity relationship study suggested the affinity of the compounds to the sigma 1 receptor was dependent on the electronic feature, Swain-Lupton's R or Sz that was derived by molecular orbital method, of R1 and R2.

Analgesics, Opioid↗

PubMed1994

Structure of ascidiacyclamide as the ethanol water solvate, a cytotoxic cyclic peptide from Ascidian.

The X-ray crystal structure determination of the C2H5OH.H2O solvate of ascidiacyclamide (C36H52N8O6S2), a cytotoxic cyclic peptide from marine tunicate Ascidian, revealed a C2-symmetric saddle-shaped rectangular conformation of the molecule. The water and ethanol molecules are located on the crystallographic diad axis and are held by hydrogen bonds and van der Waals contacts with the polar ring N atoms and nonpolar D-Val side-chain atoms, respectively. The molecular conformation and the interaction with solvent molecules are nearly the same as those of the compound with C2H5OH.2H2O [Ishida, In, Doi, Inoue, Hamada & Shioiri (1992). Biopolymers, 32, 131-143].

Animals↗

PubMed1994

Patellamide A, a cytotoxic cyclic peptide from the ascidian Lissoclinum patella.

The structure of crystals of patellamide A (13-methyl-9,23-bis(1-methylethyl)-2,16-bis(1-methylpropyl)-14,-28-di oxa-7,21- dithia-3,10,17,24,29,30,31,32- octaaza-pentacyclo[24.2.1.1(5,8).1(12,15).1(19,22]dotriac onta-1(29),5,- 8(30),15(31),19,22(32)-hexaene-4,11,18,25-tetraone methanol solvate monohydrate, C35H49N8O6S2.-CH4O.H2O), a cytotoxic cyclic peptide having a non-C2-symmetric methyl group, shows the C2-symmetric and saddle-shaped rectangular conformation where the methyl group is disordered into two C2-symmetric positions. The water and methanol solvents were located on the crystallographic diad axis and were held by hydrogen bonds and van der Waals contacts with the polar ring N atoms and non-polar D-Val side-chain atoms, respectively.

Animals↗

PubMed1994

Characteristic molecular packing in the crystal structure of tert-butoxycarbonyl-L-phenylalanyl-L-methionine methyl ester.

The molecular conformation and association of the peptide Boc-L-Phe-L-Met-OMe have been studied in the solid state by X-ray diffraction. The peptide crystallizes in the orthorhombic system, space group P2(1)2(1)2(1), with cell parameters of a = 9.821(2), b = 25.394(6), c = 28.714(8) A, V = 7161(3) A3. The structure has been solved by direct methods and refined to a final R of 0.079 for 5464 independent reflections with Fo > or = sigma(Fo). The crystal consists of three independent molecular conformations per asymmetric unit. Respective peptide backbones adopt an extended conformation with the side-chains of Phe and Met residues being arranged below and above the backbone chains. Contrary to the sheet structure most frequently observed in the crystal packing of the extended peptide conformations, three independent molecules lie spirally along the c-axis and form a pin-wheel-like crystal packing. The sheet structures formed by two of three independent molecules are almost at right angles to the backbone of the remaining molecule. This molecular packing mode would provide a possible interaction model between the intersecting beta-sheet structure and single-strand structure of polypeptide.

Amino Acid Sequence↗

PubMed1993

Cooperative face-to-face and edge-to-face aromatic interactions of tryptophan indole ring with N7-quarternized guanine and neutral cytosine bases.

In order to investigate the effect of cytosine base upon the stacking interaction of N7-quarternized guanine base with tryptophan indole ring, the X-ray crystal structure of a 1:1 complex of model compounds 1 and 2 was carried out. Contrary to the expectation of the interaction of both molecules in aqueous solution, the crystal structure showed the first example of the simultaneous recognition of the Trp indole ring by guanine and cytosine bases by the coupling of the face-to-face and edge-to-face aromatic interactions, respectively.

Cytosine↗

PubMed1993

Structure of Boc-Phe-D-Leu-Thr-OMe.

The X-ray crystal structure analysis shows that tert-butoxycarbonyl-L-phenylalanyl-D-leucine-L-threonine methyl ester takes an open conformation in which the tert-butoxycarbonyl group is located face-to-face with the D-leucine isobutyl side chain. In the crystal, the molecules, translated by twofold screw symmetry, form an infinite sheet structure through four independent hydrogen bonds.

Amino Acid Sequence↗

PubMed1993

Conformational difference between diastereomers of Dnp-Val-Aib-Gly-Leu-pNA studied by x-ray crystal analyses.

In order to investigate the conformational change of the alpha-aminoisobutyric acid (Aib) containing peptide by the D/L replacement of an amino acid residue, single crystals of two diastereomers, Dnp-L-Val-Aib-Gly-L-Leu-pNA (L-L isomer) and Dnp-D-Val-Aib-Gly-L-Leu-pNA (D-L isomer), were prepared from aqueous methanol solutions as CH3OH and CH3OH.H2O solvates, respectively, and were analyzed by the x-ray diffraction method. Molecular conformation of L-L isomer adopts consecutive two different types of beta-turns, a type II' beta-turn bent at Aib-Gly, and a type III beta-turn bent at Gly-Leu, stabilized by two intramolecular (Leu)NH...O = C(Val) and (pNA)NH...O = C(Aib) hydrogen bonds. In contrast, these two intramolecular hydrogen bonds lead the D-L isomer to a distorted 3(10)-helix conformation consisting of consecutive two type-III beta-turn of Aib-Gly-Leu sequence. The most significant structural difference between these diastereomers is the mutual orientation between the Dnp and pNA chromophores. While the extensive stacking of both the chromophores is intramolecularly formed for the folded conformation of L-L isomer, they are oriented toward an opposite direction in the open conformation of D-L isomer and are intermolecularly stacked with each other. The large separation between these diastereomers observed in the chromatography is discussed in the relation with their conformational differences.

Amino Acid Sequence↗

PubMed1993

Molecular conformation of patellamide A, a cytotoxic cyclic peptide from the ascidian Lissoclinum patella, by X-ray crystal analysis.

As part of a series of investigations into the conformational stability of a C2-symmetric or related cyclic peptide isolated from the ascidian Lissoclinum patella, the molecular conformation of patellamide A, the chemical structure of which deviates slightly for C2-symmetry, was determined by X-ray crystal analysis. Patellamide A took on a saddle-shaped rectangular form and wrapped around the water and methanol solvents. This conformation which is very similar to that of C2-symmetric ascidiacyclamide would be proposed as a possible candidate for biologically "active" conformation.

Animals↗