24 research outputs found

    Interactions of <i>B</i>/<i>C</i>-ring (A) and <i>D</i>-ring derivatives (B) with ERα LBD determined by molecular docking.

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    <p>The green dashes indicate the hydrogen bonds formed. All the structures are shown in ball and stick. The amino acids were colored according to the atom type, i.e. green for carbon, red for oxygen, blue for nitrogen and white for hydrogen. Among the amino acids in the binding site, only E353, R394 and H524 are shown in this figure. E<sub>2</sub> was colored in white. The ligands were shown in the following different colors: in <b>panel A</b>, 6α-OH-E<sub>2</sub> (yellow), 6β-OH-E<sub>2</sub> (orange), 6-keto-E<sub>2</sub> (pink), 6-dehydro-E<sub>2</sub> (red), 7-dehydro-E<sub>2</sub> (magenta), 9(11)-dehydro-E<sub>2</sub> (light blue), 11α-OH-E<sub>2</sub> (purple) and 11 β-OH-E<sub>2</sub> (green); in <b>panel B</b>, E<sub>1</sub> (magenta) estriol (16α-OH-E<sub>2</sub>) (yellow), 16β-OH-E<sub>2</sub> (orange), 16-keto-E<sub>2</sub> (pink), 17α-OH-E<sub>2</sub> (red), 15α-OH-E<sub>3</sub> (dark blue), 16α-OH-E<sub>1</sub> (light blue), 16-keto-E<sub>1</sub> (purple), 16α-OH-E<sub>2</sub>-17α (brown), 16β-OH-E<sub>2</sub>-17α (grey).</p

    The overlay of the ligand-binding domains (LBDs) of ERα and ERβ.

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    <p>The protein structures were shown in cartoon and colored green and magenta for ERα and ERβ, respectively. E<sub>2</sub> molecules were shown in stick and colored blue and red in ERα and ERβ LBD, respectively. α-Helixes and β-sheets in the ER LBDs are labeled according to references <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074615#pone.0074615-Brzozowski1" target="_blank">[14]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074615#pone.0074615-Shiau1" target="_blank">[16]</a>. Helix 2 structures are missing in both <i>X</i>-ray structures.</p

    Correlation of hydrogen bond length and log<i>RBA</i> of <i>A</i>-ring and <i>B</i>/<i>C</i>-ring derivatives.

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    <p>The hydrogen bond length data were shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074615#pone-0074615-t001" target="_blank"><b>Table 1</b></a>. The amino acids shown in the up right corner of each indicated that the hydrogen bonds were formed between 3-hydroxyl groups of the <i>A</i>-ring or <i>B</i>/<i>C</i>-ring derivatives and this specific amino acid in the binding pocket. The curve regression was performed according to the Inverse First Order equation y = y<sub>0</sub>+ a/x.</p

    The computed binding energy values (Δ<i>E</i><sub>binding</sub>) for the molecular docking study for the binding of myricetin, quercetin, chrysin or flavone with human COX I or COX II.

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    <p>The ligand-enzyme interaction energy value (Δ<i>E</i><sub>binding</sub>) was calculated using the following equation: Δ<i>E</i><sub>binding</sub> = <i>E</i><sub>complex</sub>−(<i>E</i><sub>COX</sub>+<i>E</i><sub>ligand</sub>), where <i>E</i><sub>complex</sub> was the potential energy for the complex of COX bound with the ligand, <i>E</i><sub>COX</sub> was the potential energy of the enzyme alone, and <i>E</i><sub>ligand</sub> was the potential energy for the ligand alone.</p

    Schematic depiction of the catalysis and inactivation mechanism of COX enzymes and their interaction with bioflavonoids.

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    <p>PPIX is for protoporphorin IX. Quercetin structure is shown as a representative bioactive bioflavonoid. Events in the peroxidase cycle are labeled with numbers to denote the sequence of occurrence.</p

    The 3-D QSAR/CoMFA color contour maps for COX I (A) and COX II (B).

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    <p>Note that quercetin was shown in the ball and stick format inside the field for demonstration. Oxygen, carbon, and hydrogen atoms are colored in red, gray, and blue, respectively. The contours of the steric maps are shown in yellow and green, and those of the electrostatic maps are shown in red and blue. Green contours indicate regions where a relatively bulkier substitution would increase the COX activity, whereas the yellow contours indicate areas where a bulkier substituent would decrease the COX activity. The red contours are regions where a negative-charged substitution likely would increase the COX activity whereas the blue contours showed areas where a negative-charged substitution would decrease the COX activity. Bioflavonoids with a higher ability to activate the COX enzymes are correlated with: (<b><i>i</i></b>) more bulkier substitute near green; (<b><i>ii</i></b>) less bulkier substitute near yellow; (<b><i>iii</i></b>) less negative charge near blue; and/or (<b><i>iv</i></b>) more negative charge near red. The figure in the lower panel shows the 90° rotation around the <i>x</i>-axis of the figure shown in the upper panel.</p

    Primers used in the site-directed mutagenesis study.

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    <p>The sequences that are changed for each of the mutant COX proteins developed in this study are marked with underlines.</p
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