• Bulletin of the Korean Chemical Society
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• v.34 no.9
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• pp.2629-2634
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• 2013

Fisetin is a naturally occurring flavonoid with some anti-cancer and anti-inflammation capabilities. In this study, we perform docking studies between human c-Jun N-terminal kinase 1 (JNK 1) and fisetin and proposed a binding model of fisetin and JNK 1, in which the hydroxyl groups of the B ring and oxygen at the 4-position of the C ring play key roles in binding interactions with JNK. Fluorescence quenching and saturation-transfer difference (STD) NMR experiments showed that fisetin exhibits good binding affinity to JNK, $1.32{\times}10^8M^{-1}$. The anti-inflammatory activity of fisetin was also investigated. Fisetin significantly suppressed tumor necrosis factor, the NO production, and macrophage inflammatory cytokine release in LPS-stimulated RAW264.7 mouse macrophages. We found that the anti-inflammatory cascade of fisetin was mediated through the JNK, and cyclooxygenase (COX)-2 pathways. Our findings suggest the potential of fisetin as an anti-inflammatory agent.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.728-730
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• 2003

Bond lengths, harmonic vibrational frequencies and dissociation energies of TlAt are calculated at ab initio molecular orbital and density functional theory using effective spin-orbit operator and relativistic effective core potentials. Spin-orbit effects estimated from density functional theory are in good agreement with those from ab initio calculations, implying that density functional theory with effective core potentials can be an efficient and reliable methods for spin-orbit interactions. The estimated $R_e$, $ω_e$ and $D_e$ values are 2.937 ${\AA}$, 120 $cm^{-1}$, 1.96 eV for TlAt. Spin-orbit effects generally cause the bond contraction in Group 13 elements and the bond elongation in the Group 17 elements, and spin-orbit effects on Re of TlAt are almost cancelled out. The spinorbit effects on $D_e$ of TlAt are roughly the sum of spin-orbit effects on $D_e$ of the corresponding element hydrides. Electron correlations and spin-orbit effects are almost additive in the TlAt molecule.

• BMB Reports
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• v.49 no.3
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• pp.159-166
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• 2016

Several members of tumor necrosis factor receptor (TNFR) superfamily that these members activate caspase-8 from death-inducing signaling complex (DISC) in TNF ligand-receptor signal transduction have been identified. In the extrinsic pathway, apoptotic signal transduction is induced in death domain (DD) superfamily; it consists of a hexahelical bundle that contains 80 amino acids. The DD superfamily includes about 100 members that belong to four subfamilies: death domain (DD), caspase recruitment domain (CARD), pyrin domain (PYD), and death effector domain (DED). This superfamily contains key building blocks: with these blocks, multimeric complexes are formed through homotypic interactions. Furthermore, each DD-binding event occurs exclusively. The DD superfamily regulates the balance between death and survival of cells. In this study, the structures, functions, and unique features of DD superfamily members are compared with their complexes. By elucidating structural insights of DD superfamily members, we investigate the interaction mechanisms of DD domains; these domains are involved in TNF ligand-receptor signaling. These DD superfamily members play a pivotal role in the development of more specific treatments of cancer.

• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.637-647
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• 2016

Proliferating cell nuclear antigen (PCNA) is a critical eukaryotic replication accessory factor that supports DNA binding in DNA processing, such as DNA replication, repair, and recombination. PCNA consists of three toroidal-shaped monomers that encircle double-stranded DNA. The diverse functions of PCNA may be regulated by its interactions with partner proteins. Many of the PCNA partner proteins generally have a conserved PCNA-interacting peptide (PIP) motif, located at the N- or C- terminal region. The PIP motif forms a 3₁₀ helix that enters into the hydrophobic groove produced by an interdomain-connecting loop, a central loop, and a C-terminal tail in the PCNA. Post-translational modification of PCNA also plays a critical role in regulation of its function and binding partner proteins. Structural and biochemical studies of PCNA-protein will be useful in designing therapeutic agents, as well as estimating the outcome of anticancer drug development. This review summarizes the characterization of eukaryotic PCNA in relation to the protein structures, functions, and modifications, and interaction with proteins.

• Journal of Integrative Natural Science
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• v.8 no.3
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• pp.209-213
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• 2015

Influenza A virus (H1N1) causes and spreads infectious diseases and becomes a major health threat in humans. Among the subtypes of influenza virus, neuraminidase (NA) plays an important role in viral life cycle and becomes an attractive therapeutic target. Currently two NA inhibitors namely Zanamivir and Oseltamivir are available for treating infectious diseases. Recently five naturally derived polyphenols extracted from Phellinus baumii was reported as inhibitors against NA. Molecular docking is powerful tool in computer aided drug designing which aids in exploring and elucidating the properties of the molecules from their 3D structure. Hence, in the present study, molecular docking was carried out on reported polyphenols isolated from ethanolic extract of fruiting bodies of Phellinus baumii. The objective of this work was to study the interaction and to propose the binding mode of these compounds within the binding site of H1N1 neuraminidase. The results showed these compounds had better binding energy and H-bond interactions with the important active site residues of the receptor which authenticate these compounds contributes to inhibitory activity of neuraminidase to treat influenza infection.

• Bulletin of the Korean Chemical Society
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• v.35 no.11
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• pp.3169-3174
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• 2014

Numerous studies have examined the role of flavonoids in modulating inflammatory responses in vitro. In this study, we found a novel flavonoid, 3,6,3'-trihydroxyflavone (1), with anti-inflammatory effects. Anti-inflammatory activity and mechanism of action were examined in mouse macrophages stimulated with lipopolysaccharide (LPS). Our results showed that the anti-inflammatory effects of 1 are mediated via p38 mitogen-activated protein kinase (p38 MAPK), Jun-N terminal kinase (JNK), and the extracellular-signal-regulated kinase (ERK) pathway in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Binding studies revealed that 1 had a high binding affinity to JNK1 ($1.568{\times}10^8M^{-1}$) and that the 3- and 6-hydroxyl groups of the C-ring and A-ring of 1 participated in hydrogen bonding interactions with the side chains of Asn114 and Lys55, respectively. The oxygen at the 3' position of the B-ring formed a hydrogen bond with side chain of Met111. Therefore, 1 could be a potential inhibitor of JNKs, with potent anti-inflammatory activity.

• Journal of Life Science
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• v.9 no.1
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• pp.76-83
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• 1999

Mammalial expression vectors containing GRP94, BiP, ERp72, and PDI, were introduced into FRTL5 cells. Transfected cells were selected by neomycin resistance for exogenously overexpressed proteins in the ER. The use of a reducible cross-linker, DSP, markedly improved the ability to detect noncovalent interactions of PDI, BiP and GRP94 with newly-synthesized thyroglobulin. Under normal conditions, GRP94 was found to associate transiently with early Tg folding intermediates, displaying interaction kinetics similar to those reported for another ER chaperones of BiP.

• IMMUNE NETWORK
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• v.15 no.1
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• pp.44-49
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• 2015

Interactions between microbes and epithelial cells in the gastrointestinal tract are closely associated with regulation of intestinal mucosal immune responses. Recent studies have highlighted the modulation of mucosal immunity by microbe-derived molecules such as ATP and short-chain fatty acids. In this study, we undertook to characterize the expression of the ATP-gated $P2X_7$ receptor ($P2X_7R$) on M cells and its role in gastrointestinal mucosal immune regulation because it was poorly characterized in Peyer's patches, although purinergic signaling via $P2X_7R$ and luminal ATP have been considered to play an important role in the gastrointestinal tract. Here, we present the first report on the expression of $P2X_7R$ on M cells and characterize the role of $P2X_7R$ in immune enhancement by ATP or LL-37.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2723-2728
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• 2009

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-($\alpha$-D-Man)-$\alpha$-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the $\omega$ angle transition; another minor transition is due to the $\psi$ angle transition of $\alpha$ (1 $\rightarrow$ 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega ($\omega$) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.

• Bulletin of the Korean Chemical Society
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• v.14 no.5
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• pp.583-588
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• 1993

Encapsulation capacities $(V_{gas})$ of, $H_2,\;N_2,\;CO,\;CH_4$ and CO, for $Cs_{2.5}Na_{9.5}-A (C_s-A)$ and $Na_{12}$-A (Na-A) zeolites have been measured in order to understand the effect of molecular properties on the $V_{gas}$. With appropriate number of large blocking cations on the main windows of cavities in zeolite A, gas molecules can be encapsulated in both the ${\alpha}$ -and ${\beta}$-cages, resulting in much large $V_{gas}.\;V_{gas}$ is proportional to the encapsulation pressure (Pe) and is also dependent on the molecular properties of encapsulated gases themselves, especially on intermolecular forces originated from the quadrupole moments of molecules in the molecular-dimensioned cavities of zeolite A. At the low range of Pe, molecules with larger $V_{gas}$ and intermolecular forces apparently have smaller increasing tendencies of $V_{gas}$ upon increases in Pe, showing a linear relationship between the tendencies and intermolecular forces rather than their sizes. Interactions between encapsulated molecules of $CH_4$ and framework of Cs-A have been estimated and they seem to depend on the number of encapsulated molecules per unit cell. On the basis of calculated density of $CO_2$, presence of liquid-like phase for the encapsulated molecules in the molecular dimensioned cavities of zeolite A is postulated.