• Bulletin of the Korean Chemical Society
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• v.35 no.1
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• pp.250-252
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• 2014

Lipoprotein-associated phospholipase A2 (Lp-$PLA_2$) is a crucial enzyme in atherosclerosis as a potential drug target. The most remarkable Lp-$PLA_2$ inhibitory drug is Darapladib. We determined the binding pose of Darapladib to Lp-$PLA_2$ through docking study. Darapladib formed two hydrogen bonding interactions with the side chain of Tyr160 and Gln352 and several pi-pi interactions with aromatic and aliphatic hydrophobic residues of Lp-$PLA_2$. It is known that the dietylpropan-amine moiety of Darapladib has influence on the improvement of its oral bioavailability and we supposed this in our docking results.

• Journal of the Korean Chemical Society
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• v.63 no.1
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• pp.29-36
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• 2019

A potentially tetradentate Schiff base ligand, 2-((2-((pyridin-2-ylmethylene)amino)ethyl)amino)ethan-1-ol (PMAE), and its cadmium(II) complex, [$Cd(PMAE)I_2$] (1), were prepared and characterized by elemental analysis, FT-IR, Raman, $^1H$ and $^{13}C$ NMR spectroscopies and single-crystal X-ray diffraction. In the crystal structure of 1, the cadmium atom has a slightly distorted square-pyramidal geometry and a $CdN_3I_2$ environment in which the PMAE acts as an $N_3$-donor. In the crystal packing of the complex, the alcohol and amine groups of the coordinated ligands participate in hydrogen bonding with iodide ions and form $R^2{_2}(14)$ and $R^2{_2}(8)$ hydrogen bond motifs, respectively. In addition to the hydrogen bonds, the crystal network is stabilized by ${\pi}-{\pi}$ stacking interactions between pyridine rings. The thermodynamic stability of the isolated ligand and its cadmium complex along with their charge distribution patterns were studied by DFT and NBO analysis.

• Journal of the Korean Magnetic Resonance Society
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• v.26 no.4
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• pp.46-50
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• 2022

Antifreeze proteins (AFPs) bind to the ice crystals and then are able to inhibit the freezing of body fluid at subzero temperatures. Type III AFPs are categorized into three subgroups, QAE1, QAE2, and SP isoforms, based on differences in their isoelectric points. We prepared the QAE2 (AFP11) and SP (AFP6) isoforms of the notched-fin eelpout AFP and their mutant constructs and determined their temperature gradients of amide proton chemical shifts (𝚫δ/𝚫T) using NMR. The nfeAFP11 (QAE2) has the distinct 𝚫δ/𝚫T pattern of the first 3₁₀ helix compared to the QAE1 isoforms. The nfeAFP6 (SP) has the deviated 𝚫δ/𝚫T values of many residues, indicating its backbone conformational distortion. The study suggests the distortion in the H-bonding interactions and backbone conformation that is important for TH activities.

• Advances in nano research
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• v.12 no.3
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• pp.291-300
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• 2022

The behavior of hydrogen species on the surface of the catalyst during the Lewis acid transformation to form Brønsted acid sites over the spherical silica-supported WO_x catalyst was investigated. To understand the structure-activity relationship of Lewis acid transformation and hydrogen bonding interactions, we explore the potential of using the in situ diffuse reflection infrared Fourier transform spectroscopy (DRIFTS) with adsorbed ammonia and hydrogen exposure. From the results of in situ DRIFTS measurements, Lewis acid sites on surface catalysts were transformed into new Brønsted acid sites upon hydrogen exposure. The adsorbed NH₃ on Lewis acid sites migrated to Brønsted acid sites forming NH⁴⁺. The results show that the dissociated H atoms present on the catalyst surface formed new Si-OH hydroxyl species - the new Brønsted acid site. Besides, the isolated Si-O-W species is the key towards H-bond and Si-OH formation. Additionally, the H atoms adsorbed surrounding the Si-O-W species of mono-oxo O=WO₄ and di-oxo (O=)₂WO₂ species, where the Si-O-W species are the main species presented on the Inc-SSP catalysts than that of the IWI-SSP catalysts.

• BMB Reports
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• v.45 no.8
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• pp.476-481
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• 2012

Flavodoxin (Fld) has been demonstrated to bind to ferredoxin-NADP$^+$ reductase A (FprA) in Pseudomonas putida. Two residues ($Phe^{256}$, $Lys^{259}$) of FprA are likely to be important for interacting with Fld based on homology modeling. Site-directed mutagenesis and pH-dependent enzyme kinetics were performed to further examine the role of these residues. The catalytic efficiencies of FprA-$Ala^{259}$ and FprA-$Asp^{259}$ proteins were two-fold lower than those of the wild-type FprA. Homology modeling also strongly suggested that these two residues are important for electron transfer. Thermodynamic properties such as entropy, enthalpy, and heat capacity changes of FprA-$Ala^{259}$ and FprA-$Asp^{259}$ were examined by isothermal titration calorimetry. We demonstrated, for the first time, that $Phe^{256}$ and $Lys^{259}$ are critical residues for the interaction between FprA and Fld. Van der Waals interactions and hydrogen bonding were also more important than ionic interactions for forming the FprA-Fld complex.

• Textile Coloration and Finishing
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• v.30 no.2
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• pp.63-69
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• 2018

In this study, we report on successful attempt towards the synthesis of sulfur self-doped $g-C_3N_4$ by directly heating thiourea in air. The synthesized materials were characterized using UV-vis spectral technique, FT-IR, XRD and TEM analysis. Further, the obtained material shows an excellent detection of carcinogenic TNP(Tri nitro phenol) in the presence of 10-fold excess of various other common interferences. The strong inner filter effect and molecular interactions(electrostatic, ${\pi}-{\pi}$, and hydrogen bonding interactions) between TNP and the $S-g-C_3N_4$ Nano sheets led to the fluorescence quenching of the $S-g-C_3N_4$ Nano sheets with an excellent selectivity and sensitivity towards TNP compared to that of other nitro aromatics under optimal conditions and the detection limit calculated was found to be 6.324 nM for TNP. The synthesized nanocomposite provides a promising platform for the development of sensors with improved reproducibility and stability for ultra-sensitive and selective sensing of TNP.

• Natural Product Sciences
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• v.24 no.2
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• pp.88-92
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• 2018

The present study was undertaken to investigate the isolated compounds from the stem bark of Garcinia atroviridis as potential cholinesterase inhibitors and the ligand-enzyme interactions of selected bioactive compounds in silico. The in vitro cholinesterase results showed that quercetin (3) was the most active AChE inhibitor ($12.65{\pm}1.57{\mu}g/ml$) while garcinexanthone G (6) was the most active BChE inhibitor ($18.86{\pm}2.41{\mu}g/ml$). It is noteworthy to note that compound 6 was a selective inhibitor with the selectivity index of 11.82. Molecular insight from docking interaction further substantiate that orientation of compound 6 in the catalytic site which enhanced its binding affinity as compared to other xanthones. The nature of protein-ligand interactions of compound 6 is mainly hydrogen bonding, and the hydroxyl group of compound 6 at C-10 is vital in BChE inhibition activity. Therefore, compound 6 is a notable lead for further drug design and development of BChE selective inhibitor.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2603-2608
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• 2012

A novel mononuclear supramolecule of copper(II) has been synthesized with Ippyt ligand (Ippyt=3-(4'-imidazole phenyl)-5-(pyrid-2''-yl)-1,2,4-triazole) (1). Compound 1, namely [$Cu(Ippyt)_2(H_2O)_2$], has been characterized by single-crystal X-ray diffraction, IR spectrum, elemental analysis and thermogravimetric analysis. Structure determination reveals that the elongated-octahedral geometry is formed in the vicinity of the copper (II) atom being coordinated by four nitrogen atoms from two Ippyt ligands occupying the equatorial position and two oxygen atoms from two coordinated water molecules in the axial position, which together form the $N_4O_2$ donor set. Hydrogen bonding interactions between nitrogen and oxygen atoms result in the set up of a supramolecular network architecture. Biological properties including antibacterial activity and superoxide dismutase (SOD) mimetic activity of compound 1 have been investigated by agar diffusion method and the modified Marklund method, respectively. The results indicate that compound 1 exhibits a stronger antibacterial efficiency than the parent ligand and it also has a certain radical-scavenging activity.

• Bulletin of the Korean Chemical Society
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• v.30 no.9
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• pp.2083-2086
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• 2009

Human vascular endothelial growth factor receptor 2 (hVEGFR2) is an important signaling protein involved in angiogenesis and attractive drug target in cancer therapy. It has been reported that flavonols, a class of flavonoids, have anti-angiogenic activity in various cancer cell lines. We performed receptor-oriented pharmacophore based in silico screening for identification of hVEGFR2 inhibitors from flavonol database. By comparing with three X-ray complex structures of hVEGFR2 and its inhibitors, we evaluated the specific interactions between inhibitors and receptors and determined a single pharmacophore map. This map consisted of four features, a hydrogen bonding acceptor (HBA) on Cys917, two hydrogen bonding donors on Glu917 (HBD1) and Glu883 (HBD2), and one hydrophobic interaction (Lipo) with Val846, Ala864, Val897, Val914 and Phe1045 of hVEGFR2. Using this map, we searched a flavonol database including 9 typical flavonols and proposed that five flavonols, kaempferol, quercetin, fisetin, morin, and rhamnetin can be potent inhibitors of hVEGFR2. 3-OH of C-ring and 4’-OH of B-ring of flavonols are the essential features for hVEGFR2 inhibition. This study will be helpful for understanding the mechanism of inhibition of hVEGFR2 by natural products.

• 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.