• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3429-3443
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• 2013

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

• 대한약리학회지
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• 제20권2호
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• pp.23-34
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• 1984

실험적으로 명암주기 또는 암주기에 적응시킨 백서의 간뇌 homogenate에서 opiate receptor의 일중변동 유무를 검토하고, circadian rhythm에 영향을 미치는 것으로 알려진 수종 중추작용약물의 영향을 보고 저 7 group에서 4시간 간격으로 1일 6회 maximum $^3H-morphine$ binding을 측정하여 다음과 같은 성적을 얻었다. 1) L : D, 12 : 12에 적응시킨 대조군에서 maximum $^3H-morphine$ binding은 22시에 최고에 달하는 매우 유의한 일중변동을 보였고, 24시간 평균 $^3H-morphine$ binding치는 $0.45{\pm}0.03\;pmole/mg Protein이었다. 2) 지속적인 암적응을 시킨 D : D, 12 :12군에서 $^3H-morphine$ binding의 일중변동은 14시에 최하, 그리고 2시에 최고의 binding치를 보이는 만상성의 일주변동은 보였으며 대조군의 곡선과는 그 shape, Phase, 진폭, 최고 또는 최하 binding시기 및 24시간평균 opiate수용체의 수에 현저한 차이가 있었다. 3) 지속적인 암적응, reserpine, pargyline, imipramine, amphetamine 또는 chlorpromazine 처리는 opiate receptor의 일중변동을 변화시켰다. 4) 그러나 전 실험군에서 Kd치는 변동되지 않았다. 이상 실험성적으로 백서뇌내 opiate수용체의 일중변동은 수용체의 질적변동이 아닌 수적인변동에 의하고, 지속적인 암적응이나 circadian rhythm을 변동시키는 중추성 약물들이 opiate receptor의 일중변동을 변화시킬 수 있으며, 또한 동통을 포함하여 제종 진통제의 효과가 일중변동을 일으키는 것은 opiate receptor의 일중변동과 일정한 관계가 있을 것으로 추측하였다.

• Structural Engineering and Mechanics
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• 제8권5호
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• pp.491-504
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• 1999

The initiation of toppling is explored for a uniform stack of blocks that rotates slowly about its mid-base. As the stack passes through its vertical position ($\theta$=0), it is in free-fall rotation, and a critical inclination angle ${\theta}_c$ is reached at which the toppling stack "fails" or begins to crack or separate. For tall stacks (high aspect ratios), two modes of failure are hypothesized, for which the dynamic failure analyses are shown to correlate with experimental results. These block failure modes are similar to those observed for tall, toppling masonry structures with weak binding material between their brick or stone blocks.

• 한국염색가공학회지
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• 제2권2호
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• pp.33-38
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• 1990

Nitrocellulose [NC]-Poly(vinylamine) [PVAm] blended membranes with the change of amino group contents were prepared. The sorption and permeation of a mono-sulfonic acid dye, Orange II, in the membranes were investigated by the steady-state permeation method at $50^{\circ}C$ and pH 2.2. The results were discussed in the framework of dual sorption and diffusion theory. It was found that thesorption isotherms comprise a partition and two Langmuir type adsorption having similar binding constants. One of the latter sorption modes is due to unknown adsorption sites in NC and the other is due to the amino groups in PVAm. Apparent diffusion coefficients for collective P and L dye species, $D_P\; and D_L$, were obtained. Interpretation of $D_P$ values leads to two modes of partitions; one is such that dye is immobilized in NC and the other is the dissolution of the dye into the internal water phase.

• 한국정보디스플레이학회:학술대회논문집
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• 한국정보디스플레이학회 2003년도 International Meeting on Information Display
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• pp.1112-1117
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• 2003

Polarized Fourier transform infrared (IR) absorption is used to probe molecular conformation in a ferroelectric liquid crystal (FLC) during the reorientation induced by the external field. Spectra of planar aligned cells of FLC W314 are measured as functions of IR polarizer orientation and electric field applied to the FLC. The time evolution of the dichroism of the absorbance due to biphenyl core and alkyl tail molecular vibration modes, is observed. Static IR dichroism experiments show a W314 dichroism structure in which the principal axis of dielectric tensor from molecular core vibration are tilted further from the smectic layer normal than those of the tail. This structure indicates the effective binding site in which the molecules are confined in the Sm-C phase has, on average, "zig-zag" shape and this zig-zag binding site structure is rigidly maintained while the molecular axis rotates about the layer normal during field-induced switching.

• Journal of Industrial and Engineering Chemistry
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• 제67권
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• pp.293-300
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• 2018

Lipocalins are diverse group of small extracellular proteins found in various organisms. In this study, members of 10 non-homologous lipocalin-ligand crystal complex structures were remodeled using rigid and flexible ligand modes to validate the prediction efficiency of molecular docking simulation. The modeled ligand conformations indicated a high prediction accuracy in rigid ligand mode using cluster based analysis for most cases whereas the flexible ligand mode required further considerations such as ligand binding energy and RMSD for some cases. This in silico study is expected to serve as a platform in the screening of novel ligands against lipocalin family of proteins.

• Bulletin of the Korean Chemical Society
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• 제27권9호
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• pp.1445-1449
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• 2006

Molecular tweezers based on chenodeoxycholic acid bearing different lengths of arm were synthesized andtheir anion binding affinities were evaluated by $^1H$ NMR, isothermal calorimetric titration, and ESI mass spectrometry. Molecular tweezer 6 showed a high selectivity toward $H_2PO_4\;^-$ over $Cl^-,\;Br^-,\;I^-, $ and $CH_3CO_2\;^-$ by $^1H$ NMR titration, whereas the association constant for $F^-$ revealed the largest value as determined by ITC. The selectivity of 6 towards $F^-$ was about 103 times higher than that of $Cl^-,\;H_2PO_4\;^- $, and $CH_3CO_2\;^-$. ITCexperiment of 6 with $F^-$ in a DMSO showed two binding modes; two sequential association constants $K_1\;=\;2.77\;{\times}\;10^5\;M^{-1}$ and $K_2\;=\;8.68\;{\times}\;10^6\;M^{-1}$ were found. These sequential bindings were confirmed by ESI massspectrometry. 1 : 1 and 1 : 2 complexes of 6 and $F^-$ were found at m/z 868.08 and 884.04.

• Bulletin of the Korean Chemical Society
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• 제34권6호
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• pp.1673-1678
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• 2013

Lumazine protein is a member of the riboflavin synthase superfamily and the intense fluorescence is caused by non-covalently bound to 6,7-dimethyl 8-ribityllumazine. To figure out the binding modes and the structure of the N-terminal domain of lumazine protein, the wild type of protein extending to amino acid 118 (N-LumP 118 Wt) and mutants of N-LumP 118 V41W, S48W, T50W, D64W, and A66W from Photobacterium leiognathi were purified. The biochemical properties of the wild type and mutants of N-LumP 118 proteins were analyzed by absorbance and fluorescence spectroscope. The peak of absorbance and fluorescence of lumazine ligand were shifted to longer wavelength on binding to N-LumPs. The observed absorbance value at 410 nm of lumazine bound to N-LumP 118 proteins indicate that one mole of N-LumP 118 proteins bind to one mole of ligand of lumazine. Fluorescence analysis show that the maximum peak of fluorescence of N-LumP S48W was shifted to the longest wavelength by binding with 6,7-dimethyl 8-ribityllumazine and was shown to the greatest quench effect by acrylamide among all tryptophan mutants.

• Bulletin of the Korean Chemical Society
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• 제31권5호
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• pp.1314-1318
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• 2010

The $[Ru(tpy)_2]Cl_2$ (tpy:2,2':6',2"-terpyridine) complex was synthesized and its structure was confirmed by $^1H$-NMR and elemental analysis. Its binding mode toward DNA was compared with the well-known $[Ru(bpy)_3]Cl_2$ (bpy:2,2-bipyridyl), using isotropic absorption, linear dichroism(LD) spectroscopy, and an energy minimization study. Compared to $[Ru(bpy)_3]^{2+}$, the $[Ru(tpy)_2]^{2+}$ complex exhibited very little change in its absorption pattern, especially in the MLCT band, upon binding to DNA. Furthermore, upon DNA binding, both Ru(II) complexes induced a decrease in the LD magnitude in the DNA absorption region. The $[Ru(tpy)_2]^{2+}$ complex produced a strong positive LD signal in the ligand absorption region, which is in contrast with the $[Ru(bpy)_3]^{2+}$ complex. Observed spectral properties led to the conclusion that the interaction between the ligands and DNA bases is negligible for the $[Ru(tpy)_2]^{2+}$ complex, although it formed an adduct with DNA. This conclusion implies that both complexes bind to the surface of DNA, most likely to negatively charged phosphate groups via a simple electrostatic interaction, thereby orienting to exhibit the LD signal. The energy minimization calculation also supported this conclusion.

• Bulletin of the Korean Chemical Society
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• 제31권6호
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• pp.1615-1620
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• 2010

Bis-[dipyrido[3,2-$\alpha$:2',3'-c]phenazine)$_2$(1,10-phenanthroline)$_2Ru_2$]$^{2+}$ complexes (bis-Ru(II) complexes) tethered by linkers of various lengths were synthesized and their binding properties to DNA investigated by normal absorption and linear dichroism spectra, and fluorescence techniques in this study. Upon binding to DNA, the bis-Ru(II) complex with the longest linker (1,3-bis-(4-pyridyl)-propane), exhibited a negative $LD^r$ signal whose intensity was as large as that in the DNA absorption region, followed by a complicate $LD^r$ signal in the metal-to-ligand charge transfer region. The luminescence intensity of this bis-Ru(II) complex was enhanced. The observed $LD^r$ and luminescence results resembled that of the [Ru(1,10-phenanthroline)$_2$ dipyrido[3,2-$\alpha$:2',3'-c]phenazine]$^{2+}$ complex, whose dipyrido[3,2-$\alpha$:2',3'-c]phenazine (dppz) ligand has been known to intercalate between DNA bases. Hence, it is conclusive that both dppz ligands of the bis-Ru(II) complex intercalate. The binding stoichiometry, however, was a single intercalated dppz per ~ 2.3 bases, which violates the "nearest binding site exclusion" model for intercalation. The length between the two Ru(II) complexes may be barely long enough to accommodate one DNA base between the two dppz ligands, but not for two DNA bases. When the linker was shorter (4,4'-bipyridine or 1,2-bis-(4-pyridyl)-ethane), the magnitude of the LD in the dppz absorption region, as well as the luminescence intensity of both bis-Ru(II) complexes, was half that of the bis-Ru(II) complex bearing a long linker. This observation can be elucidated by a model whereby one of the dppz ligands intercalates while the other is exposed to the aqueous environment.