• Journal of Biomedical Engineering Research
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• v.43 no.2
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• pp.71-80
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• 2022

The interaction between dual-ligand decorated particle-based delivery system and target cell under shear flow is predicted using probability model developed. We assumed the two kinds of ligand are decorated on the surface of the particle with 10% length difference. Fixed with other biophysical parameters, a study on the particle-cell interaction for the different non-specific interaction parameter is performed. To induce the firm adhesion, short ligand-receptor should be engaged. Also, it is shown that the rational design of ligand-receptor interaction, including receptor number, specific interaction parameter, kinds of ligand-receptor, etc., should be considered.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.89-100
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• 2013

생물정보학의 다양한 이론적 내용과 계산적 방법들이 갈수록 전문화 되어짐에 따라 신약 개발, 신 물질 합성, 단백질의 구조 예측 등 다양한 분야에서 필요성이 커져가고 있다. 이 중 molecular docking 기술은 단백질과 특정 분자간의 결합 형태를 분자 모델링 기법을 통해 알아내는 방법이며 신약개발 연구에 큰 영향을 미치고 있다. Molecular docking을 통하여 분자간의 결합 형태를 예측하는 과정에서 Protein-ligand complex의 정확한 에너지 측정을 가능하게 하는 scoring function이 필요하다. 그런데 본 연구에서 사용한 B-Raf kinase protein 은 active site 부분에서 ligand와 receptor 간에 aromatic ring로 인한 ${\pi}-{\pi}$ interaction이 정확한 에너지 계산을 어렵게 한다. 이러한 ${\pi}-{\pi}$ interaction 부분의 에너지를 정확하게 계산하기 위해 양자역학 계산을 실시하였다. Active site 부분에서 ligand와 receptor에서 발생하는 각각 다른 5개의 ${\pi}-{\pi}$ interaction 구조를 준비하여 Gaussian을 통해 양자역학 에너지를 계산하였다. 그리고 이러한 결과 값들이 ligand의 활성 값과 어떤 상관관계를 갖는지 살펴보았다. 그 결과 ${\pi}-{\pi}$ interaction을 양자역학으로 계산한 값이 그렇지 않은 것보다 더 좋은 상관관계를 보여주었다. 이는 특별한 구조의 영향으로 ligand와 receptor 간의 결합에너지를 정확하게 계산하기 어려운 문제에서 양자역학을 적용할 경우 더욱 좋은 결과값을 얻을 수 있었다. 또한 이러한 데이터가 신 물질 개발이나 신약 개발 등의 다양한 분야에서 계산화학 방법이 신뢰성을 얻는데 도움 될 수 있다고 생각된다.

• Translational and Clinical Pharmacology
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• v.26 no.3
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• pp.115-117
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• 2018

This tutorial explains the basic principles of mechanistic ligand-receptor interaction model, which is an operational model of agonism. A growing number of agonist drugs, especially immune oncology drugs, is currently being developed. In this tutorial, time-dependent ordinary differential equation for simple $E_{max}$ operational model of agonism was derived step by step. The differential equation could be applied in a pharmacodynamic modeling software, such as NONMEM, for use in non-steady state experiments, in which experimental data are generated while the interaction between ligand and receptor changes over time. Making the most of the non-steady state experimental data would simplify the experimental processes, and furthermore allow us to identify more detailed kinetics of a potential drug. The operational model of agonism could be useful to predict the optimal dose for agonistic drugs from in vitro and in vivo animal pharmacology experiments at the very early phase of drug development.

• Bulletin of the Korean Chemical Society
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• v.18 no.9
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• pp.976-981
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• 1997

The magnetic susceptibilities of molybdenum ions with 4d1 electronic configuration in the octahedral crystal field were calculated on the basis of ligand field theory. The experimental magnetic susceptibilities for molybdenum ions, which are stabilized at the octahedral site in the perovskite lattice of Ba2ScMoⅤO6 and Sr2YMoⅤO6, were compared with the theoretical ones. We have tried to fit their temperature dependence of magnetic susceptibility with ligand field parameters, spin-orbit coupling constant ζSO, and orbital reduction parameter κ according to intermediate field coupling and strong field theory. Strong field coupling theory could not explain experimental curves without unrealistically large axial ligand field, since it ignores the mixing up between different state via spin-orbit interaction and ligand field. On the other hand, the intermediate field coupling theory could successfully reproduce experimental data in octahedral and trigonal ligand field. The fitting result demonstrates not only the fact that spin-orbit interaction is primarily responsible for the variation of magnetic behavior but also the fact that effective orbital overlap, enhanced by cubic crystal structure, reduces significantly orbital angular momentum as indicated by κ parameter.

• Journal of the Korean Chemical Society
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• v.36 no.6
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• pp.802-811
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• 1992

The conformations of several carbene-olefin-transition metal complexes[$(CO)_4M$-(CHX)olefin] (X: $OCH_3,\;NHCH_3,\;SCH_3$, M: C, Mo, W) have been studied by means of Extend Huckel calculations. In the case of $d^6$ transition metal octahedral complexes, it is shown that the two main factors which determine the optimal conformation are metal-to-ligand back-donation and direct ligand-ligand interaction at the metal, but the ligand-ligand interaction dominates the situation for a metal that is coordinated to $\pi$ acceptor ligands and to $\pi$ donor group on the carbene. The relative amounts of both factors depend strongly on the electronic nature of the ligands at the metal. The greater electron donating ability of nitrogen stabilizes amino-substituted carbene complexes compared with their alkoxyl substituted analogues. This interaction is optimal when the $\pi$ systems of the carbene and olefin are coplanar. The introduction of the $\pi$ donor group on the carbene carbon increases also the importance of the ligand-ligand interaction.

• YAKHAK HOEJI
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• v.60 no.2
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• pp.78-84
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• 2016

N-Phenylthiourea derivatives and catechol oxidase receptor complex was studied using molecular mechanics method. The starting structure was adopted from the protein databank and the calculation of energy minimization and molecular dynamics was performed with AMBER package. The molecular dynamics showed that the simulation time span of 20 ns was long enough to observe the interaction profile and stationary ligand-receptor configuration in the complex. The conformation of the ligand was related to the interaction to the receptor and the efficacy was also interpreted in this context.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.125-131
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• 2018

Chemical shift perturbation (CSP) is a simple NMR technique for studying binding of a protein to various ligands. CSP is the only technique that can directly provide both a value for the dissociation constant and a binding site from the same set of measurements. To accurately analyze the CSP data, the exact binding mode such as multiple binding, should be carefully considered. In this review, we analyzed systematically the CSP data with multiple modes. This analysis might provide insight into the mechanism on how proteins selectively recognize their target ligands to achieve the biological function.

• Journal of Biomedical Engineering Research
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• v.43 no.2
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• pp.94-101
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• 2022

Recent advancement of micro/nano technology enables the development of diverse micro/nano particle-based delivery systems. Due to the multi-functionality and engineerability, particle-based delivery system are expected to be a promising method for delivery to the target cell. Since the particle-based delivery system should be delivered to the various kinds of target cell, including the cardiovascular system, cancer cell etc., it is frequently decorated with multiple kinds of targeting molecule(s) to induce specific interaction to the target cell. The surface decorated molecules interact with the cell surface expressed molecule(s) to specifically form a firm adhesion. Thus, in this study, the probability of adhesion is estimated to predict the possibility to form a firm adhesion for the multi-ligand decorated particle-based delivery system.

• Bulletin of the Korean Chemical Society
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• v.26 no.3
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• pp.393-398
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• 2005

The stability constants for the diaza-18-crown-6 ethers 2-6 and alkali metal cations ($Na^+,\;K^+,\;Rb^+\;and\;Cs^+$) were determined using potentiometry in 95% methanol. For each metal ion the stability constants of the partiallyfluorinated ligands 3-6 were larger than that of the non-fluorinated ligand 2, which might reflect an interaction between fluorine atoms and alkali metal cations. The stability constant of the ligand 4 was larger than that of the ligand 5 for each metal cation tested. This finding was also supported by the results of cation-induced chemical shifts in $^1H-,\;^{19}F$-NMR and extraction experiment. The potentiometry and NMR results as well as the X-ray crystal structures revealed that the position and number of fluorine atoms in the benzyl side arms was crucial for the enhanced interaction between a ligand and an alkali metal.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.4-4
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• 2003

A large number of in-vitro experiments on the inhibition of kinases and pretenses are reported in literature, and compiled by ProLINT database. Using this powerful wealth of knowledge, we have carried our an analysis of ligand specificity of these two classes of proteins. Each of the pretenses and kinases included in the database has been assigned a consensus ligand fragment signature, based on the available information about its interaction with different ligands. A set of 43 fragments efficiently represent every ligand. We have then organized the consensus fragment signatures for every protein in form of a cluster-tree diagram. This tree is also constructed from other sequence, structure and physical considerations. Cluster-cluster comparison between these analyzes provide a valuable information about ligand specific interactions and similarities between proteins.