• Bulletin of the Korean Chemical Society
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• 제14권4호
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• Molecules and Cells
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• 제42권10호
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• pp.721-728
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• 2019

Non-structural protein 1 (NS1) of influenza virus has been shown to inhibit the innate immune response by blocking the induction of interferon (IFN). In this study, we isolated two single-stranded RNA aptamers specific to NS1 with $K_d$ values of $1.62{\pm}0.30nM$ and $1.97{\pm}0.27nM$, respectively, using a systematic evolution of ligand by exponential enrichment (SELEX) procedure. The selected aptamers were able to inhibit the interaction of NS1 with tripartite motif-containing protein 25 (TRIM25), and suppression of NS1 enabled retinoic acid inducible gene I (RIG-I) to be ubiquitinated regularly by TRIM25. Additional luciferase reporter assay and quantitative real-time PCR (RT-PCR) experiments demonstrated that suppression of NS1 by the selected aptamers induced IFN production. It is noted that viral replication was also inhibited through IFN induction in the presence of the selected aptamers. These results suggest that the isolated aptamers are strongly expected to be new therapeutic agents against influenza infection.

• 통합자연과학논문집
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• 제5권1호
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• pp.32-37
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• 2012

Chemokine receptor antagonists have potential applications in field of drug discovery. Although the chemokine receptors are G-protein-coupled receptors, their cognate ligands are small proteins (8 to 12 kDa), and so inhibiting the ligand/receptor interaction has been challenging. The application of structure-based in-silico methods to drug discovery is still considered a major challenge, especially when the x-ray structure of the target protein is unknown. Such is the case with human CCR2 and CCR5, the most important members of the chemokine receptor family and also a potential drug target. Herein, we review the success stories of combined receptor modeling/mutagenesis approach to probe the allosteric nature of chemokine receptor binding by small molecule antagonists for CCR2 and CCR5 using Rhodopsin as template. We also urged the importance of recently available ${\beta}2$-andrenergic receptor as an alternate template to guide mutagenesis. The results demonstrate the usefulness and robustness of in-silico 3D models. These models could also be useful for the design of novel and potent CCR2 and CCR5 antagonists using structure based drug design.

• 통합자연과학논문집
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• 제5권1호
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• pp.22-26
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• 2012

Chemokine receptor antagonists have potential applications in field of drug discovery. Although the chemokine receptors are G-protein-coupled receptors, their cognate ligands are small proteins (8 to 12 kDa), and so inhibiting the ligand/receptor interaction has been challenging. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, targeting both CCR2 and CCR5 could be a useful strategy. Because of the importance of these receptors, providing information regarding the binding site is of prime importance. Herein, we report the comparison of CCR2 of CCR5 binding sites both sequentially as well as structurally. We also urged the importance of crucial residues in the binding site, to facilitate the development of dual antagonists targeting both the receptors. These results could also be useful for the design of novel and potent dual CCR2 and CCR5 antagonists using structure based drug design.

• Natural Product Sciences
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• 제25권3호
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• pp.215-221
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• 2019

Inflammation is the crucial biological process of immune system which acts as body's defense and protective response against the injuries or infection. However, the systemic inflammation devotes the adverse effects such as multiple inflammation associated diseases. One of the best ways to treat this entity is by blocking the tumor necrosis factor alpha ($TNF-{\alpha}$) and TNF-related apoptosis-inducing ligand (TRAIL) to avoid the proinflammation cytokines production. Thus, this study aims to evaluate the potency of Sambucus bioactive compounds as anti-inflammation through in silico approach. In order to assess that, molecular docking was performed to evaluate the interaction properties between the $TNF-{\alpha}$ or TRAIL with the ligands. The 2D structure of ligands were retrieved online via PubChem and the 3D protein modeling was done by using SWISS Model. The prediction results of the study showed that caffeic acid (-6.4 kcal/mol) and homovanillic acid (-6.6 kcal/mol) have the greatest binding affinity against the $TNF-{\alpha}$ and TRAIL respectively. This evidence suggests that caffeic acid and homovanillic acid may potent as anti-inflammatory agent against the inflammation associated diseases. Finally, this study needs further examination and evaluation to validate the potency of Sambucus bioactive compounds.

• 분석과학
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• 제19권1호
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• pp.9-17
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• 2006

생체 물질의 농도, 두께 및 특정 생체 물질의 분석을 위한 반응 속도론적 자료를 검출하는 능력 그리고 antigen/antibody, ligand/receptor, protein/protein 및 DNA/DNA 상호작용을 포함하는 다양한 생체물질간의 상호작용에 대한 분석에 적용되고, 자연 환경중 오염물질의 분석 등 다양하게 적용되는 표면 플라즈몬 공명 센서를 제작하였다. 또한 표면 플라즈몬 공명 센서를 제어하고 검출기로부터의 데이타(data)를 personal computer로 받아들이기 위해 data acquisition board를 이용하여 LabVIEW program을 만들었다.

• IMMUNE NETWORK
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• 제24권4호
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• pp.24.1-24.8
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• 2024

Complement C5a receptor (C5aR) signaling in immune cells has various functions, inducing inflammatory or anti-inflammatory responses based on the type of ligand present. The Co1 peptide (SFHQLPARSRPLP) has been reported to activate C5aR signaling in dendritic cells. We investigated the effect of C5aR signaling via the Co1 peptide on macrophages. In peritoneal macrophages, the interaction between C5aR and the Co1 peptide activated the mTOR pathway, resulting in the production of pro-inflammatory cytokines. Considering the close associations of mTOR signaling with IL-6 and TNF-α in macrophage training, our findings indicate that the Co1 peptide amplifies β-glucan-induced trained immunity. Overall, this research highlights a previously underappreciated aspect of C5aR signaling in trained immunity, and posits that the Co1 peptide is a potentially effective immunomodulator for enhancing trained immunity.

• Journal of Microbiology and Biotechnology
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• 제22권3호
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• pp.378-384
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• 2012

In aquatic invertebrates, particularly marine gastropods, organotin compounds induce irreversible sexual abnormality in females, which is termed imposex, at very low concentrations. Organotin compounds are agonists for nuclear receptors such as RXRs and $PPAR{\gamma}$. However, the imposex phenomenon has not been reported to act as an antagonist on estrogen receptors in other species, including vertebrates and invertebrates. In order to gain insights into the antagonistic activity of organotin compounds on estrogen receptors (ERs), we examined the inhibitive effect of these compounds on estradiol-dependent ${\beta}$-galactosidase activity using the yeast two-hybrid detection system consisting of a combination of the human estrogen receptor ($hER{\beta}$) ligand-binding domain and the co-activator steroid receptor co-activator-1 (SRC1). Tributyltin-hydroxide (TBT-OH) and triphenyltin-chlorine (TPT-Cl) exhibited an inhibitive effect on $E_2$-dependent transcriptional activity, similar to antagonistic chemicals such as 4-hydroxytamoxifen (OHT) or ICI 182,780, at a very low concentration of $10^{-14}$ M TBT or $10^{-10}$ M TPT, respectively. The yeast growth and transcriptional activity with transcriptional factor GAL4 did not exhibit any effect at the tested concentration of TBT or TPT. Moreover, the yeast two-hybrid system using the interaction between p53 and the T antigen of SV40 large did not describe any effect at the tested concentration of OHT or ICI 182,780. However, the interaction between p53 and T antigen was inhibited at a TBT or TPT concentration of $10^{-9}$ M, respectively. These results indicate that TBT and TPT act as inhibitors of ER-dependent reporter gene transcriptional activation and of the interaction between $hER{\beta}$ LBD and the co-activator SRC1 in the yeast two-hybrid system. Consequently, our data could partly explain the occurrence of organotin compound-induced imposex on the endocrine system of mammals, including humans.

• 분석과학
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• 제12권5호
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• pp.421-427
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• 1999

메탄올에 녹인 $Co(NCS)_2$와 클로로포름에 녹인 bbpe (1,2-bis(2,2'-bipyridyl-6-yl)ethane)를 서로 확산시켜 시간에 따라 비율이 다른 두 가지 형태의 결정을 단리하였다. 두 결정은 X-ray 결정학, 원소분석, IR 및 열분석에 의해 $trans-Co^{II}(NCS)_2(bbpe)$와 $trans-Co^{II}(NCS)_2(bbpe){\cdot}2CHCl_3$로 확인되었다. 용매화 차이만 있을 뿐 두 결정의 근본 구조는 bbpe 리간드가 사배위자로 코발트 원자에 배위하고 있는 유사한 구조로 판명되었다. 코발트 원자 주위는 두 개의 NCS기가 서로 trans에 위치하고 있고 모든 배위자가 원자로 이루어져 있는 전형적인 팔면체를 이루고 있다. 유연성 있는 리간드 구조 때문에 먼저 $trans-Co^{II}(NCS)_2(bbpe)$이 형성되고 결국은 $trans-Co^{II}(NCS)_2(bbpe){\cdot}2CHCl_3$로 변환되는 것으로 생각된다. 열역학적으로 안정한 용매화된 결정은 NCS 기의 S원자와 클로로포름의 Cl원자의 약한 작용 때문인 것으로 해석된다. 따라서 본 시스템의 결정모양과 색이 클로로포름에 매우 민감한 물질이다.

• 대한화학회지
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• 제54권6호
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• pp.687-695
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• 2010

L이 urea, acetamide, semicrabazide, formamide 인 thiocyanato (L) Cobaloxime 착물을 합성하고 특성을 규명하였다. Thiocyanato(L)cobaloximes (SCNCo$(DH)_2$(L))과 benzyl (aquo) cobaloxime $PhCH_2Co(DH)_2(OH_2)$를 반응시켜 일반 분자식 $PhCH_2Co(DH)_2SCNCo(DH_2)(L)$를 갖는 일련의 thiocyanato로 연결된 dicobaloximes 생성물을 얻었다. Thiocyanato 리간드의 다리결합을 포함하고 있는 dicobaloximes의 조성에 대한 증거로 말단의 thiocyanocobaloxime (SCNCo$(DH)_2$(L))으로부터 dicobaloxime이 형성되면서 vCN이 $20-45cm^{-1}$ 증가하게 되는 적외선 데이터를 들 수 있다. 이러한 두 일련의 물질에 대한 더많은 특성을 ($^1H$, $^{13}C$) NMR, LCMS 및 원소분석을 통하여 확인하였다. Thiocyanato (L) cobaloximes 및 thiocyanato로 연결된 dicobaloxime의 항균 활성은 E. Coli에 의해 조사하였다. 두 단량체와 이합체 모두의 DNA-결합 행동은 분광학적 방법 및 점성도 측정을 통하여 조사하였다. 그 결과 이합체 착물은 calf-thymus DNA와 DNA의 염기쌍에 말단의 벤질 고리를 통해 사이에 끼인 형태로 결합되어 있음을 나타내었다. 단량체 착물은 DNA와 상호작용하지 않는 것으로 관찰되었다.