• 통합자연과학논문집
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• 제5권4호
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• pp.216-219
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• 2012

Structure-based drug design possibly benefit from in silico methods that precisely predict the binding affinity of small molecules to target macromolecules. There are many limitations arise from the difficulty of predicting the binding affinity of a small molecule to a biological target with the current scoring functions. There is thus a strong interest in novel methodologies based on MD simulations that claim predictions of greater accuracy than current scoring functions, helpful for a regular use designed for drug discovery in the pharmaceutical industry. Herein, we report a short review on free energy calculations using MMPBSA method a useful method in structure based drug discovery.

• 대한의생명과학회지
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• 제13권2호
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• pp.127-133
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• 2007

Heterotrimeric GTP binding proteins (G proteins) mediate signal generated by neurotransmitter and hormones. Among all G proteins, Go is the most abundant in brain but its role in brain is not clearly understood. To determine the function of the alpha subunit of Go (Go$\alpha$), we search for the interacting partner of Go$\alpha$ in brain using yeast two-hybrid system. A resistant to inhibitor of cholinesterase (Ric-8B) was identified as a Go$\alpha$ interacting protein. We confirmed interaction between Go$\alpha$ and Ric-8b employing in vitro affinity binding assay and showed that the Ric-8b increased the function of Go$\alpha$. Our findings indicate that Ric-8b is possible guanine nucleotide exchange factor for Go$\alpha$.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2013년도 제44회 동계 정기학술대회 초록집
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• pp.84-84
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• 2013

FcBP consisting of 13 amino acids specifically binds to Immunoglobulin G Fc domain. Initially, we utilized this peptide for preparation of antibody chip as a PEG composite for enhanced solubility. After then, the peptide conjugate was immobilized on agarose resin, resulting in highly efficient affinity column for antibody purification. The efficiency was comparable to commercial Protein A column. Recently, this peptide was conjugated with cell penetratingpeptide (CPP) on a backbone of GFP, affording antibody transducer, which carries antibody into live cells by simple mixing of antibody and the transducer in cell culture media. Antibody transduction into cells was monitored by live cell imaging. More recently, the FcBP was fused to ferritin cage, which consists of 24 ferritin protein molecules. The FcBP-ferritin cage showed greatly increased binding affinity to human IgG. Its binding was analyzed by QCM and SPR analysis. Finally, it was selectively delivered by Herceptin to SKBR3, a breast cancer cell, over MCF10A, non-tumorigenic cells.

• Bulletin of the Korean Chemical Society
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• 제34권3호
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• pp.749-752
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• 2013

Trehalose-tethered monomeric and dimeric berberines were synthesized in 50% and 30% from the reaction of berberrubine with 6-tosyl-${\alpha}$,${\alpha}^{\prime}$-trehalose and 6,6'-ditosyl-${\alpha}$,${\alpha}^{\prime}$-trehalose, respectively, and fully characterized by MS (HR and ESI) and NMR ($^1H$, $^{13}C$, COSY and HSQC). Spectrophotometric and spectrofluorimetric titrations indicated that compared with berberine, trehalose-tethered monomeric berberine had comparable DNA-binding affinity toward calf-thymus DNA, whereas trehalose-spaced dimeric berberine exhibited higher DNA-binding affinity. The potential application of these conjugates is also briefly discussed.

• 한국동물학회지
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• 제37권4호
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• pp.495-503
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• 1994

Hemolymph SHBP (hJHBP) was partially purified from last instar larvae of Bombyx zori by gel filtration and their optimal reaction conditions of dextrin coated charcoal binding assay were determined. Dissociation constant (KD) of hJHBP for JH III was calculated to be 1.45 $\times$ 10-7 M at $4^{\circ}C.$ The molecular weight of hJHBP was estimated to be 30 kDa by gel filtration on a calibrated Sephadex G-100 column and 33 kDa by SDS-PAGE. These results indicate that hSHBP consists of a single polvpeptide chain. Isoelectric point of hJHBP was found to be pH 5.1 and 19 of the first 20 amino acid residues were determined from N-terminus of purified hJHBP.

• 대한약학회:학술대회논문집
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• 대한약학회 2002년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2
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• pp.365.1-365.1
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• 2002

Since adenosine A3 receptor has been cloned from rat brain. a number of compounds have been synthesized and evaluated for the binding affinity to this receptor. Among these. 2-chloro-N6-(3-iodobenzyl)-adenosine-5'-methylcarboxamide (2-CI-IB-MECA) has been found to be one of the most selective agonists (Ki = 1.0 nM) for rat adenosine A3 receptor. On the basis of the high binding affinity of 2-CI-IB-MECA to adenosine A3 receptor. it was interesting to find out whether 2'-hydroxyl group of 2-CI-IB-MECA is essential for the binding affnity to the receptor. (omitted)

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1995년도 춘계학술대회
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• pp.100-100
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• 1995

Several behavioral studies have suggested that ginseng total saponin (GTS) antagonizes morphine actions. Based on these observations, we conducted biochemical studies to elucidate the cellular mechanism of GTS actions. morphine hydrochloride (10mg/kg, sc) and/or on (400mg/kg, oral ) were administered to mice for 14 consecutive days. Ligand binding studies were conducted from striatal membranes. For opioid receptors, morphine increased the affinity but decreased the maximal binding sites for $^3$H naloxone. GTS partially recovered it. In case of dopamine receptors, morphine increased affinity and maximal binding sites for 3H spiperone. and GTS partially blocked it. These results suggest that morphine affects cellular events by modulating opioid receptors and that opioid receptors interact with dopamine receptors to change the mental status. GTS could be helpful for the treatment of morphine- induced mental disorders.

• 대한화학회지
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• 제67권4호
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• pp.226-235
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• 2023

Chikungunya fever has a high morbidity rate in humans and is caused by chikungunya virus. There are no treatments available until now for this particular viral disease. The present study was carried out by selecting 19 flavonoids, which are available naturally in fruits, vegetables, tea, red wine and medicinal plants. The molecular docking of selected 19 flavonoids was carried out against the Chikungunya virus capsid protein using the Autodock4.2 software. Binding affinity analysis based on the Intermolecular interactions such as Hydrogen bonding and hydrophobic interactions and drug-likeness properties for all the 19 flavonoids have been carried out and it is found that the top four molecules are Chrysin, Fisetin, Naringenin and Biochanin A as they fit to the chikungunya protein and have binding energy of -8.09, -8.01, -7.6, and 7.3 kcal/mol respectively. This result opens up the possibility of applying these compounds in the inhibition of chikungunya viral protein.

• 생명과학회지
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• 제28권2호
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• pp.195-200
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• 2018

베타아사론은 널리 알려진 석창포의 주요 효능 성분이다. 본 연구에서는 모기의 oviposition 페로몬 성분인 MOP와 석창포 효능성분 베타아사론의 열대집모기 후각 단백질 CquiOBP1 활성 부위에 대한 친화도 분석 실험을 컴퓨터 분자결합 분석 방법을 통해 비교하였다. CquiOBP1 후각 단백질의 3차원 구조 정보는 PDB database (PDB ID: 3OGN)를 활용하였다. In silico 결합 분석을 수행하기 위해 PyRx, Autodock Vina, Discovery Studio Version 4.5, and NX-QuickPharm 프로그램을 각 분석 조건에 따라 활용하였다. CquiOBP1 후각단백질 활성 부위에 대한 베타아사론의 결합친화도는 -6.40 kcal/mol으로 나왔으며 이는 -6.00 kcal/mol으로 나온 MOP의 결합친화도 보다 훨씬 더 높고 효율적인 것으로 분석되었다. 리간드와 상호작용 하는 CquiOBP1단백질 활성 부위의 아미노산들 가운데 TRP114가 공히 MOP와 베타아사론과 결합 하였다. CquiOBP1 단백질 활성부위의 아미노산들을 전혀 다른 전기적 성질을 지닌 아미노산으로 치환 시킨 후 분자결합 분석을 해 본 결과 리간드들의 X,Y,Z Grid 값에 현격한 변화가 유도되었으며 결합 친화도 또한 감소되었다. 이러한 결과를 통하여 베타아사론은 CquiOBP1 단백질 활성을 조절하는 리간드로서 효과적으로 작용할 것으로 보인다. 결론적으로 석창포 추출물 또는 베타아사론은 곤충기피제 신물질 연구 개발 분야에 효율적으로 활용할 수 있을 것으로 사료된다.

• 한국어병학회지
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• 제14권1호
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• pp.31-36
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• 2001

해수에 적응된 뱀장어, Anguilla japonica의 장 세포막으로부터 새로운 clonidine의 결합부위가 있음이 밝혀졌다. Clonidine의 특이적인 결합부위는 적어도 2개의 부위 (high affinity $K_d=1.4{\pm}0.3$ nMn= 5, low affinity $K_d=175{\pm}34$ nM)를 가지고 있었다. 2nM [$^3H$]clonidine의 특이적인 결합은 $20^{\circ}C$, pH 7.5에서 최적 결합능을 가지고 있었고, 라벨되지 않은 clonidine에 의해 가역적인 반응을 보였다. 이러한 결합은 adrenaline, yohimbine과 rauwolscine에 의한 저해능은 약하였다. 그리고 대부분의 결합부위는 $\alpha_2$-adrenoceptor와는 상이하였다. Clonidine의 특이적인 결합은 다양한 imidazoline/guanidinium약물에 의해 억제되었다. Competition 실험의 결과, 2nM[$^3H$]clonidine의 치환 rank order는 다음과 같다. guanabenz > cirazoline = naphazoline=UK14,304= ST587 $\geq$ clonidine $\geq$ idazoxan = RX821002 = tolazoline > ST93 = oxymetazoline = amiloride = ST91 > yohimbine = efaroxan = rauwolscine $\geq$ adrenaline = ST567 = histamine = agmatine. 이러한 순서는 포유류에 분류된 imidazoline receptorl($I_1$), imidazoline receptor 2($I_2$) 및 imidazoline/guanidinium receptive sites(IGRS)형태와는 틀리기 때문에 새로운 imidazoline receptor라고 생각된다. 지금까지 보고된 포유류의 세포와 조직에서 IGRS의 생리학적인 역할은 명확하지 않지만, 해수뱀장어 장은 IGRS의 세포에 있어서의 역할 그리고 IGRS의 내인성(內因性) ligand가 무엇인가에 대한 좋은 모델이 될 수 있다고 생각되어진다.