• 생명과학회지
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• 제17권6호통권86호
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• pp.783-790
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• 2007

G protein-coupled receptor, (GPCR)는 세포외부의 신호를 인식 시 G 단백질을 활성화시켜 신호를 전달하며 kinase에 의한 인산화를 통하여 지속적인 신호전달을 억제한다. 외부 신호물질이 없는 조건에서도 활성을 나타내는 항활성 돌연변이종(CAM)은 GPCR의 신호전달 이상에 기인한 질병 치료나 활성화 구조변화의 좋은 연구대상이다. 희미한 빛을 인식하는 시각수용체인 로돕신의 CAM으로는 salt bridge에 직접적인 영향을 미치는 돌연변이인 G90D, El13Q, 그리고 K296E와, 직접적인 영향이 없는 돌연변이인 E134q와 M25Y등 두 가지 계통의 종류가 알려져 있다. 본 연구에서는 각각의 돌연변이가 복합된 mutant를 구성하여 agonist와 inverse agonist에 대한친화도와 로돕신 kinase에 대한 활성을 조사하여 각 종에서의 구조변화의 차이를 분석하였다. 로돕신 mutant의constitutive activity는 all-trans-retinal에 대한 친화도에 비례하며 11-cis-retinal에 대한 친화도와는 역상관 관계를 보여준다. 같은 계통에 속하는 돌연변이가 합쳐진 복합 mutant는 단일 mutant에 비하여 미약한 정도의 로돕신 kinase 항활성화 증가를 보여주나, 다른 계통에 속하는 두 가지 돌연변이가 합쳐진 mutant는 항활성화가 크게 증가되었음을 보여주었다. 이 결과는 다른 계통에 속하는 mutant에서는 상이한 구조변화가 일어나며 로돕신이완전한 활성화에 이르기 위해서는 최소한 두 가지 종류의 돌연변이에 의하여 생기는 구조변화들이 함께 일어나야함을 의 미 한다. G protein 활성화와 유사한 항활성화 분석 결과는 rhodopsin kinase가 인식하는 로돕신의 활성화상태 구조가 G protein이 인식하는 구조와 유사함을 의미한다. 특히 가장 강한 활성을 나타내는 El13Q/E134Q/M257Y는 활성화상태 GPCR 단백질의 결정 시도에 이용 될 수 있을 것이다.

• Natural Product Sciences
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• 제28권2호
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• pp.45-52
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• 2022

The identification of Plasmodium falciparum enoyl acyl-carrier protein reductase (pfENR) is considered as a potential biological target against malaria. Trema orientalis is considered a rich source of phytochemicals useful in malaria treatment. This study evaluated the in-vitro inhibitory activity of the extract and isolated compounds of T. orientalis leaf; the isolated compounds and the analogues of the most active compound were subjected to in-silico molecular docking studies on pfENR. The methanolic extract of T. orientalis was subjected to repeated chromatographic separation which led to the isolation of some compounds. The isolated compounds from the plant were examined for their antimalarial activity using β-hematin inhibition assay. Virtual screening via molecular docking and ADMET studies were conducted to gain insight into the mechanism of binding of ligand and to identify effective pfENR inhibitors. The isolated compounds and the analogues of the most active isolates were gotten from PubChem library for use in docking study. Hexacosanol and β-sitosterol showed inhibition of the β-hematin formation. The docking results showed that hexacosanol, β-sitosterol and the analogues of β-sitosterol displayed binding energy ranging between -6.1 kcal/mol and -11.6 kcal/mol. Sitosterol glucoside has the highest docking score. Some of the ligands showed more binding affinity than known bioactive compounds used as reference. Analogues of β-sitosterol has been shown to be potential inhibitors of pfENR, therefore, the findings from this study suggest that sitosterol glucoside and ergosterol peroxide could act as antimalarial agents after further lead optimisation investigations.

• 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.

• BMB Reports
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• 제40권2호
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• pp.239-246
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• 2007

Riboflavin synthase from Escherichia coli is a homotrimer of 23.4 kDa subunits and catalyzes the formation of one molecule each of riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione by the transfer of a 4-carbon moiety between two molecules of the substrate, 6,7- dimethyl-8-ribityllumazine. Each subunit comprises two closely similar folding domains. Recombinant expression of the N-terminal domain is known to provide a $C_2$-symmetric homodimer. In this study, the binding properties of wild type as well as two mutated proteins of N-terminal domain of riboflavin synthase with various ligands were tested. The replacement of the amino acid residue A43, located in the second shell of riboflavin synthase active center, in the recombinant N-terminal domain dimer reduces the affinity for 6,7-dimethyl-8-ribityllumazine. The mutation of the amino acid residue C48 forming part of activity cavity of the enzyme causes significant $^{19}F$ NMR chemical shift modulation of trifluoromethyl derivatives of 6,7-dimethyl-8-ribityllumazine in complex with the protein, while substitution of A43 results in smaller chemical shift changes.

• Asian Pacific Journal of Cancer Prevention
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• 제16권18호
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• pp.8191-8196
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• 2016

Inhibition of EGFR-EGF interactions forms an important therapeutic rationale in treatment of non-small cell lung carcinoma. Established inhibitors have been successful in reducing proliferative processes observed in NSCLC, however patients suffer serious side effects. Considering the narrow therapeutic window of present EGFR inhibitors, the present study centred on identifying high efficacy EGFR inhibitors through structure based virtual screening strategies. Established inhibitors - Afatinib, Dacomitinib, Erlotinib, Lapatinib, Rociletinib formed parent compounds to retrieve similar compounds by linear fingerprint based tanimoto search with a threshold of 90%. The compounds (parents and respective similars) were docked at the EGF binding cleft of EGFR. Patch dock supervised protein-protein interactions were established between EGF and ligand (query and similar) bound and free states of EGFR. Compounds ADS103317, AKOS024836912, AGN-PC-0MXVWT, GNF-Pf-3539, SCHEMBL15205939 were retrieved respectively similar to Afatinib, Dacomitinib, Erlotinib, Lapatinib, Rociletinib. Compound-AGN-PC-0MXVWT akin to Erlotinib showed highest affinity against EGFR amongst all the compounds (parent and similar) assessed in the study. Further, AGN-PC-0MXVWT brought about significant blocking of EGFR-EGF interactions in addition showed appreciable ADMET properties and pharmacophoric features. In the study, we report AGN-PC-0MXVWT to be an efficient and high efficacy inhibitor of EGFR-EGF interactions identified through computational approaches.

• BMB Reports
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• 제40권5호
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• pp.731-739
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• 2007

The purpose of this study was to develop paclitaxel-loaded poly(lactide-co-glycolide) (PLGA) nanoparticles coated with cationic SM5-1 single-chain antibody (scFv) containing a polylysine (SMFv-polylys). SM5-1 scFv (SMFv) is derived from SM5-1 monoclonal antibody, which binds to a 230 kDa membrane protein specifically expressed on melanoma, hepatocellular carcinoma and breast cancer cells. SMFv-polylys was expressed in Escherichia coli and purified by cation-exchange chromatography. Purified SMFv-polylys was fixed to paclitaxel-loaded PLGA nanoparticles to form paclitaxel-loaded PLGA nanoparticles coated with SMFv-polylys (Ptx-NP-S). Ptx-NP-S was shown to retain the specific antigen-binding affinity of SMFv-polylys to SM5-1 binding protein-positive Ch-hep-3 cells. Finally, the cytotoxicity of Ptx-NP-S was evaluated by a non-radioactive cell proliferation assay. It was demonstrated that Ptx-NP-S had significantly enhanced in vitro cytotoxicity against Ch-hep-3 cells as compared with non-targeted paclitaxel-loaded PLGA nanoparticles. In conclusion, our results suggest that cationic SMFv-polylys has been successfully generated and may be used as targeted ligand for preparing cancer-targeted nanoparticles.

• 대한의생명과학회지
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• 제12권2호
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• pp.73-79
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• 2006

Nebulin is a giant ($600{\sim}900$ kDa), modular sarcomeric protein proposed to regulate the assembly, and to specify the precise lengths of actin filamints in vertebrate skeletal muscles. Recently, There is an evidence that the nebulin also expressed in non muscle tissue, brain and liver. We identified a new isoform of nebulin from adult brain library by PCR screening. It contains two simple-repeats exon 165, 166 and linker-repeats exon $154{\sim}161$ except exon 159. The nebulin modules M160 to M170 (exon 150 to exon 161) has been shown to bind desmin. In mature striated muscle, desmin intermediate filaments surround Z-discs and link individual myofibrils laterally at their Z-discs and to other intracellular structures, including the costameres and the intercalated discs of the sarcolemma, sarcoplasmic reticulum, mitochondria, T-tubules, and nuclei. Therefore, it is an interesting possibility that the differential splice pathways within the linker region of nebulin modify the affinity of nebulin's interaction with desmin. The specific interactions of nebulin and desmin were confirmed in vivo by yeast two hybrid experiments. To verify in the cellular level the interaction between nebulin isoform and desmin, we transfected COS-7 cell with EGFP-tagged nebulin and DsRed-tagged desmin. Based on evidence showing that despite exon 159 was deleted, the new isoform of nebulin was interact with desmin. This suggest that nebulin in brain may interact with another intermediate filament. The conservation of these ligand-binding capacity in brain and skeletal nebulins suggest that nebulins may have conserved roles in brain and skeletal muscle.

• 대한약침학회지
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• 제18권2호
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• pp.7-18
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• 2015

Objectives: Lawsone (1,4 naphthoquinone) is a non redox cycling compound that can be catalyzed by DT diaphorase (DTD) into 1,2,4-trihydroxynaphthalene (THN), which can generate reactive oxygen species by auto oxidation. The purpose of this study was to evaluate the toxicity of the phytomarker 1,4 naphthoquinone and its metabolite THN by using the molecular docking program AutoDock 4. Methods: The 3D structure of ligands such as hydrogen peroxide ($H_2O_2$), nitric oxide synthase (NOS), catalase (CAT), glutathione (GSH), glutathione reductase (GR), glucose 6-phosphate dehydrogenase (G6PDH) and nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) were drawn using hyperchem drawing tools and minimizing the energy of all pdb files with the help of hyperchem by $MM^+$ followed by a semi-empirical (PM3) method. The docking process was studied with ligand molecules to identify suitable dockings at protein binding sites through annealing and genetic simulation algorithms. The program auto dock tools (ADT) was released as an extension suite to the python molecular viewer used to prepare proteins and ligands. Grids centered on active sites were obtained with spacings of $54{\times}55{\times}56$, and a grid spacing of 0.503 was calculated. Comparisons of Global and Local Search Methods in Drug Docking were adopted to determine parameters; a maximum number of 250,000 energy evaluations, a maximum number of generations of 27,000, and mutation and crossover rates of 0.02 and 0.8 were used. The number of docking runs was set to 10. Results: Lawsone and THN can be considered to efficiently bind with NOS, CAT, GSH, GR, G6PDH and NADPH, which has been confirmed through hydrogen bond affinity with the respective amino acids. Conclusion: Naphthoquinone derivatives of lawsone, which can be metabolized into THN by a catalyst DTD, were examined. Lawsone and THN were found to be identically potent molecules for their affinities for selected proteins.

• 대한약리학회지
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• 제26권2호
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• pp.167-176
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• 1990

비스테로이드성 항에스트로젠제는 표적기관에서 estrogen 수용체와 상경적으로 결합하므로써 estrogen의 작용을 억제하는 것으로 알려져 있다. 비스테로이드성 항에스트로젠제는 대체로 triphenylethylene계로서 tamoxifen, clomiphene, LYl17018등이 있으며 표적기관에서 estrogen의 작용을 억제하기 때문에 estrogen과 관련된 질환을 치료하는데 이용되어 오고 있다. 본 연구에서는 생후 21-23일된 미성숙 흰쥐를 재료로 항에스트로젠제중 tamoxifen과 LY117018이 자궁세포 성장에 어떠한 영향을 미치며 어떠한 기전으로 estrogen의 작용을 길항하는지를 규명하고자, 항에스트로젠제가 estrogen작용의 중요 지포에 미치는 영향을 비교 관찰하여 다음과 같은 결과를 얻었다. Tamoxifen과 LY117018은 자궁세포에서 estrogen의 영향이 없는 경우에는 estrogen agonist로, estrogen작용하에서는 estrogen antagonist로서 작용하였다. Estrogen 작용의 여러 가지 지표에 대해 tamoxifen이 LY117018보다 agonistic effect는 더 컸으나, antagonistic effect는 LY117018이 더 큰 것으로 나타났다. Estrogen 수용체에 대한 결합능은 LY117018이 estradiol보다는 약간 낮았으나 용량에 비례하여 estrogen 수용체와 결합하였다. 그러나 tamoxifen은 estrogen 수용체에 대한 결합이 아주 낮았다. Estrogen 수용체에 대한 binding affinity는 estradiol(100%), LY117018(77%), tamoxifen(6.3%) 순으로 나타났다. 항에스트로젠제의 생체내 투여는 estrogen 존재 유무에 따라 estrogen 수용체 농도에 agonist 또는 antagonist로 작용하였다. 항에스트로젠제의 단독투여는 progesterone 수용체 생성을 증가시키나, estrogen에 의하여 유도된 progesterone 수용체 생성을 억제하였다. 이상의 결과로 보아, tamoxifen과 LY117018은 estrogen유무에 따라 흰쥐 자궁세포에서 estrogen antagonist로서 뿐만 아니라 agonist로서도 작용함을 알 수 있다. 그러나 estrogen수용체와의 결합능력이 아주 낮은 tamoxifen은, 용량에 비례하여 estrogen수용체에 결합하므로써 작용하는 LY117018과는 다른 기전으로 작용하는 것으로 생각된다.