• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.201-207
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• 2011

Peroxisome proliferator-activated receptors (PPARs) are members of nuclear receptors and their activation induces regulation of fatty acid storage and glucose metabolism. Therefore, the $PPAR\gamma$ is a major target for the treatment of type 2 diabetes mellitus. In order to generate pharmacophore model, 1080 known agonists database was constructed and a training set was selected. The Hypo7, selected from 10 hypotheses, contains four features: three hydrogen-bond acceptors (HBA) and one general hydrophobic (HY). This pharmacophore model was validated by using 862 test set compounds with a correlation coefficient of 0.903 between actual and estimated activity. Secondly, CatScramble method was used to verify the model. Hence, the validated Hypo7 was utilized for searching new lead compounds over 238,819 and 54,620 chemical structures in NCI and Maybridge database, respectively. Then the leads were selected by screening based on the pharmacophore model, predictive activity, and Lipinski's rules. Candidates were obtained and subsequently the binding affinities to $PPAR\gamma$ were investigated by the molecular docking simulations. Finally the best two compounds were presented and would be useful to treat type 2 diabetes.

• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3199-3205
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• 2013

The inclusion behavior of sulfobutylether-${\beta}$-cyclodextrin (SBE-${\beta}$-CD) with perphenazine (PPH) was first studied by flow injection (FI)-chemiluminescence (CL) analysis with proposed $lg[(I_0-I_s)/I_s]=lgK_{P-CD}+nlg[C_{PPH}]$ model and molecular docking. Results showed that a 1:1 complex of SBE-${\beta}$-CD/PPH could online form, with the formation constant $K_{P-CD}$ of $2.57{\times}10^7Lmol^{-1}$ at 298 K. The thermodynamic parameters showed that the inclusion behavior of SBE-${\beta}$-CD/PPH was a spontaneous process by hydrophobic interaction. The molecular docking results revealed PPH entered into the larger cavity of SBE-${\beta}$-CD with two hydrogen bonds. Based on the linear relationship of the decrement of luminol/SBE-${\beta}$-CD/PPH CL intensity against the logarithm of PPH concentration ranging from 0.03 to 30.0 ng $mL^{-1}$, the present FI-CL analysis using luminol/SBE-${\beta}$-CD/PPH system was successfully applied to PPH determination in biological fluids and tablets with recoveries from 94.5 to 105.6% and RSDs less than 2.6% (n = 5).

• Genomics & Informatics
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• v.12 no.4
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• pp.268-275
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• 2014

The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire's disease. The increasing development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this, the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.

• Journal of Ginseng Research
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• v.47 no.2
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• pp.274-282
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• 2023

Background: Ginsenoside compound K (CK) stimulated activation of the PI3K-Akt signaling is one of the major mechanisms in promoting cell survival after stroke. However, the underlying mediators remain poorly understood. This study aimed to explore the docking protein of ginsenoside CK mediating the neuroprotective effects. Materials and methods: Molecular docking, surface plasmon resonance, and cellular thermal shift assay were performed to explore ginsenoside CK interacting proteins. Neuroscreen-1 cells and middle cerebral artery occlusion (MCAO) model in rats were utilized as in-vitro and in-vivo models. Results: Ginsenoside CK interacted with recombinant human PTP1B protein and impaired its tyrosine phosphatase activity. Pathway and process enrichment analysis confirmed the involvement of PTP1B and its interacting proteins in PI3K-Akt signaling pathway. PTP1B overexpression reduced the tyrosine phosphorylation of insulin receptor substrate 1 (IRS1) after oxygen-glucose deprivation/reoxygenation (OGD/R) in neuroscreen-1 cells. These regulations were confirmed in the ipsilateral ischemic hemisphere of the rat brains after MCAO/R. Ginsenoside CK treatment reversed these alterations and attenuated neuronal apoptosis. Conclusion: Ginsenoside CK binds to PTP1B with a high affinity and inhibits PTP1B-mediated IRS1 tyrosine dephosphorylation. This novel mechanism helps explain the role of ginsenoside CK in activating the neuronal protective PI3K-Akt signaling pathway after ischemia-reperfusion injury.

• Journal of Integrative Natural Science
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• v.8 no.1
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• pp.75-79
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• 2015

Thromboxane A2 receptors (TXA2-R) are the G protein coupled receptors localized on cell membranes and intracellular structures and play pathophysiological role in various thrombosis/hemostasis, modulation of the immune response, acute myocardial infarction, inflammatory lung disease, hypertension and nephrotic disease. TXA2 receptor antagonists have been evaluated as potential therapeutic agents for asthma, thrombosis and hypertension. The role of TXA2 in wide spectrum of diseases makes this as an important drug target. Hence in the present study, homology modeling of TXA2 receptor was performed using the crystal structure of squid rhodopsin and night blindness causing G90D rhodopsin. 20 models were generated using single and multiple templates based approaches and the best model was selected based on the validation result. We found that multiple template based approach have given better accuracy. The generated structures can be used in future for further binding site and docking analysis.

• The Transactions of The Korean Institute of Electrical Engineers
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• v.57 no.11
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• pp.2074-2079
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• 2008

This paper presents a software toolbox with $Matlab^{(R)}$ developed for the various performance analysis of an automatic guidance system of the Bimodal Tram. The Bimodal Tram is a new kind of transportation vehicle which could be an all-wheel steered multiple-articulated vehicle. This vehicle has to be equipped with an automatic guidance, traction/braking, and docking system, In the stage of developing such a system, its validities and performances should be verified under various operation conditions. For the purpose of doing these things through simulation, this toolbox has been developed and demonstrated well by applying it to the KRRI model.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.340.3-341
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• 2002

During the research for the development of antitumor agents. we found the 3-arylisoquinoline derivatives exhibited potent cytotoxicity against human tumor cell lines. For extending our study on these compounds. indeno［1.2-c］isoquinolines were chosen as the next research target due to previous studied data of the compounds that showed potent topoisomerase I inhibition activity as well as cytotoxicity against many kinds of tumor cell lines. Retrosynthetic consideration of indeno[1.2-d]isoquinolines indicates that the coupling of o-methyltoluamide with o-hydroxymethylbenxonitrile might afford 3-arylisoquinoline which could be translerred to the aldehtde. Indeno [1.2-c]isoquinolines can be formed by and inframolecular ring cyclization method. Various derlvatives of this compound including 11-alkoxy-6-methyl-6H. 11H-indeno[1.2-c]isoquinolin-5-one and biological activity will be presented with the docking model with topisomerase 1 enzyme.

• Journal of Integrative Natural Science
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• v.11 no.2
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• pp.87-92
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• 2018

5-Hydroxytryptamine receptor 7 ($5-HT_7R$) is one of G-Protein coupled receptors, which is found to be involved in the pathophysiology of various neurological disorders including depression, sleep disorders, memory deficiency and neuropathic pain. After activation of $5-HT_7R$ by serotonin, it activates the production of the intracellular signaling molecule cyclic AMP. The availability of 3D structure of the receptor would enhance the development of new drugs. Hence, in the present study, homology modelling of human 5-hydroxytryptamine receptor 7 ($5-HT_7R$) was performed using comparative modelling (Easy Modeller) and threading (I-TASSER) approaches. The generated models were validated using Ramachandran plot and ERRAT plot and the best models were selected based on the validation results. The 3D model developed here could be useful for identifying crucial residues and further docking study.

• Computational Structural Engineering
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• v.22 no.4
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• pp.89-94
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• 2009

최근에 선박의 도킹해석은 3차원 전선 구조 해석을 통해 수행되어 왔으나 도킹해석 모델을 구성하는데 많은 시간과 노력이 필요하였다. 전선구조해석 모벨을 만들기 위해 필요한 선박구조 도면이 완성되기 전인 초기 설계단계에서 도킹시 반목배치를 조기에 확정하고, 구조 안정성을 확보하기 위한 노력이 요구되어 왔기 때문에 간이화된 도킹 해석 프로그램을 개발하게 되었다. 2차원 격자구조를 이용한 도킹해석기법을 통해 얻은 반목에서의 지지력이 3차원 전선해석모델을 사용하여 얻은 반목에서의 반력 결과와 비교해 타당한 결과를 보여 주고 있음을 확인하였다. 간이화된 도킹용 해석 프로그램을 개발하였으며, 다음과 같은 기능을 갖추어 사용자가 쉽게 격자 구조 모델을 생생하고 해석을 수행할 수 있도록 구성하였다. 향후 각 요소의 단면 특성치를 자동으로 산정하는 기능이 추가되어야 한다. 그리고 부유식 도크(Floating dock)에서의 도킹해석은 본 개발의 대상이 된 건식 도크(Dry dock)에서의 경우와 다른 고려사항이 추가되어야 하기 때문에 향후 추가적인 연구와 개발을 통해 새로운 기능으로 포함될 것이다.

• Journal of Integrative Natural Science
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• v.7 no.4
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• pp.234-240
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• 2014

C-C chemokine receptor type 4 (CCR4) is a chemokine receptor with seven transmembrane helices and it belongs to the GPCR family. It plays an important role in asthma, lung disease, atopic dermatitis, allergic bronchopulmonary aspergillosis, cancer, inflammatory bowel disease, the mosquito-borne tropical diseases, such as dengue fever and allergic rhinitis. Because of its role in wide spectrum of disease processes, CCR4 is considered to be an important drug target. Three dimensional structure of the protein is essential to determine the functions. In the present study homology modeling of human CCR4 was performed based on crystal structure of CCR5 chemokine receptor. The generated models were validated using various parameters. Among the generated homology models the best one is selected based on validation result. The model can be used for performing further docking studies to identifying the critical interacting residues.