• The Korean Journal of Physiology and Pharmacology
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• 제28권1호
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• pp.59-72
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• 2024

To investigate the mechanism of Wenshen Xuanbi Decoction (WSXB) in treating osteoarthritis (OA) via network pharmacology, bioinformatics analysis, and experimental verification. The active components and prediction targets of WSXB were obtained from the TCMSP database and Swiss Target Prediction website, respectively. OA-related genes were retrieved from GeneCards and OMIM databases. Protein-protein interaction and functional enrichment analyses were performed, resulting in the construction of the Herb-Component-Target network. In addition, differential genes of OA were obtained from the GEO database to verify the potential mechanism of WSXB in OA treatment. Subsequently, potential active components were subjected to molecular verification with the hub targets. Finally, we selected the most crucial hub targets and pathways for experimental verification in vitro. The active components in the study included quercetin, linolenic acid, methyl linoleate, isobergapten, and beta-sitosterol. AKT1, tumor necrosis factor (TNF), interleukin (IL)-6, GAPDH, and CTNNB1 were identified as the most crucial hub targets. Molecular docking revealed that the active components and hub targets exhibited strong binding energy. Experimental verification demonstrated that the mRNA and protein expression levels of IL-6, IL-17, and TNF in the WSXB group were lower than those in the KOA group (p < 0.05). WSXB exhibits a chondroprotective effect on OA and delays disease progression. The mechanism is potentially related to the suppression of IL-17 and TNF signaling pathways and the down-regulation of IL-6.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
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• pp.247.2-248
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• 2003

The three-dimensional quantitative structure-activity relationship (3D-QSAR) approach using comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) was applied to 62 derivatives known as COX-2 selective inhibitors. Partial least square (PLS) analyses produced good predicted models with q2 value of 0.803 (s=0.285, F=215.401, r2=0.951) and 0.769 (s=0.192, F=245.364, r2=0.980) for CoMFA and CoMSIA, respectively. (omitted)

• Journal of Ginseng Research
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• 제47권5호
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• pp.662-671
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• 2023

Background: 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, has prominent benefits for the central nervous system, especially in improving learning and memory. However, its transcriptional targets in brain tissue remain unknown. Methods: In this study, we first used mass spectrometry-based drug affinity responsive target stability (DARTS) to identify the potential proteins of ginsenosides and intersected them with the transcription factor library. Second, the transcription factor PURA was confirmed as a target of PPD by biolayer interferometry (BLI) and molecular docking. Next, the effect of PPD on the transcriptional levels of target genes of PURA in brain tissues was determined by qRT-PCR. Finally, bioinformatics analysis was used to analyze the potential biological features of these target proteins. Results: The results showed three overlapping transcription factors between the proteomics of DARTS and transcription factor library. BLI analysis further showed that PPD had a higher direct interaction with PURA than parent ginsenosides. Subsequently, BLI kinetic analysis, molecular docking, and mutations in key amino acids of PURA indicated that PPD specifically bound to PURA. The results of qRT-PCR showed that PPD could increase the transcription levels of PURA target genes in brain. Finally, bioinformatics analysis showed that these target proteins were involved in learning and memory function. Conclusion: The above-mentioned findings indicate that PURA is a transcription target of PPD in brain, and PPD upregulate the transcription levels of target genes related to cognitive dysfunction by binding PURA, which could provide a chemical and biological basis for the study of treating cognitive impairment by targeting PURA.

• Advances in aircraft and spacecraft science
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• 제7권3호
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• pp.271-290
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• 2020

The paper describes the analysis of deployment strategies and trajectories design suitable for executing the inspection of an operative spacecraft in orbit through re-usable CubeSats. Similar missions have been though indeed, and one mission recently flew from the International Space Station. However, it is important to underline that the inspection of an operative spacecraft in orbit features some peculiar characteristics which have not been demonstrated by any mission flown to date. The most critical aspects of the CubeSat inspection mission stem from safety issues and technology availability in the following areas: trajectory design and motion control of the inspector relative to the target, communications architecture, deployment and retrieval of the inspector, and observation needs. The objectives of the present study are 1) the identification of requirements applicable to the deployment of a nanosatellite from the mother-craft, which is also the subject of the inspection, and 2) the identification of solutions for the trajectories to be flown along the mission phases. The mission for the in-situ observation of Space Rider is proposed as reference case, but the conclusions are applicable to other targets such as the ISS, and they might also be useful for missions targeted at debris inspection.

• 통합자연과학논문집
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• 제8권1호
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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.

• KSBB Journal
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• 제25권4호
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• pp.344-350
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• 2010

This paper demonstrates a microfluidic chip incorporating patterned hollow silica beads that can be effectively used for chemotaxis assay. The hollow silica bead has been exploited to develop a carrier for chemoattractant to induce cell migration. The microfluidic chip contains a patterned array of microfabricated docks which can hold only one bead per docking site. The hollow bead placed inside microfluidic chip releases chemotactic reagent (PDGF-BB) around its periphery in a controlled fashion which generates a signal for chemotatic migration of fibroblast cells. The number of cells migrated close to each bead has been assessed. On-chip cell migration assay showed a remarkable result proving the high efficiency and reliable accuracy in quantitative analysis. Therefore, the device could be extensively used in cell migration assay and other various studies related to cellular movements.

• 전기학회논문지
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• 제57권11호
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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.

• Interdisciplinary Bio Central
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• 제2권2호
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• pp.6.1-6.5
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• 2010

Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.

• 통합자연과학논문집
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• 제11권2호
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• pp.101-106
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• 2018

Corticotropin - releasing hormone receptor 1 (CRHR1) forms an integral part of the pathophysiology of disorders like post-traumatic stress disorder, stress, anxiety, addiction, and depression. Hence it is essential to look for new, potent and structure-specific inhibitors of CRHR1. We have analysed the protein-protein interaction complexes of the CRHR1 receptor with its native ligand CRF and full agonist Sauvagine. The structure of Sauvagine was predicted using homology modelling. We have identified that the residues TYR253, ASP254, GLU256, GLY265, ARG1014 and LY1060 are important in the formation of protein-protein complex formation. Future studies on these residues could throw light on the crucial structural features required for the formation of CRHR1-inhibitor complex and in studies that try to solve the structural complexities of CRHR1.

• 전산구조공학
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• 제22권4호
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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.