• Genomics & Informatics
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• v.15 no.1
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• pp.19-27
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• 2017

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

• Herbal Formula Science
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• v.28 no.1
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• pp.91-115
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• 2020

Objective : This study's purpose was to review the clinical studies of Galgeun-tang. Method : We searched papers about Galgeun-tang using KISS, RISS, OASIS, PUBMED and J-stage. The key words we used were "Galgeuntang", "Kakkonto", "Ge gen tang", and "Pueraria Decoction". Papers not matched with inclusion criteria were excluded. Results : Until today, there have been 223 studies on Galgeun-tang. Of these, 25 studies were classified as clinical research papers. There were 4 cases of fever, 5 cases of inflammation on respiratory system, 3 cases of head, neck and shoulder disorder, 2 cases of diarrhea, 6 cases of pharmacokinetics and interaction, 5 cases of side effect. Conclusion : It can be seen that Galgeun-tang has established the basis for application to the purpose of treating fever (common cold, influenza), inflammation on respiratory system (nasal obstruction, maxillary sinus retention cyst, mucoid pseudomonas aeruginosa chronic lower respiratory tract infection), head, neck and shoulder disorder (temporomandibular disorders, shoulder stiffness, tetanus), and diarrhea. On the other hand, considering 4 cases of side effect on drug eruption, caution should be exercised when observing the progress of the patient taking Galgeun-tang.

• Korean Chemical Engineering Research
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• v.44 no.1
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• pp.1-9
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• 2006

Biodevices composed of biomolecular layer by mimicking the natural functions of cells and the interaction mechanisms of the constituted biomolecules have been developed in various industrial fields such as medical diagnosis, drug screening, electronic device, bioprocess, and environmental pollution detection. To construct biodevices such as bioelectronic devices (biomolecular diode, bio-information storage device and bioelectroluminescence device), protein chip, DNA chip, and cell chip, biomolecules including DNA, protein, and cells have been used. Fusion technology consisting of immobilization technology of biomolecules, micro/nano-scale patterning, detection technology, and MEMs technology has been used to construct the biodevices. Recently, nanotechnology has been applied to construct nano-biodevices. In this paper, the current technology status of biodevice including its fabrication technology and applications is described and the future development direction is proposed.

• The Journal of Korean Medicine
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• v.32 no.4
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• pp.1-24
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• 2011

Backgrounds: Danggui, one of the major herbs in Korean traditional medicine consists of three species: Angelica gigas of Korea, Angelica sinensis of China, and Angelica acutiloba of Japan. Despite its importance in Korean traditional medicine, recognition of the clinical differences between its three species is insufficient. Objectives: The purpose of the present review is to suggest evidence in using Angelica gigas, Angelica sinensis, and Angelica acutiloba distinctively in clinic, by comparing their pharmacological effects and bioactive compounds. Methods: We searched articles published from 2000 to 2009 in Pubmed, EMbase, and RISS. The search keywords were "Angelica gigas", "Angelica sinensis", "Angelica acutiloba", "dongquei", "toki", "Angelicae Radix", "Archangelica officinalis Hoffm.", "Garden Angelica", "Chinese angelica root", "tangkuei", and "danggui". 861 articles were searched. Among them, we selected 143 articles which met our inclusion criteria. Results: This review summarizes active constituents, experimental studies, clinical studies, pharmacokinetics, side effects and toxicity, drug interaction, and industrial use of Angelica gigas, Angelica sinensis, and Angelica acutiloba. Conclusions: While Angelica sinensis and Angelica acutiloba are relatively similar, Angelica gigas is quite different from the others in main active constituents and genetic form. The main experimental studies of Danggui are cardiovascular studies, central nervous system studies and anti-cancer activity. Even though there were cases in which the three species show similar pharmacological effects, the mechanism was not always shared. Therefore, distinguished use of Angelica gigas, Angelica sinensis and Angelica acutiloba is needed.

• Journal of Pharmaceutical Investigation
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• v.40 no.2
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• pp.85-90
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• 2010

Docetaxel-loaded liposomes were prepared by emulsion-solvent evaporation method, then coated with chitosan at room temperature and lyophilized. This system was designed in order to improve solubility and stability of docetaxel in the GI tract for oral drug delivery. The solubilizing effect of some frequently used solubilizers and/or liposome was determined. Among the results docetaxel-loaded liposomes prepared with 0.5% TPGS as a solubilizer showed 100-fold higher solubility than docetaxel. In a stability test, mean particle size of different liposome formulations was measured by a particle size analyzer in simulated gastric fluid (SGF) and in simulated intestinal fluid (SIF). The particle size of uncoated liposomes was significantly increased compared with that of chitosan-coated liposomes in SGF, however, there was no significant difference between coated and uncoated liposome in SIF. It is evident that chitosan-coated liposomes were more stable in GI conditions. The release characteristics of docetaxel-loaded liposomes were also investigated in three buffer solutions (pH 1.2, 4.0, 6.8). Docetaxel release did not occur in pH 1.2 for 4 hrs. However, in pH 4.0 and 6.8 conditions, docetaxel was gradually released over 24 hrs as a sustained release. It seems that aggregation and precipitation of particles by electrostatic interaction might protect docetaxel from being released. In Conclusion, the results from this study show that the chitosan-coated liposomes may be useful in enhancing solubility and GI stability of docetaxel.

• The Journal of Korean Medicine
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• v.33 no.3
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• pp.200-230
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• 2012

Objectives: Ginseng, Panax ginseng C. A., white ginseng, has been used for thousands of years in Traditional Korean Medicine. Red ginseng can be made by a steaming process of white ginseng changing a variety of ginsenosides and ingredients such as dencichine. This article reviews red ginseng for mechanisms for pharmacodynamics and toxicity based on the content of ginseng's active ingredients, ginsenoside changed by steaming. Methods: The following electronic databases were searched: PubMed, Science Direct and Chinese Scientific Journals full text database (CQVIP), and KSI (Korean Studies Information) from their respective inceptions to June 2012. Results: Compared with unsteamed ginseng, the content of ginsenosides Rg2, Rg3, Rg5, Rh1, Rh2 and Rk1 called red ginseng-specific ginsenosides increased after the steaming process. Different ginsenosides have shown a wide variety of effects such as lowering or raising blood sugar and blood pressure or stimulating or sedating the nervous system. Especially, the levels of Rg2, Rg3, Rg5, Rh1, Rh2 and Rk1 were increased by the steaming process, showing a variety of pharmacodynamics in biological systems. Also, various processing methods such as puffing and fermentation have been developed in processing crude ginseng or red ginseng, affecting the content of ginseng's ingredients. The safety issue could be the most critical, specifically, on changed ginseng's ingredients such as dencichine. The level of dencichine was significantly reduced in red ginseng by the steaming process. In addition, the possible toxicity for red ginseng was affected by cytochrome P450, a herbal-drug interaction. Conclusions: The variety of pharmacological and toxicological properties should be changed by steaming process of Panax ginseng C. A., white ginseng. Even if it is not sure whether the steaming process of white ginseng would be better pharmacologically, it is sure that steaming reduces the level of dencichine causing a lower toxicity to the nervous system.

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.647-655
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• 2008

Microsomal prostaglandin E2 synthase (mPGES-1) is a potent target for pain and inflammation. Various QSAR (quantitative structure activity relationship) analyses used to understand the factors affecting inhibitory potency for a series of MK886 analogues. We derived four QSAR models utilizing various quantum mechanical (QM) descriptors. These QM models indicate that steric, electrostatic and hydrophobic interaction can be important factors. Common pharmacophore hypotheses (CPHs) also have studied. The QSAR model derived by best-fitted CPHs considering hydrophobic, negative group and ring effect gave a reasonable result (q2 = 0.77, r2 = 0.97 and Rtestset = 0.90). The pharmacophore-derived molecular alignment subsequently used for 3D-QSAR. The CoMFA (Comparative Molecular Field Analysis) and CoMSIA (Comparative Molecular Similarity Indices Analysis) techniques employed on same series of mPGES-1 inhibitors which gives a statistically reasonable result (CoMFA; q2 = 0.90, r2 = 0.99. CoMSIA; q2 = 0.93, r2 = 1.00). All modeling results (QM-based QSAR, pharmacophore modeling and 3D-QSAR) imply steric, electrostatic and hydrophobic contribution to the inhibitory activity. CoMFA and CoMSIA models suggest the introduction of bulky group around ring B may enhance the inhibitory activity.

• Journal of Ginseng Research
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• v.39 no.2
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• pp.141-147
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• 2015

Background: Adipocytes, which are the main cellular component of adipose tissue, are the building blocks of obesity. The nuclear hormone receptor $PPAR{\gamma}$ is a major regulator of adipocyte differentiation and development. Obesity, which is one of the most dangerous yet silent diseases of all time, is fast becoming a critical area of research focus. Methods: In this study, we initially aimed to investigate whether the ginsenoside Rf, a compound that is only present in Panax ginseng Meyer, interacts with $PPAR{\gamma}$ by molecular docking simulations. After we performed the docking simulation the result has been analyzed with several different software programs, including Discovery Studio, Pymol, Chimera, Ligplus, and Pose View. All of the programs identified the same mechanism of interaction between $PPAR{\gamma}$ and Rf, at the same active site. To determine the drug-like and biological activities of Rf, we calculate its absorption, distribution, metabolism, excretion, and toxic (ADMET) and prediction of activity spectra for substances (PASS) properties. Considering the results obtained from the computational investigations, the focus was on the in vitro experiments. Results: Because the docking simulations predicted the formation of structural bonds between Rf and $PPAR{\gamma}$, we also investigated whether any evidence for these bonds could be observed at the cellular level. These experiments revealed that Rf treatment of 3T3-L1 adipocytes downregulated the expression levels of $PPAR{\gamma}$ and perilipin, and also decreased the amount of lipid accumulated at different doses. Conclusion: The ginsenoside Rf appears to be promising compound that could prove useful in antiobesity treatments.

• Archives of Pharmacal Research
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• v.29 no.1
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• pp.50-58
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• 2006

Translationally controlled tumor protein (TCTP), also known as histamine releasing factor (HRF), is found abundantly in different eukaryotic cell types. The sequence homology of TCTP between different species is very high, belonging to the MSS4/DSS4 superfamily of proteins. TCTP is involved in both cell growth and human late allergy reaction, as well as having a calcium binding property; however, its primary biological functions remain to be clearly elucidated. In regard to many possible functions, the TCTP of Plasmodium falciparum (Pf) is known to bind with an antimalarial agent, artemisinin, which is activated by heme. It is assumed that the endoperoxide-bridge of artemisinin is opened up by heme to form a free radical, which then eventually alkylates, probably to the Cys14 of PfTCTP. Study of the docking of artemisinin with heme, and subsequently with PfTCTP, was carried out to verify the above hypothesis on the basis of structural interactions. The three dimensional (3D) structure of PfTCTP was built by homology modeling, using the NMR structure of the TCTP of Schizosaccharomyces pombe as a template. The quality of the model was examined based on its secondary structure and biological function, as well as with the use of structure evaluating programs. The interactions between artemisinin, heme and PfTCTP were then studied using the docking program, FlexiDock. The center of the peroxide bond of artemisinin and the Fe of heme were docked within a short distance of $2.6{\AA}$, implying the strong possibility of an interaction between the two molecules, as proposed. When the activated form of artemisinin was docked on the PfTCTP, the C4-radical of the drug faced towards the sulfur of Cys14 within a distance of $2.48{\AA}$, again suggesting the possibility of alkylation having occurred. These results confirm the proposed mechanism of the antimalarial effect of artemisinin, which will provide a reliable method for establishing the mechanism of its biological activity using a molecular modeling study.

• YAKHAK HOEJI
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• v.30 no.1
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• pp.42-46
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• 1986

The binding characteristics of five cephalosporins, cefamandole, ceftriaxone, cefoxitin, latamoxef, and cefotetan to bovine serum albumin (BSA) was examined by UV difference spectrophotometry. 2-(4'-hydroxybenzeneazo) benzoic acid was used as the spectrophotometric probe. Competitive bindings between the probe and cephalosporins were observed. Based on the Scatchard plot, the BSA appeared to have two classes of binding sites in BSA binding with cephalosporins. The number of primary binding sites appears to be one, secondary binding sites appears to be three. The binding constants were found as follows: BSA-HBAB; $K_1^{obs}$=8.39$\times$$10^4$ $M^{-1}$, $K_2^{obs}$=1.60$\times$$10^4$ $M^{-1}$, BSA-Cefamandole; $K_1^{obs}$=5.44$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=0.74$\times$$10^3$ $M^{-1}$, BSA-Cefotriaxone; $K_1^{obs}$=6.78$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=0.88$\times$$10^3$ $M^{-1}$, BSA-Cefoxitin; $K_1^{obs}$=7.24$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=1.13$\times$$10^3$ $M^{-1}$, BSA-Latamoxef; $K_1^{obs}$=8.87$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=1.92$\times$$10^3$ $M^{-1}$, BSA-Cefotetan; $K_1^{obs}$=15.41$\times$$10^3$ $M^{-1}$, $K_2^{obs}$=2.7$\times$$10^3$ $M^{-1}$.