• Title/Summary/Keyword: docking

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Variation in bioactive principles and bioactive compounds of Rosa rugosa fruit during ripening (해당화 열매 성숙단계에 따른 생리활성 및 기능성 물질 변화 분석)

  • Kwak, Minjeong;Eom, Seung Hee;Gil, Jinsu;Kim, Ju-Sung;Hyun, Tae Kyung
    • Journal of Plant Biotechnology
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    • v.46 no.3
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    • pp.236-245
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    • 2019
  • Fruit ripening is a genetically programmed process involving a number of biochemical and physiological processes assisted by variations in gene expression and enzyme activities. This process generally affects the phytochemical profile and the bioactive principles in fruits and vegetables. To appraise the variation in bioactive principles of fruits from Rosa rugosa during its ripening process, we analyzed the changes in antioxidant and anti-elastase activities and polyphenolic compounds during the four ripening stages of fruits. Overall, an extract of unripe fruits contained the highest levels of total phenolic and flavonoid contents, radical scavenging activity, reducing power, oxygen radical antioxidant capacity, and elastase inhibitory activity, compared with the extracts of fruits at other stages of ripening. Additionally, we found that the reduction of flavonoid content occurs because of decreased transcriptional levels of genes involved in flavonoid biosynthesis pathway during the ripening process. Based on HPLC analysis, we found that the extract of unripe fruits contained the highest amount of myricetin, caffeic acid, chlorogenic acid, syringic acid, and p-coumaric acid and suggested that the antioxidant and anti-elastase activities of the extract obtained from stage 1, should be mediated by the presence of these compounds. Additionally, we analyzed the interaction sites and patterns between these compounds and elastase using the structure-based molecular docking approach, and suggested that chlorogenic acid strongly interacted with elastase. Together, these findings suggest that the maturity of fruits has profound effects on the pharmaceutical value of R. rugosa.

A Sliding Mode Control of an Underwater Robotic Vehicle under the Influence of Thrust Dynamics (추진기의 동역학을 고려한 무인잠수정의 슬라이딩 모드 제어)

  • Choi, Hyeung-Sik;Park, Han-Il;Roh, Min-Shik;So, Myung-Ok
    • Journal of Advanced Marine Engineering and Technology
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    • v.33 no.8
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    • pp.1203-1211
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    • 2009
  • The dynamics of underwater vehicles can be greatly influenced by the dynamics of the vehicle thrusters. The control of the state of the hovering or very slow motion of the underwater vehicle is most important for automatic docking or control of the manipulator of the vehicle. The dynamics of the thruster based on the electric motor is nonlinear and has uncertain parameters. Since the dynamics of the vehicle coupled with the dynamics of the thruster is nonlinear and has uncertain parameters, a robust control is very effective for a desired motion tracking of the uncertain and nonlinear vehicle. In this paper a study was performed on the robust control scheme of the very slow motion or hovering motion of the underwater vehicle actuated by the electric motor. Also, a concurrent control on the state of the vehicle with nonlinearity and uncertain parameters was performed. A sliding mode control algorithm out of robust controllers was designed and applied, which compensates the nonlinear forces and uncertain parameters of the vehicle and actuator. Through a computer simulation, the proposed control scheme was compared with a linear PD controller and its superior performance was validated.

Protein target identification of ginsenosides in skeletal muscle tissues: discovery of natural small-molecule activators of muscle-type creatine kinase

  • Chen, Feiyan;Zhu, Kexuan;Chen, Lin;Ouyang, Liufeng;Chen, Cuihua;Gu, Ling;Jiang, Yucui;Wang, Zhongli;Lin, Zixuan;Zhang, Qiang;Shao, Xiao;Dai, Jianguo;Zhao, Yunan
    • Journal of Ginseng Research
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    • v.44 no.3
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    • pp.461-474
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    • 2020
  • Background: Ginseng effectively reduces fatigue in both animal models and clinical trials. However, the mechanism of action is not completely understood, and its molecular targets remain largely unknown. Methods: By screening for proteins that interact with the primary components of ginseng (ginsenosides) in an affinity chromatography assay, we have identified muscle-type creatine kinase (CK-MM) as a potential target in skeletal muscle tissues. Results: Biolayer interferometry analysis showed that ginsenoside metabolites, instead of parent ginsenosides, had direct interaction with recombinant human CK-MM. Subsequently, 20(S)-protopanaxadiol (PPD), which is a ginsenoside metabolite and displayed the strongest interaction with CK-MM in the study, was selected as a representative to confirm direct binding and its biological importance. Biolayer interferometry kinetics analysis and isothermal titration calorimetry assay demonstrated that PPD specifically bound to human CK-MM. Moreover, the mutation of key amino acids predicted by molecular docking decreased the affinity between PPD and CK-MM. The direct binding activated CK-MM activity in vitro and in vivo, which increased the levels of tissue phosphocreatine and strengthened the function of the creatine kinase/phosphocreatine system in skeletal muscle, thus buffering cellular ATP, delaying exercise-induced lactate accumulation, and improving exercise performance in mice. Conclusion: Our results suggest a cellular target and an initiating molecular event by which ginseng reduces fatigue. All these findings indicate PPD as a small molecular activator of CK-MM, which can help in further developing better CK-MM activators based on the dammarane-type triterpenoid structure.

Brain Wave Control Effect of Smart-wave via Docking into the Odorant-binding Protein (스마트 웨이브 조성물질의 odorant 결합 단백질에 대한 분자 결합 친화도 비교 분석 및 후각 흡입으로 유도되는 뇌파 변화 연구)

  • Kim, Dong-Chan
    • Journal of Life Science
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    • v.26 no.3
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    • pp.346-352
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    • 2016
  • Aroma inhalation therapy has traditionally been used not only in alternative medicinal treatment but also in psychotherapy. In the first stage of the study, the in silico molecular binding affinity of the major ingredients of Smart-Wave (SW) on the active site of the odorant-binding protein (OBP) was compared with that of citrate anions. The binding affinity of the chemical mixture formula of the major ingredients of SW on the OBP was relatively higher than that of citrate anions. In addition, nasal inhalation of SW had a positive effect upon changes in brain waves. Eighteen healthy volunteers participated in the experiment. The study consisted of measurements of the brain’s meditation level recordings in the pre- and post-SW inhalation periods as compared with negative (EV) and positive (HB) control groups. After SW inhalation, all the subjects stated that they felt “fresher” and that the SW trial group had significantly changed the brain’s meditation in a positive way. SW inhalation also converted EV-induced unstable brain meditation wave patterns into more stable patterns. Collectively, the results of this empirical study strongly suggest that the SW mixture activates the OBP and controls the mental state by regulating brain waves. The results provide scientific evidence that the SW formula has potential as an effective mental-stress controller.

Curcumin and its Analogues (PGV-0 and PGV-1) Enhance Sensitivity of Resistant MCF-7 Cells to Doxorubicin through Inhibition of HER2 and NF-kB Activation

  • Meiyanto, Edy;Putri, Dyaningtyas Dewi Pamungkas;Susidarti, Ratna Asmah;Murwanti, Retno;Sardjiman, Sardjiman;Fitriasari, Aditya;Husnaa, Ulfatul;Purnomo, Hari;Kawaichi, Masashi
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.1
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    • pp.179-184
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    • 2014
  • Chemoresistance of breast cancer to doxorubicin is mediated mainly through activation of NF-kB and over expression of HER2. Curcumin and its analogues (PGV-0 and PGV-1) exert cytotoxic effects on T47D breast cancer cells. Suppression of NF-kB activation is suggested to contribute to this activity. The present study aimed to explore the effects of curcumin, PGV-0, and PGV-1 singly and in combination with doxorubicin on MCF-7/Dox cells featuring over-expression of HER2. In MTT assays, curcumin, PGV-0, and PGV-1 showed cytotoxicity effects against MCF-7/Dox with IC50 values of $80{\mu}M$, $21{\mu}M$, and $82{\mu}M$ respectively. These compounds increased MCF-7/Dox sensitivity to doxorubicin. Cell cycle distribution analysis exhibited that the combination of curcumin and its analogues with Dox increased sub G-1 cell populations. Curcumin and PGV-1 but not PGV-0 decreased localization of p65 into the nucleus induced by Dox, indicating that activation of NF-kB was inhibited. Molecular docking of curcumin, PGV-0, and PGV-1 demonstrated high affinity to HER2 at ATP binding site. This interaction were directly comparable with those of ATP and lapatinib. These findings suggested that curcumin, PGV-0 and PGV-1 enhance the Dox cytotoxicity to MCF-7 cells through inhibition of HER2 activity and NF-kB activation.

A Novel Suberoylanilide Hydroxamic Acid Histone Deacetylase Inhibitor Derivative, N25, Exhibiting Improved Antitumor Activity in both Human U251 and H460 Cells

  • Zhang, Song;Huang, Wei-Bin;Wu, Li;Wang, Lai-You;Ye, Lian-Bao;Feng, Bing-Hong
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.10
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    • pp.4331-4338
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    • 2014
  • $N^1$-(2, 5-dimethoxyphenyl)-$N^8$-hydroxyoctanediamide (N25) is a novel SAHA cap derivative of HDACi, with a patent (No. CN 103159646). This invention is a hydroxamic acid compound with a structural formula of $RNHCO(CH_2)6CONHOH$ (wherein R=2, 5dimethoxyaniline), a pharmaceutically acceptable salt which is soluble. In the present study, we investigated the effects of N25 with regard to drug distribution and molecular docking, and anti-proliferation, apoptosis, cell cycling, and $LD_{50}$. First, we designed a molecular approach for modeling selected SAHA derivatives based on available structural information regarding human HDAC8 in complex with SAHA (PDB code 1T69). N25 was found to be stabilized by direct interaction with the HDAC8. Anti-proliferative activity was observed in human glioma U251, U87, T98G cells and human lung cancer H460, A549, H1299 cells at moderate concentrations ($0.5-30{\mu}M$). Compared with SAHA, N25 displayed an increased antitumor activity in U251 and H460 cells. We further analyzed cell death mechanisms activated by N25 in U251 and H460 cells. N25 significantly increased acetylation of Histone 3 and inhibited HDAC4. On RT-PCR analysis, N25 increased the mRNA levels of p21, however, decreased the levels of p53. These resulted in promotion of apoptosis, inducing G0/G1 arrest in U251 cells and G2/M arrest in H460 cells in a time-dependent and dose-dependent manner. In addition, N25 was able to distribute to brain tissue through the blood-brain barrier of mice ($LD_{50}$: 240.840mg/kg). In conclusion, our findings demonstrate that N25 will provide an invaluable tool to investigate the molecular mechanism with potential chemotherapeutic value in several malignancies, especially human glioma.

Association of Insulin Receptor Substrate-1 G972R Variant with Non-small Cell Lung Cancer Risk

  • Lee, Chang Youl;Ahn, Chul Min;Jeon, Jeong Hee;Kim, Hyung Jung;Kim, Se Kyu;Chang, Joon;Kim, Sung Kyu;Chang, Yoon Soo
    • Tuberculosis and Respiratory Diseases
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    • v.67 no.1
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    • pp.8-13
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    • 2009
  • Background: The insulin receptor substrate-1 (IRS-1) is the primary docking molecule for the insulin-like growth factor I receptor (IGF-IR), and is required for activation of the phosphatidylinositol 3'-kinase (PI3K) pathway. IRS-1 activation of the (PI3K) pathway regulates IGF-mediated survival, enhancement of cellular motility and apoptosis. Therefore, we attempted to ascertain whether IRS-1 genetic variations affect an individual's risk for non-small cell lung cancer (NSCLC). Methods: Two-hundred and eighteen subjects, either diagnosed with NSCLC or control subjects, were matched by age, gender and smoking status. Genomic DNA from each subject was amplified by PCR and analyzed according to the restriction fragment length polymorphism (RFLP) profile to detect the IRS-1 G972R polymorphism. Results: The frequencies of each polymorphic variation, in the control population, were as follows: GG=103 (94.5%) and GR=6 (5.5%); for the NSCLC subjects, the genotypic frequencies were as follows: GG=106 (97.2%) and GR=3 (2.8%). We could not demonstrate statistically significant differences in the genotypic distribution between the NSCLC and the control subjects (p=0.499, Fisher's Exact test). The relative risk of NSCLC, associated with the IRS-1 G972R polymorphic variation, was 1.028 (95% CI; 0.63~9.90). In addition, we found no differences between polymorphic variants with regard to the histological subtype of NSCLC. Conclusion: We did not observe any noteworthy differences in the frequency of the IRS-1 G972R polymorphism in NSCLC patients, compared to control subjects. These results suggest suggesting that, in our study population, the IRS-1 G972R polymorphism does may not appear to be associated with an increased risk of NSCLC.

A Study on Trade Structure of Furniture and Port Logistics Business Model in North-east Asia (동북아 가구류 무역구조 분석을 통한 항만물류 비즈니스 모델의 탐색)

  • Oh, Yong-Sik;Kwon, Moon-Kyu;Koo, Kyoung-Mo
    • Journal of Korea Port Economic Association
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    • v.30 no.3
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    • pp.231-257
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    • 2014
  • In general, furniture industry, with its high foreign dependency, has serious logistics issues that are commonly raised in such countries as Korea, China and Japan. This leads to my different possibilities & ways of rationalizing the logistics systems that utilize port hinterlands. Thus the purpose of the present paper is to create new logistics systems which will work effectively across the three countries. In this research study, we came up with 2 logistics models in which the port hinterland of Busan serves as the distribution center for furniture industry, and the models were suggested as the cooperative logistics business systems for the North-east asian region. In the proposed models, 'Busan furniture logistics center' has the dual functions of 'the cross-docking center from China to Japan' and 'the assembly & delivery center for furniture imported by Japan'. To have this logistics business center materialized, we propose that policy-level supports from the relevant port authorities be provided in the following three aspects: overseas investment promotion focused on the furniture industry of Japan, protection & enhancement of competitiveness for the port of Busan, and uilization plans for the new port hinterland of the city.

Relative Navigation Study Using Multiple PSD Sensor and Beacon Module Based on Kalman Filter (복수 PSD와 비콘을 이용한 칼만필터 기반 상대항법에 대한 연구)

  • Song, Jeonggyu;Jeong, Junho;Yang, Seungwon;Kim, Seungkeun;Suk, Jinyoung
    • Journal of the Korean Society for Aeronautical & Space Sciences
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    • v.46 no.3
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    • pp.219-229
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    • 2018
  • This paper proposes Kalman Filter-based relative navigation algorithms for proximity tasks such as rendezvous/docking/cluster-operation of spacecraft using PSD Sensors and Infrared Beacon Modules. Numerical simulations are performed for comparative analysis of the performance of each relative-navigation technique. Based on the operation principle and optical modeling of the PSD Sensor and the Infrared Beacon Module used in the relative navigation algorithm, a measurement model for the Kalman filter is constructed. The Extended Kalman Filter(EKF) and the Unscented Kalman Filter(UKF) are used as probabilistic relative navigation based on measurement fusion to utilize kinematics and dynamics information on translational and rotation motions of satellites. Relative position and relative attitude estimation performance of two filters is compared. Especially, through the simulation of various scenarios, performance changes are also investigated depending on the number of PSD Sensors and IR Beacons in target and chaser satellites.

Pharmacophore Modeling, Virtual Screening and Molecular Docking Studies for Identification of New Inverse Agonists of Human Histamine H1 Receptor

  • Thangapandian, Sundarapandian;Krishnamoorthy, Navaneethakrishnan;John, Shalini;Sakkiah, Sugunadevi;Lazar, Prettina;Lee, Yu-No;Lee, Keun-Woo
    • Bulletin of the Korean Chemical Society
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    • v.31 no.1
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    • pp.52-58
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    • 2010
  • Human histamine H1 receptor (HHR1) is a G protein-coupled receptor and a primary target for antiallergic therapy. Here, the ligand-based three-dimensional pharmacophore models were built from a set of known HHR1 inverse agonists using HypoGen module of CATALYST software. All ten generated pharmacophore models consist of five essential features: hydrogen bond acceptor, ring aromatic, positive ionizable and two hydrophobic functions. Best model had a correlation coefficient of 0.854 for training set compounds and it was validated with an external test set with a high correlation value of 0.925. Using this model Maybridge database containing 60,000 compounds was screened for potential leads. A rigorous screening for drug-like compounds unveiled RH01692 and SPB00834, two novel molecules for HHR1 with good CATALYST fit and estimated activity values. The new lead molecules were docked into the active site of constructed HHR1 homology model based on recently crystallized squid rhodopsin as template. Both the hit compounds were found to have critical interactions with Glu177, Phe432 and other important amino acids. The interpretations of this study may effectively be deployed in designing of novel HHR1 inverse agonists.