• Genomics & Informatics
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• v.14 no.3
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• pp.104-111
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• 2016

Zika virus (ZIKV) is a mosquito borne pathogen, belongs to Flaviviridae family having a positive-sense single-stranded RNA genome, currently known for causing large epidemics in Brazil. Its infection can cause microcephaly, a serious birth defect during pregnancy. The recent outbreak of ZIKV in February 2016 in Brazil realized it as a major health risk, demands an enhanced surveillance and a need to develop novel drugs against ZIKV. Amodiaquine, prochlorperazine, quinacrine, and berberine are few promising drugs approved by Food and Drug Administration against dengue virus which also belong to Flaviviridae family. In this study, we performed molecular docking analysis of these drugs against nonstructural 3 (NS3) protein of ZIKV. The protease activity of NS3 is necessary for viral replication and its prohibition could be considered as a strategy for treatment of ZIKV infection. Amongst these four drugs, berberine has shown highest binding affinity of -5.8 kcal/mol and it is binding around the active site region of the receptor. Based on the properties of berberine, more similar compounds were retrieved from ZINC database and a structure-based virtual screening was carried out by AutoDock Vina in PyRx 0.8. Best 10 novel drug-like compounds were identified and amongst them ZINC53047591 (2-(benzylsulfanyl)-3-cyclohexyl-3H-spiro[benzo[h]quinazoline-5,1'-cyclopentan]-4(6H)-one) was found to interact with NS3 protein with binding energy of -7.1 kcal/mol and formed H-bonds with Ser135 and Asn152 amino acid residues. Observations made in this study may extend an assuring platform for developing anti-viral competitive inhibitors against ZIKV infection.

• Journal of Advanced Marine Engineering and Technology
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• v.39 no.4
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• pp.399-404
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• 2015

The cost of fuel in ships has recently increased due to a rapid increase in international oil prices and international restrictions regarding the greenhouse effect generated from the burning of fuel. Therefore, different methods for changing the hull designs for improving energy efficiency, developing coating for reducing friction resistances, developing additives for improving engine thermal efficiency, and low-speed operation for reducing fuel consumption have been considered. The developments of high-speed, large-scale, and energy-saving vessels are deemed essential to adapt to the recent high oil price era. Therefore, it is important to analyze Precisely the qualitative and quantitative changes in the resistance value of the local areas of the hull surface. In this study, the engine performance before and after docking was analyzed to examine friction resistance caused by marine growth on the hull as a basic study for improving the energy efficiency. The result was then presented by comparing it with the previous data for 2.5 years between docks to investigate the performance of the main engine, the change in friction resistances and loads, the fuel consumption and ship speed.

• Journal of Ginseng Research
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• v.39 no.4
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• pp.406-413
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• 2015

Background: Pathogenesis-related 10 (PR-10) proteins are small, cytosolic proteins with a similar three-dimensional structure. Crystal structures for several PR-10 homologs have similar overall folding patterns, with an unusually large internal cavity that is a binding site for biologically important molecules. Although structural information on PR-10 proteins is substantial, understanding of their biological function remains limited. Here, we showed that one of the PgPR-10 homologs, PgPR-10.3, shares binding properties with flavonoids, kinetin, emodin, deoxycholic acid, and ginsenoside Re (1 of the steroid glycosides). Methods: Gene expression patterns of PgPR-10.3 were analyzed by quantitative real-time PCR. The three-dimensional structure of PgPR-10 proteins was visualized by homology modeling, and docking to retrieve biologically active molecules was performed using AutoDock4 program. Results: Transcript levels of PgPR-10.3 expressed in leaves, stems, and roots of 3-wk-old ginseng plantlets were on average 86-fold lower than those of PgPR-10.2. In mature 2-yr-old ginseng plants, the mRNA of PgPR-10.3 is restricted to leaves. Ginsenoside Re production is especially prominent in leaves of Panax ginseng Meyer, and the binding property of PgPR-10.3 with ginsenoside Re suggests that this protein has an important role in the control of secondary metabolism. Conclusion: Although ginseng PR-10.3 gene is expressed in all organs of 3-wk-old plantlets, its expression is restricted to leaves in mature 2-yr-old ginseng plants. The putative binding property of PgPR-10.3 with Re is intriguing. Further verification of binding affinity with other biologically important molecules in the large hydrophobic cavity of PgPR-10.3 may provide an insight into the biological features of PR-10 proteins.

• Journal of Ginseng Research
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• v.44 no.5
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• pp.690-696
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• 2020

Background: As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis. Methods: The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor. Results: Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively. Conclusion: This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.

• Maxillofacial Plastic and Reconstructive Surgery
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• v.29 no.5
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• pp.429-438
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• 2007

Transport distraction osteogenesis has been introduced recently to correct skeletal malformations and discrepancies in the maxillofacial area. To reconstruct 3-dimensitonal mandibular shape, this transport distraction can be considered with the use of reconstruction plate. A 23-years-old male having unilateral mandibular body and angle defects, who had been operated of partial mandibular resection due to unicystic ameloblastoma, was treated by transport distraction procedures with ThreadLock transport $distractor^{(R)}$ (KLS Martin Co., Germany) through the rail of reconstruction plate (Osteomed Co., USA). After being distracted 35 mm defect from mandibular angle to body, and consolidated for 16 weeks, allogenic bone graft on docking site was performed with removal of transgingival pin. For more than 13 weeks follow up period after consolidation period, gradual increase of radiopacity in the radiographic examination was shown, and the curved mandibular continuity according to the reconstruction plate was made firmly. These transport distraction osteogenesis in the mandible was able to be considered as the good and minimally invasive technique for the reconstruction of mandibular discontinuity. Young patient was also very satisfactory for these results.

• Ocean Systems Engineering
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• v.2 no.3
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• pp.217-228
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• 2012

As the size of container ships continues to increase, not many existing harbors can host the super-container ship due to its increased draft and the corresponding dredging requires huge budget. In addition, the minimization of waiting and loading/offloading time is the most important factor in harbor competitiveness. In this regard, mobile-harbor concept has been developed in Korea to achieve much improved harbor capacity and efficiency. In developing the concept, one of the most important elements is the operability of crane between two or more floating bodies in side-by-side arrangement. The container ship is to be stationed through a hawser connection to an outside-harbor fixed-pile station with the depth allowing its large draft. The mobile harbors with smart cranes are berthed to the sides of its hull for loading/offloading containers and transportation. For successful operation, the relative motions between the two or more floating bodies with hawser/fender connections have to be within allowable range. Therefore, the reliable prediction of the relative motions of the multiple floating bodies with realistic mooring system is essential to find the best hull particulars, hawser/mooring/fender arrangement, and crane/docking-station design. Time-domain multi-hull-mooring coupled dynamic analysis program is used to assess the hydrodynamic interactions among the multiple floating bodies and the global performance of the system. Both collinear and non-collinear wind-wave-current environments are applied to the system. It is found that the non-collinear case can equally be functional in dynamics view compared to the collinear case but undesirable phenomena associated with vessel responses and hawser tensions can also happen at certain conditions, so more care needs to be taken.

• Journal of Marine Bioscience and Biotechnology
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• v.6 no.2
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• pp.102-109
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• 2014

Cetaceans (whales, dolphins, and porpoises) are aquatic mammals that experienced drastic changes during the transition from terrestrial to aquatic environment. Morphological changes include streamlined body, alterations in the face, transformation of the forelimbs into flippers, disappearance of the hindlimbs and the acquisition of flukes on the tail. For a prolonged diving, cetaceans acquired hypoxia-resistance by developing various anatomical and physiological changes. However, molecular mechanisms underlying these adaptations are still limited. CREB-binding protein (CREBBP) is a transcriptional co-activator critical for embryonic development, growth control, metabolic homeostasis and responses to hypoxia. Natural selection analysis of five cetacean CREBBPs compared with those from 15 terrestrial relatives revealed strong purifying selection, supporting the importance of its role in mammals. However, prediction for amino acid changes that elicit functional difference of CREBBP identified three cetacean specific changes localized within a region required for interaction with SRCAP and in proximal regions to KIX domain of CREBBP. Mutations in CREBBP or SRCAP are known to cause craniofacial and skeletal defects in human, and KIX domain of CREBBP serves as a docking site for transcription factors including c-Myb, an essential regulator of haematopoiesis. In these respects, our study provides interesting insights into the functional adaptation of cetacean CREBBP for aquatic lifestyle.

• Molecules and Cells
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• v.43 no.3
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• pp.222-227
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• 2020

Inositol polyphosphate multikinase (IPMK) is required for the biosynthesis of inositol phosphates (IPs) through the phosphorylation of multiple IP metabolites such as IP3 and IP4. The biological significance of IPMK's catalytic actions to regulate cellular signaling events such as growth and metabolism has been studied extensively. However, pharmacological reagents that inhibit IPMK have not yet been identified. We employed a structure-based virtual screening of publicly available U.S. Food and Drug Administration-approved drugs and chemicals that identified the antidepressant, vilazodone, as an IPMK inhibitor. Docking simulations and pharmacophore analyses showed that vilazodone has a higher affinity for the ATP-binding catalytic region of IPMK than ATP and we validated that vilazodone inhibits IPMK's IP kinase activities in vitro. The incubation of vilazodone with NIH3T3-L1 fibroblasts reduced cellular levels of IP5 and other highly phosphorylated IPs without influencing IP4 levels. We further found decreased Akt phosphorylation in vilazodone-treated HCT116 cancer cells. These data clearly indicate selective cellular actions of vilazodone against IPMK-dependent catalytic steps in IP metabolism and Akt activation. Collectively, our data demonstrate vilazodone as a method to inhibit cellular IPMK, providing a valuable pharmacological agent to study and target the biological and pathological processes governed by IPMK.

• Proceedings of the Korean Institute of Navigation and Port Research Conference
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• 2009.06a
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• pp.435-438
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• 2009

A navigation aid buoy is a kind of safety facility for maritime navigation with a purpose of leading the vessels for navigating, docking and sail off. An advanced rechargeable battery is required for stable power supply for navigation aid buoy as the high magnitude LED lamps, real time location/control for navigation aids and e-Navigation support systems with maritime climate observation equipments have recently been deployed. This study is focused on the lithium battery, especially lithium polymer battery which is believed to be safer than the other types of batteries. The lithium polymer battery reviewed in this study is designed with $LiFePO_4$-based cathode, which has superior safety features to the oxide-based cathodes. Besides, a 3.6kWh battery pack has been built with the above-mentioned unit cells for the purpose of comparative research with lead acid battery system.

• KIPS Transactions on Software and Data Engineering
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• v.8 no.10
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• pp.421-426
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• 2019

In this paper, we propose a method to visualize the geometric features of the contact region between proteins in a protein complex. When proteins or ligands are represented as curved surfaces with irregularities, the property that the two surfaces contact each other without intersections is called shape compatibility. Protein-Protein or Protein-Ligand docking researches have shown that shape complementarity, chemical properties, and entropy play an important role in finding contact regions. Usually, after finding a region with high shape complementarity, we can predict the contact region by using residual polarity and hydrophobicity of amino acids belonging to this region. In the research for predicting the contact region, it is necessary to investigate the geometrical features of the contact region in known protein complexes. For this purpose, it is essential to visualize the geometric features of the molecular surface. In this paper, we propose a method to find the contact region, and visualize the geometric features of it as normal vectors and mean curvatures of the protein complex.