• Proceedings of the Korean Information Science Society Conference
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• 2007.10b
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• pp.17-21
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• 2007

Drug discovery is a long process with a low rate of successful new therapeutic discovery regardless of the advances in information technologies. Identification of candidate proteins is an essential step for the drug discovery and it usually requires considerable time and efforts in the drug discovery. The drug discovery is not a logical, but a fortuitous process. Nevertheless, considerable amount of information on drugs are accumulated in UniProt, NCBI, or DrugBank. As a result, it has become possible to try to devise new computational methods classifying drug target candidates extracting the common features of known drug target proteins. In this paper, we devise a method for drug target protein classification by using weighted feature summation and Support Vector Machine. According to our evaluation, the method is revealed to show moderate accuracy $85{\sim}90%$. This indicates that if the devised method is used appropriately, it can contribute in reducing the time and cost of the drug discovery process, particularly in identifying new drug target proteins.

• Molecules and Cells
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• v.26 no.2
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• pp.175-180
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• 2008

$I{\kappa}B$ kinase (IKK), the pivotal kinase in signal-dependent activation of nuclear factor-${\kappa}B$ (NF-${\kappa}B$), is composed of multiple protein components, including IKK ${\alpha}/{\beta}/{\gamma}$ core subunits. To investigate the regulation of the IKK complex, we immunoaffinity purified the IKK complex, and by MALDI-TOF mass spectrometry identified a splice variant of zinc finger protein 268 (ZNF268) as a novel IKKinteracting protein. Both the full-length and the spliced form of the ZNF268 protein were detected in a variety of mammalian tissues and cell lines. The genes were cloned and expressed by in vitro transcription/translation. Several deletion derivatives, such as KRAB domain (KRAB) on its own, the KRAB/spacer/4-zinc fingers (zF4), and the spacer/4-zinc fingers (zS4), were ectopically expressed in mammalian cells and exhibited had different subcellular locations. The KRAB-containing mutants were restricted to the nucleus, while zS4 was localized in the cytosol. TNF-${\alpha}$-induced NF-${\kappa}B$ activation was examined using these mutants and only zS4 was found to stimulate activation. Collectively, the results indicate that a spliced form of ZNF268 lacking the KRAB domain is located in the cytosol, where it seems to play a role in TNF-${\alpha}$-induced NF-${\kappa}B$ activation by interacting with the IKK complex.

• BMB Reports
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• v.49 no.11
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• pp.585-586
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• 2016

Extracellular vesicles (EVs) are natural carriers of biomolecules that play central roles in cell-to-cell communications. Based on this, there have been various attempts to use EVs as therapeutic drug carriers. From chemical reagents to nucleic acids, various macromolecules were successfully loaded into EVs; however, loading of proteins with high molecular weight has been huddled with several problems. Purification of recombinant proteins is expensive and time consuming, and easily results in modification of proteins due to physical or chemical forces. Also, the loading efficiency of conventional methods is too low for most proteins. We have recently proposed a new method, the so-called exosomes for protein loading via optically reversible protein-protein interaction (EXPLORs), to overcome the limitations. Since EXPLORs are produced by actively loading of intracellular proteins into EVs using blue light without protein purification steps, we demonstrated that the EXPLOR technique significantly improves the loading and delivery efficiency of therapeutic proteins. In further in vitro and in vivo experiments, we demonstrate the potential of EXPLOR technology as a novel platform for biopharmaceuticals, by successful delivery of several functional proteins such as Cre recombinase, into the target cells.

• Bulletin of the Korean Chemical Society
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• v.27 no.9
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• pp.1285-1286
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• 2006

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1023-1024
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• 2013

• Journal of the Korea Society of Computer and Information
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• v.21 no.1
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• pp.115-123
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• 2016

In this study, we collect various side effect pairs which are appeared frequently at many drugs, and select side effect pairs that have higher severity. For every selected side effect pair, we extract common genetic networks which are shared by side effects' genes and drugs' target genes based on PPI(Protein-Protein Interaction) network. For this work, firstly, we gather drug related data, side effect data and PPI data. Secondly, for extracting common genetic network, we find shortest paths between drug target genes and side effect genes based on PPI network, and integrate these shortest paths. Thirdly, we develop a classification model which uses this common genetic network as a classifier. We calculate similarity score between the common genetic network and genetic network of a drug for classifying the drug. Lastly, we validate our classification model by means of AUC(Area Under the Curve) value.

• Proceedings of the Korea Information Processing Society Conference
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• 2022.11a
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• pp.63-65
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• 2022

DDI(Drug-Drug Interaction)는 병원에서 발생하는 약물이상반응의 30%를 유발하는 부작용이지만, 현실적으로 모든 약물쌍의 DDI 를 기존 in vivo, in vitro 방식으로 예측하는 것은 불가능하다. 그렇기에, 다양한 in silico 방식의 DDI 예측 모델이 연구되고 있다. 본 연구에서는, 단백질 네트워크 상에서 RWR(Random Walk with Restart) 알고리즘을 통해 약물과 직접적으로 상호작용하는 단백질과 간접적으로 상호작용하는 단백질의 정보를 사용하여 DDI 를 예측하는 모델을 개발하였다. 이 모델을 통하여 기존에 발견하지 못한 DDI 를 새롭게 발견하고, 신약 개발 시에도, 신약과 함께 복용 시 문제를 일으킬 수 있는 약물을 예측하여 약물 이상반응을 방지하고자 한다.

• Macromolecular Research
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• v.16 no.6
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• pp.481-488
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• 2008

Apoptosis is a natural cell suicide mechanism to maintain homeostasis. However, many of the diseases encountered today are caused by aberrant apoptosis where excessive apoptosis leads to neurodegenerative disorders, ischemic heart disease, autoimmune disorders, infectious diseases, etc. A variety of antiapoptotic agents have been reported to interfere with the apoptosis pathway. These agents can be potential drug candidates for the treatment or prevention of diseases caused by dysregulated apoptosis. Obviously, world-wide pharmaceutical and biotechnology companies are gearing up to develop antiapoptotic drugs with some products being commercially available. Polymeric drug delivery systems are essential to their success. Recent R&D efforts have focused on the chemical or bioconjugation of antiapoptotic proteins with the protein transduction domain (PTD) for higher cellular uptake with antibodies for specific targeting as well as with polymers to enhance the protein stability and prolonged effect with success observed both in vivo and in vitro. All these different fusion antiapoptotic proteins provide promising results for the treatment of dysregulated apoptosis diseases.

• Archives of Pharmacal Research
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• v.27 no.1
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• pp.1-12
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• 2004

Initial burst is one of the major challenges in protein-encapsulated microparticle systems. Since protein release during the initial stage depends mostly on the diffusional escape of the protein, major approaches to prevent the initial burst have focused on efficient encapsulation of the protein within the microparticles. For this reason, control of encapsulation efficiency and the extent of initial burst are based on common formulation parameters. The present article provides a literature review of the formulation parameters that are known to influence the two properties in the emulsion-solvent evaporation/extraction method. Physical and chemical properties of encapsulating polymers, solvent systems, polymer-drug interactions, and properties of the continuous phase are some of the influential variables. Most parameters affect encapsulation efficiency and initial burst by modifying solidification rate of the dispersed phase. In order to prevent many unfavorable events such as pore formation, drug loss, and drug migration that occur while the dispersed phase is in the semi-solid state, it is important to understand and optimize these variables.

• Bulletin of the Korean Chemical Society
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• v.32 no.10
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• pp.3553-3554
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• 2011