• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2006-2010
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• 2013

Leukocyte common antigen-related phosphatase (LAR) has been considered a promising target for the development of therapeutics for neurological diseases. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule LAR inhibitors. Five of these inhibitors revealed micromolar inhibitory activities with the associated $IC_{50}$ values ranging from 2 to 6 ${\mu}M$. Because the newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of LAR are discussed in detail.

• The Plant Pathology Journal
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• v.33 no.6
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• pp.529-542
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• 2017

Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3359-3365
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• 2010

The incorporation of microwave irradiation with the prevalent "click chemistry" is currently of considerable synthetic interest. We describe here the introduction of such laboratorial shortcut into carbohydrate-based drug discovery, resulting in the rapid formation of a series of triazole-linked salicylic $\beta$-D-O-glycosides with biological activities. All "clicked" products were achieved in excellent yields ($\approx$ 90%) within only a quarter. In addition, based on the structural characteristics of the afforded glycomimetics, their inhibitory activities were evaluated toward protein tyrosine phosphatases 1B (PTP1B) and a panel of homologous protein tyrosine phosphatases (PTPs). Docking simulation was also conducted to plausibly propose binding modes of this glycosyl salicylate series with the enzymatic target.

• Proceedings of the Korean Information Science Society Conference
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• 2010.06b
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• pp.514-517
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• 2010

그리드 인프라를 활용하여 대규모 계산 자원이 필요한 가상 스크리닝(Virtual Screening)에 관한 연구가 국제 WISDOM 프로젝트를 중심으로 활발하게 진행 중에 있다. 기존의 연구들은 싱글 클러스터나 개인의 컴퓨터를 중심으로 계산 자원을 활용하는 방식으로 연구가 진행이 되었다. WISDOM을 중심으로 대규모 말라리아(Malaria), 조류 독감(Avian Flu) 에 대한 대규모 신약 후보 탐색에 관한 연구들이 진행이 되었으며 한국과학기술정보연구원(KISTI)의 그리드 개발팀은 2007년도부터 국제 공동 파트너로 연구에 참여하고 있다. 공동연구에 참여하면서 신약 연구 개발자들이 Docking 및 그리드 자원을 활용하기 위한 접근 방식에 있어서 기존 방식들을 활용하기 어려운 점과 검색된 신약 물질을 분석하는 도구의 활용이 어려움이 많아 그리드 기반의 가상스크리닝 도구인 DrugScreenr-G(이하, DSG-G 클라리언트)를 개발하게 되었다. 본 논문은 개발된 DSG-G 클라이언트에 관한 개발 및 구조에 관한 내용이다.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.92-93
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• 2002

With the recent development of combinatorial chemistry, recombinant biotechnology and rational drug design, millions of compounds are being produced in the laboratories of pharmaceutical companies. These new drug candidates are evaluated their efficacy and toxicity through in vivo animal model studies which is very important in drug development. From these studies, very successful drug candidates are selected. (omitted)

• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3345-3349
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• 2013

Hsp90 shows great promise as a therapeutic target due to its potential to disable multiple signaling pathways simultaneously. In this study, we discovered that a natural product, butein moderately inhibited the growth of drug-resistant cancer cells (A2780cis and H1975), and brought about the degradation of oncogenic Hsp90 client proteins. The study demonstrated that butein would be a therapeutic lead to circumvent drug-resistance in cancer chemotherapy. The structure-based screening, synthesis, and biological evaluation of butein are described herein.

• Biomolecules & Therapeutics
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• v.29 no.2
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• pp.234-247
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• 2021

We used a heterozygous gene deletion library of fission yeasts comprising all essential and non-essential genes for a microarray screening of target genes of the antifungal terbinafine, which inhibits ergosterol synthesis via the Erg1 enzyme. We identified 14 heterozygous strains corresponding to 10 non-essential [7 ribosomal-protein (RP) coding genes, spt7, spt20, and elp2] and 4 essential genes (tif302, rpl2501, rpl31, and erg1). Expectedly, their erg1 mRNA and protein levels had decreased compared to the control strain SP286. When we studied the action mechanism of the non-essential target genes using cognate haploid deletion strains, knockout of SAGA-subunit genes caused a down-regulation in erg1 transcription compared to the control strain ED668. However, knockout of RP genes conferred no susceptibility to ergosterol-targeting antifungals. Surprisingly, the RP genes participated in the erg1 transcription as components of repressor complexes as observed in a comparison analysis of the experimental ratio of erg1 mRNA. To understand the action mechanism of the interaction between the drug and the novel essential target genes, we performed isobologram assays with terbinafine and econazole (or cycloheximide). Terbinafine susceptibility of the tif302 heterozygous strain was attributed to both decreased erg1 mRNA levels and inhibition of translation. Moreover, Tif302 was required for efficacy of both terbinafine and cycloheximide. Based on a molecular modeling analysis, terbinafine could directly bind to Tif302 in yeasts, suggesting Tif302 as a potential off-target of terbinafine. In conclusion, this genome-wide screening system can be harnessed for the identification and characterization of target genes under any condition of interest.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2655-2659
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• 2014

Dual specificity protein phosphatase 4 (DUSP4) has been considered a promising target for the development of therapeutics for various human cancers. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule DUSP4 inhibitors. As a consequence of the virtual screening with the modified scoring function to include an effective molecular solvation free energy term, five micromolar DUSP4 inhibitors are found with the associated $IC_{50}$ values ranging from 3.5 to $10.8{\mu}M$. Because these newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of DUSP4 are discussed in detail.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.263-269
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• 2008

Hydrazinocurcumin (HC), a synthetic derivative of curcumin, has been reported to inhibit angiogenesis via unknown mechanisms. Understanding the molecular mechanisms of the drug's action is important for the development of improved compounds with better pharmacological properties. A genome-wide drug-induced haploinsufficiency screening of fission yeast gene deletion mutants has been applied to identify drug targets of HC. As a first step, the 50% inhibition concentration $(IC_{50})$ of HC was determined to be $2.2{\mu}M$. The initial screening of 4,158 mutants in 384-well plates using robotics was performed at concentrations of 2, 3, and $4{\mu}M$. A second screening was performed to detect sensitivity to HC on the plates. The first screening revealed 178 candidates, and the second screening resulted in 13 candidates, following the elimination of 165 false positives. Final filtering of the condition-dependent haploinsufficient genes gave eight target genes. Analysis of the specific targets of HC has shown that they are related to septum formation and the general transcription processes, which may be related to histone acetyltransferase. The target mutants showed 65% growth inhibition in response to HC compared with wild-type controls, as shown by liquid culture assay.

• Proceedings of the Korea Contents Association Conference
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• 2007.11a
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• pp.569-573
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• 2007

e-Science is a new paradigm to increase the research efficiency by applying the state-of-the-art information technology to the classical research methodology. Among the research fields influenced by e-Science, Biology and Bioinformatics are the fields that are using IT very actively. And virtual screening, a procedure for the drug discovery, is one of the bioinformatics applications which requires a large amount of computing resources. In this paper, WISDOM, which is a e-Science project to design a new drug for Malaria and Avian flu, and related projects are introduced and the joint research between KISTI and Chun-nam university planned for the virtual screening research is explained.