• The Plant Pathology Journal
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• 제33권6호
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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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• 제30권10호
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• pp.2213-2216
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• 2009

A novel carbazole functionalized bis-$\beta$-diketone type organic ligand, 1,1′-(2,6-bispyridyl)bis-3-(9-ethylcarbazole- 3-yl)-1,3-propanedione ($H_2L$) and its corresponding lanthanide complexes $Eu_2(L)_3\;and\;Tb_2(L)_3$ were successfully prepared. The ligand and complexes were characterized in detail based on FT-IR spectra, $^1H$ NMR and elemental analysis. The observed UV-Vis absorption and photoluminescence properties of the complexes were investigated, it shows that the Eu(III) and Tb(III) ions can be sensitized efficiently by the ligand ($H_2L$) to some extent, in particular, the complex $Tb_2(L)_3$ exhibits a more excellent luminescence property than the Eu(III) complex. Meanwhile, the introduction of the carbazole moiety can enlarge the $\Pi$-conjugated system of the ligand and enhance the luminescent intensity of the complexes. The results show that the complexes would be used as excellent luminescent materials.

• Macromolecular Research
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• 제13권5호
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• pp.391-396
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• 2005

The polymerization of methyl methacrylate (MMA) was carried out using CuBr/bidentate phosphorus ligand catalyst systems. MMA polymerization with CuBr/phosphine-phosphinidene (PP) exhibited high conversion ($\~80\%$) in 5 h at $90^{\circ}C$ along with a linear increase of ln($[M]_0/[M]$) versus time, indicating constant concentration of the propagating radicals during the polymerization. The molecular weight of the prepared PMMA tended to increase with conversion, suggesting the living polymerization characteristic of the system. On the other hand, a large difference between the measured and theoretical molecular weight and a broad molecular weight distribution were observed, implicating possible incomplete control over the polymerization. This may have been caused by the low deactivation rate constant ($\kappa_{deact}$) of the system. The low $\kappa_{deact}$, would result in irreversible generation of radicals instead of reversible activation/deactivation process of ATRP. Polymerizations performed at different ligand to CuBr ratios and different monomer to initiator ratios did not afford better control over the polymerization, suggesting that the controllability of CuBr/phosphorus ligand system for ATRP is inherently limited.

• EDISON SW 활용 경진대회 논문집
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• 제2회(2013년)
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• pp.89-100
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• 2013

생물정보학의 다양한 이론적 내용과 계산적 방법들이 갈수록 전문화 되어짐에 따라 신약 개발, 신 물질 합성, 단백질의 구조 예측 등 다양한 분야에서 필요성이 커져가고 있다. 이 중 molecular docking 기술은 단백질과 특정 분자간의 결합 형태를 분자 모델링 기법을 통해 알아내는 방법이며 신약개발 연구에 큰 영향을 미치고 있다. Molecular docking을 통하여 분자간의 결합 형태를 예측하는 과정에서 Protein-ligand complex의 정확한 에너지 측정을 가능하게 하는 scoring function이 필요하다. 그런데 본 연구에서 사용한 B-Raf kinase protein 은 active site 부분에서 ligand와 receptor 간에 aromatic ring로 인한 ${\pi}-{\pi}$ interaction이 정확한 에너지 계산을 어렵게 한다. 이러한 ${\pi}-{\pi}$ interaction 부분의 에너지를 정확하게 계산하기 위해 양자역학 계산을 실시하였다. Active site 부분에서 ligand와 receptor에서 발생하는 각각 다른 5개의 ${\pi}-{\pi}$ interaction 구조를 준비하여 Gaussian을 통해 양자역학 에너지를 계산하였다. 그리고 이러한 결과 값들이 ligand의 활성 값과 어떤 상관관계를 갖는지 살펴보았다. 그 결과 ${\pi}-{\pi}$ interaction을 양자역학으로 계산한 값이 그렇지 않은 것보다 더 좋은 상관관계를 보여주었다. 이는 특별한 구조의 영향으로 ligand와 receptor 간의 결합에너지를 정확하게 계산하기 어려운 문제에서 양자역학을 적용할 경우 더욱 좋은 결과값을 얻을 수 있었다. 또한 이러한 데이터가 신 물질 개발이나 신약 개발 등의 다양한 분야에서 계산화학 방법이 신뢰성을 얻는데 도움 될 수 있다고 생각된다.

• IMMUNE NETWORK
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• 제3권1호
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• pp.29-37
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• 2003

Background: CC chemokine receptor (CCR) 7 and cognate CCR7 ligands, CCL21 (formerly secondary lymphoid tissue chemokine [SLC]) and CCL19 (formerly Epstein-Barr virus-induced molecule 1 ligand chemokine [ELC]), were known to establish microenvironment for the initiation of immune responses in secondary lymphoid tissue. As described previously, coadministration of DNA vaccine with CCR7 ligand-encoding plasmid DNA elicited enhanced humoral and cellular immunity via increasing the number of dendritic cells (DC) in secondary lymphoid tissue. The author hypothesized here that CCR7 ligand DNA could effectively expand memory CD4+ T cells to protect from viral infection likely via increasing DC number. Methods: To evaluate the effect of CCR7 ligand DNA on the expansion of memory CD4+ T cells, DO11.10.BALB/c transgenic (Tg)-mice, which have highly frequent ovalbumin $(OVA)_{323-339}$ peptide-specific CD4+ T cells, were used. Tg-mice were previously injected with CCR7 ligand DNA, then immunized with $OVA_{323-339}$ peptide plus complete Freund's adjuvant. Subsequently, memory CD4+ T cells in peripheral blood lymphocytes (PBL) were analyzed by FACS analysis for memory phenotype ($CD44^{high}$ and CD62 $L^{low}$) at memory stage. Memory CD4+ T cells recruited into inflammatory site induced with OVA-expressing virus were also analyzed. Finally, the protective efficacy against viral infection was evaluated. Results: CCR7 ligand DNA-treated Tg-mice showed more expanded $CD44^{high}$ memory CD4+ T cells in PBL than control vector-treated animals. The increased number of memory CD4+ T cells recruited into inflammatory site was also observed in CCR7 ligand DNA-treated Tg-mice. Such effectively expanded memory CD4+ T cell population increased the protective immunity against virulent viral infection. Conclusion: These results document that CCR7 and its cognate ligands play an important role in intracellular infection through establishing optimal memory T cell. Moreover, CCR7 ligand could be useful as modulator in DNA vaccination against viral infection as well as cancer.

• Bulletin of the Korean Chemical Society
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• 제31권5호
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• pp.1283-1288
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• 2010

A novel polyaminopolycarboxylate ligand with many coordination sites, N,N,$N^1,N^1,N^2,N^2$-[( 2,4,6-tri(aminomethyl)-pyridine]hexakis(acetic acid) (TPHA), was designed and synthesized and its lanthanide complexes $Na_6Tb_2$(TPHA)$Cl_6{\cdot}14H_2O$, $Na_6Eu_2$(TPHA)$Cl_6{\cdot}8H_2O$, $Na_6Gd_2$(TPHA)$Cl_6{\cdot}11H_2O$ and $Na_6Sm_2$(TPHA)$Cl_6{\cdot}9H_2O$ were successfully prepared. The ligand and the complexes were characterized by elemental analysis, IR, mass, NMR and TG-DTA. The TG-DTA studies indicated that the complexes had a high thermal stability, whose initial decomposition temperature was over $270^{\circ}C$. The luminescence properties of the complexes in solid state were investigated and the results suggested that $Tb^{3+}$ and $Eu^{3+}$ ions could be sensitized efficiently by the ligand, especially the Tb(III) complex displayed a very strong luminescence intensity (> 10000) and only displayed characteristic metal-centered luminescence. Also, the correlative comparison between the structure of ligand and luminescence properties showed how the number of the coordination atoms of ligand can be a prominent factor in the effectiveness of ligand-to-metal energy transfer.

• 대한화학회지
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• 제36권6호
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• pp.802-811
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• 1992

카르벤-올레핀-전이금속착물들[$(CO)_4M=CHX(CH_2=CH_2)$] (X: $OCH_3,\;NHCH_3,\;SCH_3$, M: C, Mo, W)의 형태에 대하여 확장된 Huckel 방법으로 계산하여 연구하였다. $d^6$ 전이금속 8면체 착물에서는 두 개의 인자 즉 금속에서 리간드로의 역제공과 리간드-리간드 상호작용이 안정한 형태를 결정해 준다는 사실이 밝혀졌지만 카르벤에 $\pi$-전자를 수용하는 리간드와 $\pi$-전자를 주는 기가 배위되어 있을 때 리간드-리간드 상호작용이 우세하므로 착물이 형태를 결정해 주는 주요한 인자라고 예측된다.

• Bulletin of the Korean Chemical Society
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• 제28권2호
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• pp.173-174
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• 2007

• Bulletin of the Korean Chemical Society
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• 제22권2호
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• pp.231-233
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• 2001

• 한국식품위생안전성학회지
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• 제21권3호
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• pp.171-180
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• 2006

Peroxisome proliferator-activated receptor-gamma$(PPAR{\gamma})$ 는 DNA와 결합하기 위해 retinoid-X receptor(RXR)와 heterodimer를 형성해야만 한다. 그리고 전사에 대한 최대활성은 수용체에 대한 리간드 특이성에 의하는 것으로 생각되고 있다. 활성화된 $(PPAR{\gamma})$ 와 $(PPAR{\gamma})$ 리간드는 종양억제 PTEN의 조절을 통해 종양세포의 성장에 영향을 끼치게 된다. 본 연구의 목적은 $(PPAR{\gamma})$ ligand, ciglitazone그리고 RXR ligand로 동시에 자극하였을 때 급성전골수성백혈병(APL) 세포에 대해 이들이 함께 PTEN upregulate를 조절할 수 있는지를 결정하기 위함이다. 그리고 이들 세포의 성장과 분화주기에 대해 강력한 억제 능이 있는지를 결정하고자 하였다. 즉, 사람의 백혈병세포주인 HL-60세포에 all-trans-retinol과 ciglutazone을 노출시킨 뒤 PTEN 발현에 대한 측정을 위해 RT-PCR법으로 PTEN mRNA 발현 정도를 확인하고 western blot으로 분석하였다 세포주기의 분석은 propidium iodide(PI) 염색법과 FACScan으로 분석하였고, HL-60 cells에서 $(PPAR{\gamma})$ ligand, ciglitazone, 그리고 RXR ligand, retinoic acid 그리고 upregulated PTEN 발현에 대한 time- and dose-dependent방법으로 각각 확인하였던 바 ciglitazone과 retinoic acid를 동시 조합하여 처치하였을 때 유의적인 효과를 인정할 수 있었다. 더욱이 이들 혼합 물질은 세포의 성장과 G, phase를 동시 억제하는 능력이 있었다. 그러므로 $(PPAR{\gamma})$의 활성에 있어 RXR heterodimer가 사람의 백혈병세포에 대한 조절 경로로서 존재하며, PTEN의 upregulation을 통해 백혈병을 조절하기 때문에 백혈병의 예방 및 치료 접근에 $(PPAR{\gamma})$와 RXR ligands가 중요한 역할을 할 것이다.