• Bulletin of the Korean Chemical Society
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• 제29권3호
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• pp.656-662
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• 2008

Antagonists of the d -opioid receptor are effective in overcoming resistance against analgesic drugs such as morphine. To identify novel antagonists of the d -opioid receptor that display high potency and low resistance, we performed 3D-QSAR analysis using chemical feature-based pharmacophore models. Chemical features for d -opioid receptor antagonists were generated using quantitative (Catalyst/HypoGen) and qualitative (Catalyst/HipHop) approaches. For HypoGen analysis, we collected 16 peptide and 16 non-peptide antagonists as the training set. The best-fit pharmacophore hypotheses of the two antagonist models comprised identical features, including a hydrophobic aromatic (HAR), a hydrophobic (HY), and a positive ionizable (PI) function. The training set of the HipHop model was constructed with three launched opioid drugs. The best hypothesis from HipHop included four features: an HAR, an HY, a hydrogen bond donor (HBD), and a PI function. Based on these results, we confirm that HY, HAR and PI features are essential for effective antagonism of the d -opioid receptor, and determine the appropriate pharmacophore to design such antagonists.

• Bulletin of the Korean Chemical Society
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• 제34권8호
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• pp.2387-2393
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• 2013

Benzotriazole is an important synthetic auxiliary for potential clinical applications. A series of benzotriazoles as potential antiproliferative agents by inhibiting histone deacetylase (HDAC) were recently reported. Three-dimensional quantitative structure-activity relationship (3D-QSAR), including comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), were performed to elucidate the 3D structural features required for the antiproliferative activity. The results of both ligand-based CoMFA model ($q^2=0.647$, $r^2=0.968$, ${r^2}_{pred}=0.687$) and CoMSIA model ($q^2=0.685$, $r^2=0.928$, ${r^2}_{pred}=0.555$) demonstrated the highly statistical significance and good predictive ability. The results generated from CoMFA and CoMSIA provided important information about the structural characteristics influence inhibitory potency. In addition, docking analysis was applied to clarify the binding modes between the ligands and the receptor HDAC. The information obtained from this study could provide some instructions for the further development of potent antiproliferative agents and HDAC inhibitors.

• Molecular & Cellular Toxicology
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• 제2권3호
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• pp.216-221
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• 2006

The cholinesterase-inhibiting organophosphorous (OP) compounds known as nerve agents are highly toxic. The principal toxic mechanism of OP compounds is the inhibition of acethylcholine esterase (AChE) by phosphorylation of its catalytic site. The reversible competitive inhibition of AChE may prevent the subsequent OP intoxication. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) was performed to investigate the relationship between the 29 compounds with structural diversity and their bioactivities against AChE. In particular, predictive models were constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The results indicate reasonable model for CoMFA ($q^{2}=0.453,\;r^{2}=0.697$) and CoMSIA ($q^{2}=0.518,\;r^{2}=0.696$). The presence of steric and hydophobic group at naphtyl moiety of the model may lead to the design of improved competitive inhibitors for organophosphorous intoxication.

• Bulletin of the Korean Chemical Society
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• 제30권11호
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• pp.2717-2722
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• 2009

The use of the classification and regression tree (CART) methodology was studied in a quantitative structure-activity relationship (QSAR) context on a data set consisting of the binding affinities of 39 imidazobenzodiazepines for the α1 benzodiazepine receptor. The 3-D structures of these compounds were optimized using HyperChem software with semiempirical AM1 optimization method. After optimization a set of 1481 zero-to three-dimentional descriptors was calculated for each molecule in the data set. The response (dependent variable) in the tree model consisted of the binding affinities of drugs. Three descriptors (two topological and one 3D-Morse descriptors) were applied in the final tree structure to describe the binding affinities. The mean relative error percent for the data set is 3.20%, compared with a previous model with mean relative error percent of 6.63%. To evaluate the predictive power of CART cross validation method was also performed.

• 대한암한의학회지
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• 제11권1호
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• pp.95-103
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• 2006

Objective: Gami-Samhwang-San, a herbal prescription for obesity treatment, is composed of seven crude herbs such as Ephedrae Herba, Scutellariae Radix, Acori Gramineri Rhizoma, Polygalae Radix, Typhae Pollen, Armeniacae Semen, Nelumbo Folium. This study was aimed to evaluate marker substances in n-butanol fraction (SH-21-B) from Gami-Samhwang-San by high performance liquid chromatography (HPLC). And we predicted inhibition activity of major compounds of Gami-Samhwang-San using Quantitative Structure Activity Relationships (QSAR) Methods: The separation was performed on a YMC J,sphere-H80 CI8(250${\times}$4.6 mm I.D) column by gradient elution with $H_3PO_4$ buffers in acetonitrile as the moblie phase at a flow-rate of 1.0ml/min. Results: HPLC was employed to determine the quantities and the qualities of several marker substances such as ephedrine, pseudoephedirne, baicalin, ${\beta}-asarone$, tenuifoliside, naringenin, amygdalin and hyperoside in the SH-21-B. Conclusion: We suggest this results could be a useful evidence for quality control of SH-21-B.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.210-218
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• 2004

Poly(ADP-ribose)polymerase-1 (PARP-1) is a nuclear enzyme involved in various physical functions related to genomic repair, and PARP inhibitors have therapeutic application in a variety of neurological diseases. Docking and the QSAR (quantitative structure-activity relationships) studies for 52 PARP-1 inhibitors were conducted using FlexX algorithm, comparative molecular field analysis (CoMFA), and hologram quantitative structure-activity relationship analysis (HQSAR). The resultant FlexX model showed a reasonable correlation (r$^{2}$ = 0.701) between predicted activity and observed activity. Partial least squares analysis produced statistically significant models with q$^{2}$ values of 0.795 (SDEP=0.690, r$^{2}$=0.940, s=0.367) and 0.796 (SDEP=0.678, r$^{2}$ = 0.919, s=0.427) for CoMFA and HQSAR, respectively. The models for the entire inhibitor set were validated by prediction test and scrambling in both QSAR methods. In this work, combination of docking, CoMFA with 3D descriptors and HQSAR based on molecular fragments provided an improved understanding in the interaction between the inhibitors and the PARP. This can be utilized for virtual screening to design novel PARP-1 inhibitors.

• 농약과학회지
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• 제12권1호
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• pp.18-23
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• 2008

기질 분자로서 6-bromobenzo-[4,5]imidazo[$1,2{\alpha}$]pyridin-8,9-diones 유도체의 photosystem II의 저해활성에 관한 3차원적인 정량적 구조와 활성과의 관계(3D-QSARs)들을 비교 분자장분석(CoMFA)과 비교분자 유사성 지수분석(CoMSIA) 방법으로 각각 검토하였다. CoMFA 모델은 CoMSIA 모델보다 높은 예측성과 상관성을 갖는 모델이었다. 또한 최적화된 CoMFA 2 모델의 기여도는 입체장(90.4%)에 가장 의존적이었다. CoMFA 등고도 분석으로부터, 치환기(R)로서 모체로 연결되는 탄소원자(ipso carbon)에 곁가지를 가진 치환체가 도입될수록 저해활성이 증가할 것으로 보인다. 또한, imidazol 고리와 pyridine 고리 사이의 위치에 양하전을 가질수록 활성이 높을 것으로 예상되며 친수성을 띄는 선 형태의 치환기가 도입되는 경우에 활성이 개선될 것으로 판단되었다.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
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• pp.247.2-248
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• 2003

The three-dimensional quantitative structure-activity relationship (3D-QSAR) approach using comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) was applied to 62 derivatives known as COX-2 selective inhibitors. Partial least square (PLS) analyses produced good predicted models with q2 value of 0.803 (s=0.285, F=215.401, r2=0.951) and 0.769 (s=0.192, F=245.364, r2=0.980) for CoMFA and CoMSIA, respectively. (omitted)

• Archives of Pharmacal Research
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• 제27권5호
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• pp.467-470
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• 2004

Comparative molecular field analysis and comparative molecular similarity indices analysis were performed on twenty five analogues of pimarane COX-2 inhibitor to optimize their cyclooxygenase-2 (COX-2) selective anti-inflammatory activities.

• 농약과학회지
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• 제7권2호
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• pp.100-107
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• 2003

일련의 새로운 N-치환-phenyl-3,4,5,6-tetrahydrophthalimide 유도체를 합성하여 $R_2=Sub.X$ 치환기들의 변화에 따르는 발아 전, 벼(Oryza sativa L.)와 논피(Echinochloa crus-galli) 의 줄기와 뿌리에 대한 생장 저해활성 $(pI_{50})$과의 관계 (QSAR)는 물론, 기질 유도체와 protox의 기질인 protogen 분자 사이의 구조적인 분자 유사성을 연구하였다. 두 초종간 및 부위별, 생장 저해활성은 비례관계를 보였으며 벼 보다는 논피에 대하여 약간 강한 저해활성을 나타내었다. QSAR식으로부터 논피의 생장 저해활성은 기질 분자중 음으로 하전된 원자들의 표면적이 클수록 증가하므로 $R_2=Sub.X$ 치환기로서 전자 밀게가 치환되어야 할 것으로 추측되었다. 또한, 기질 유도체와 protogen 분자 사이의 유사성을 검토한 결과, 기질 유도체들의 유사성 지수(S)는 대략 0.8 이상으로 비교적 큰 유사성을 나타내었으나 두 초종의 생장 저해활성과의 상관성은 낮은 편이었다.