• Bulletin of the Korean Chemical Society
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• 제30권11호
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• pp.2739-2748
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• 2009

Hologram and three dimensional quantitative structure activity relationship (3D QSAR) studies for a series of anilinobipyridine JNK3 inhibitors were performed using various alignment-based comparative molecular field analysis (COMFA) and comparative molecular similarity indices analysis (CoMSIA). The in vitro JNK3 inhibitory activity exhibited a strong correlation with steric and electrostatic factors of the molecules. Using four different types of alignments, the best model was selected based on the statistical significance of CoMFA ($q_2\;=\;0.728,\;r_2\;=\;0.865$), CoMSIA ($q_2\;=\;0.706,\;r_2\;=\;0.960$) and Hologram QSAR (HQSAR: $q_2\;=\;0.838,\;r_2\;=\;0.935$). The graphical analysis of produced CoMFA and CoMSIA contour maps in the active site indicated that steric and electrostatic interactions with key residues are crucial for potency and selectivity of JNK3 inhibitors. The HQSAR analysis showed a similar qualitative conclusion. We believe these findings could be utilized for further development of more potent and selective JNK3 inhibitors.

• 통합자연과학논문집
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• 제5권3호
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• pp.168-174
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• 2012

Gal (1-3) receptors are members of GPCR superfamily with seven transmembrane helices. The neuropeptide galanin mediates its effects through the receptor subtypes Gal1, Gal2, and Gal3 and has been implicated in anxiety and depression related behaviors. Galanin receptors are considered to be important targets for the development of novel antidepressant drugs. Owing to the importance of these receptors, a short communication about the sequential and structural studies about the functional Galanin (1-3) receptors has been reported. Structural studies have been hampered due to the lack of X-ray crystal structures. However with the availability of templates with close homologs comparative modeling could be encouraging. Sequence analysis was done for each receptors and homology modeling of each receptors were done with recently reported templates. Comparative analyses were done between these receptors to identify the relationships between them sequentially. Phylogram was generated between these receptors to identify the close homologue between this receptor and found that Gal2 and Gal3 receptors are closer. Our results could be useful for further structure based drug design targeting Gal1, Gal2 and Gal3 receptors.

• Journal of Plant Biotechnology
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• 제47권4호
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• pp.273-282
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• 2020

In Vietnam, Celastrus hindsii Benth, a medicinal plant rich in secondary metabolites, has been used to alleviate distress caused by ulcers, tumors, and inflammation for generations. The occurrence of two phenotypes, Broad Leaf (BL) and Narrow Leaf (NL), has raised questions about the selection of appropriate varieties for conservation and crop improvement to enhance medicinal properties. This study examined molecular differences in C. hindsii by comparing protein profiles between the NL and BL types using 2D-PAGE and MS. Peptide sequences and proteins were identified by matching MS data against the MSPnr100 databases and verified using the MultiIdent tool on ExPASy and the Blast2GO software. Our results revealed notable variations in protein abundance between the NL and BL proteomes. Selected proteins were confidently identified from 12 protein spots, thereby highlighting the molecular variation between NL and BL proteomes. Upregulated proteins in BL were found to be associated with flavonoid and amino acid biosynthesis as well as nuclease metabolism, which probably attributed to the intraspecific variations. Several bioactive proteins identified in this study can have applications in cancer therapeutics. Therefore, the BL phenotype characterized by healthier external morphological features has higher levels of bioactive compounds and could be better suited for medicinal use.

• Journal of the Korean Data and Information Science Society
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• 제19권3호
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• pp.903-911
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• 2008

Association rule mining searches for interesting relationships among items in a given large database. Association rules are frequently used by retail stores to assist in marketing, advertising, floor placement, and inventory control. Many data is most quantitative data. There is a need for partitioning techniques to quantitative data. The partitioning process is referred to as binning. We introduce several binning methods ; parameter mean binning, equi-width binning, equi-depth binning, clustering-based binning. So we apply these binning methods to several distribution types of quantitative data and present the best binning method for association rule discovery.

• 통합자연과학논문집
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• 제4권3호
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• pp.216-221
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• 2011

c-Jun N-terminal kinase-3 (JNK-3) has been shown to mediate neuronal apoptosis and make the promising therapeutic target for neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, and other CNS disorders. In order to better understand the structural and chemical features of JNK-3, comparative molecular field analysis (CoMFA) was performed on a series of 3,5-disubstituted quinolines derivatives. The best predictions were obtained CoMFA model ($q^2$=0.707, $r^2$=0.972) and the statistical parameters from the generated 3D-QSAR models were indicated that the data are well fitted and have high predictive ability. The resulting contour map from 3D-QSAR models might be helpful to design novel and more potent JNK3 derivatives.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2007년도 International Meeting of the Microbiological Society of Korea
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• pp.123-126
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• 2007

• 통합자연과학논문집
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• 제4권4호
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• pp.266-272
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• 2011

Focal adhesion kinase (FAK) is a potential target for the treatment of primary cancers as well as prevention of tumor metastasis. To understand the structural and chemical features of FAK inhibitors, we report comparative molecular field analysis (CoMFA) for the series of 7H-pyrrolo(2,3-d)pyrimidines. The CoMFA models showed good correlation between the actual and predicted values for training set molecules. Our results indicated the ligand-based alignment has produced better statistical results for CoMFA ($q^2$ = 0.505, $r^2$ = 0.950). Both models were validated using test set compounds, and gave good predictive values of 0.537. The statistical parameters from the generated 3D-QSAR models were indicated that the data are well fitted and have high predictive ability. The contour map from 3D-QSAR models explains nicely the structure-activity relationships of FAK inhibitors and our results would give proper guidelines to further enhance the activity of novel inhibitors.

• 통합자연과학논문집
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• 제4권2호
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• pp.99-102
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• 2011

Effect of protonation and deprotonation of ionization compounds is an important application in Comparative molecular field analysis (CoMFA). There are enough information's were reported about different CoMFA applications such as Series design and selection of training set, Geometries and optimizations of molecules, Effect of partial atomic charges, bioactive conformations and alignment, Interaction energy fields, Effects of different grid spacing etc. However limited information's are available about the ionization of compounds. This study aimed at the critical review of about the effects of protonation of ionizable molecules and its impact on the predictability of CoMFA models. We also discussed about previous implications and the things needed to be considered to come for a final conclusion about its impact on CoMFA predictability.

• 통합자연과학논문집
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• 제5권1호
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• pp.6-12
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• 2012

c-Jun N-terminal kinase-3 (JNK-3) has been identified as a promising target for neuronal apoptosis and has the effective therapeutic for neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, and other CNS disorders. Herein, we report the essential structural and chemical parameters for JNK-3 inhibitors utilizing comparative molecular field similarity indices analysis (CoMSIA) using the derivatives of 3,5-disubstituted quinolines. The best predictions were obtained CoMSIA model (q2=0.834, r2=0.987) and the statistical parameters from the generated 3D-QSAR models were indicated that the data are well fitted and have high predictive ability. The resulting contour map from 3D-QSAR models might be helpful to design novel and more potent JNK3 derivatives.

• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1344-1349
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• 2004

Titin-cap (TCAP), one of the abundant transcripts in skeletal muscles, was nvestigated in this study in cattle because of its role in regulating the proliferation and differentiation of myoblasts by interacting with the myostatin gene. From the 5, and 3, RACE experiments, full-length TCAP coding sequence was identified, comprising 166 amino acids. The amino acid comparison showed high sequence similarities with previously identified human (95.8%) and mouse (95.2%) TCAP genes. The TCAP expression, addressed by northern blot, is limited in muscle tissues as indicated by Valle et al. (1997). The radiation hybrid analysis localized the gene on BTA19, where the comparative human and porcine counterparts are on HSA17 and SSC12. A few muscle-related genetic disorders were mapped on HSA17 and some growth-related QTLs were identified on SSC12. The bovine TCAP gene found in this study opens up new possibilities for the investigation of muscle-related genetic diseases as well as meat yield traits in cattle.