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QSAR modeling to design selective histone deacetylase 8 (HDAC8) inhibitors
Guang Ping Cao,Sundarapandian Thangapandian,손민경,Raj Kumar,Yeung-Joon Choi,Yongseong Kim,Yong Jung Kwon,Hyong-Ha Kim,Jung-Keun Suh,Keun Woo Lee 대한약학회 2016 Archives of Pharmacal Research Vol.39 No.10
HDAC8 inhibitors have become an attractive treatment for cancer. This study aimed to facilitate the identification of potential chemical scaffolds for the selective inhibition of histone deacetylase 8 (HDAC8) using in silico approaches. Non-linear QSAR classification and regression models of HDAC8 inhibitors were developed with support vector machine. Mean impact valuebased sequential forward feature selection and grid search strategy were used for molecular descriptor selection and parameter optimization, respectively. The generated QSAR models were validated by leave-one-out cross validation and an external test set. The best QSAR classificationmodel yielded 84 % of accuracy on the external test prediction and Matthews correlation coefficient is 0.69. The best QSAR regression model showed low root-meansquare error (0.63) and high squared correlation coefficient (0.53) for the test set. The validated QSAR models together with various drug-like properties, molecular docking and molecular dynamics simulation were sequentially used as a multi-step query in chemical database virtual screening. Finally, two hit compounds were discovered as new structural scaffolds which can be used for further in vitro and in vivo activity analyses. The strategy used in this study could be a promising computational strategy which can be utilized for other target drug design.
Application of rare earth as mordant for the dyeing of ramie fabrics with natural dyes
Guang Hong Zheng,Hong Bin Fu,Guang Ping Liu 한국화학공학회 2011 Korean Journal of Chemical Engineering Vol.28 No.11
Selecting appropriate metallic compounds as mordants is essential for dyeing with natural dyes. This paper presents the application of rare earth compounds as mordant for the dyeing of ramie fabrics with four kinds of natural dyes. The influences of pre-mordanting, simultaneous mordanting, and post-mordanting on the dyeing effect were explored. The post-mordanting was proved to give rise to the highest dye uptake. The effects of dyeing conditions including dyeing temperature and time, dyeing bath pH and the concentration of rare earth on the dye uptake were investigated systematically. The fabrics dyed with natural dyes in presence of rare earth as mordant exhibited high color shade stability in the baths with pH varying from being acidic to neutral and alkaline. Employing rare earth as mordant apparently raised the color fastness to washing, rubbing and light of the ramie fabrics dyed with the natural extracts. In comparison with the commonly used metallic salts, using rare earth chlorides as mordants can greatly reduce the ionic concentration employed in natural dyeing. This study proved that rare earth would be a kind or promising environmentally friendly mordant in natural dyeing.
Ping Fan,Zhuang-Hao Zheng,Jing-Ting Luo,Guang-Xing Liang,Dong-Ping Zhang 대한금속·재료학회 2015 ELECTRONIC MATERIALS LETTERS Vol.11 No.3
In this study, AZO thin films prepared by direct current reactive magnetron sputtering using a Zn-Al alloy target and In with varied content were doped through the prefabricated layer doping method in order to optimize their thermoelectric properties. The effects of In content on the room temperature microstructure and thermoelectric properties of the AZO thin films were investigated. It was found that the absolute value of the Seebeck coefficient of the thin films increases stably after In doping and reaches 153 μV·K−1 when the In content is 0.71%. Though the electrical conductivity of In-doped thin films is smaller than those of the un-doped films, the power factor of the thin films shows a significant increase after In doping with a maximum value of 2.22 × 10−4 W·m−1·K−2, which is several times that of the un-doped films.
Guang-Ping Li,Xiao-Yan Wang,Yong Zhang 대한배뇨장애요실금학회 2018 International Neurourology Journal Vol.22 No.4
Purpose: OnabotulinumtoxinA (BoNT-A) is a promising therapy for treating neurogenic detrusor overactivity (NDO) in individuals with spinal cord injury (SCI). This systematic review and meta-analysis aimed to carry out an in-depth review and to make an objective estimation of the efficacy and safety of BoNT-A on NDO after SCI. Methods: The PubMed, Embase, and Cochrane databases were searched for all relevant articles published from 2001 to 2016 that referred to NDO, SCI, and BoNT-A or botulinum toxin A. All data were recorded in an Excel spreadsheet by 2 individual reviewers. Review Manager version 5.3 was used to carry out the meta-analysis. Results: This analysis included 17 studies involving 1,455 patients. Compared with placebo and baseline, BoNT-A was effective in increasing maximum cystometric capacity, volume at first involuntary detrusor contraction, cystometric bladder capacity (all P<0.00001), compliance (P=0.001), and the number of patients with complete dryness (P=0.0003), and decreasing detrusor pressure, the number of patients with no involuntary detrusor contractions, the maximum flow rate, the incidence of detrusor overactivity (all P<0.00001), and the number of urinary incontinence episodes (P=0.001). There were no statistically significant differences between doses of 200 U and 300 U or between injections into the detrusor and submucosa. There were no life-threatening adverse events. Conclusions: BoNT-A is effective and safe in treating NDO after SCI. There were no statistically significant differences between doses of 200 U and 300 U or between injecting into the detrusor and submucosa. However, more high-quality randomized controlled trials are still needed.
Classification of HDAC8 Inhibitors and Non-Inhibitors Using Support Vector Machines
Cao, Guang Ping,Thangapandian, Sundarapandian,John, Shalini,Lee, Keun-Woo Korean Society for Bioinformatics 2012 Interdisciplinary Bio Central (IBC) Vol.4 No.1
Introduction: Histone deacetylases (HDAC) are a class of enzymes that remove acetyl groups from ${\varepsilon}$-N-acetyl lysine amino acids of histone proteins. Their action is opposite to that of histone acetyltransferase that adds acetyl groups to these lysines. Only few HDAC inhibitors are approved and used as anti-cancer therapeutics. Thus, discovery of new and potential HDAC inhibitors are necessary in the effective treatment of cancer. Materials and Methods: This study proposed a method using support vector machine (SVM) to classify HDAC8 inhibitors and non-inhibitors in early-phase virtual compound filtering and screening. The 100 experimentally known HDAC8 inhibitors including 52 inhibitors and 48 non-inhibitors were used in this study. A set of molecular descriptors was calculated for all compounds in the dataset using ADRIANA. Code of Molecular Networks. Different kernel functions available from SVM Tools of free support vector machine software and training and test sets of varying size were used in model generation and validation. Results and Conclusion: The best model obtained using kernel functions has shown 75% of accuracy on test set prediction. The other models have also displayed good prediction over the test set compounds. The results of this study can be used as simple and effective filters in the drug discovery process.
Guang-Hong Chen,Chun-Ping Jen,Ching-Te Huang,Hsin-Hui Wu,Tatyana N. Zamay,Anna S. Zamay 한국바이오칩학회 2014 BioChip Journal Vol.8 No.2
Detecting rare cells, such as circulatingtumor cells (CTCs), circulating fetal cells, and stemcells, is vital during medical diagnostics and characterization. During carcinogenesis, cancer cells detachfrom the primary tumor into the blood stream, becomingCTCs. Typical rare cell samples are consideredany sample that contains less than 1000 target cellsper milliliter. The volumes of microfluidic devicestypically range from several microliters to nanoliters;this is excessively small for experimenting using lowconcentrationsamples. This study involved isolatingcancerous cells in an open-top chamber with sub-millilitervolumes (0.1 mL) of blood samples by using alysis buffer solution for red blood cells (RBCs), as wellas concentrating cells employing the dielectrophoreticforce generated using stepping electric fields,which were produced using a handheld electric modulethat comprised a voltage-frequency converterand an operational amplifier. To increase the samplevolume, an open-top chamber was fabricated on andbonded to a glass substrate by using circular microelectrodes. The concentrations of cancer cells andRBCs were adjusted to 500 cells/mL and 4×105 cell/mL, respectively, for the experiments. To reduce theinterference of blood cells during detection and isolateCTCs, the RBCs in the sample were lysed in alysis buffer solution before the proposed chip wasused to dielectrophoretically manipulate the rare cancerouscells. The findings indicated that the lysis bufferlysed the erythrocytes and the survivability levelsof the cancerous cells (HeLa and MCF-7) remainedhigh in the lysis buffer. The positive dielectrophoreticcancerous cells were guided based on the direction ofthe stepping electric field because of movement in thehigh-electric-field region; hence, the cancerous cellsconcentrated and collected at the central electrode.