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.

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.

Aircraft Object Tracking Using Point Feature Matching based on SIFT

Guang-Ping Cao,Pill-Do Kang,Jung-Soo Jun,Yong-Ho Moon,Seok-Wun Ha 한국정보통신학회 2010 2016 INTERNATIONAL CONFERENCE Vol.3 No.1

창의성 마인드셋, 목표지향성, 창의적 자기효능감, 영역 창의성의 구조적 관계

조아평(Ya-ping Cao),최지은(Ji-Eun Choi) 한국영재교육학회 2022 영재와 영재교육 Vol.21 No.1

본 연구 목적은 중국 대학생의 창의성 마인드셋, 목표지향성, 창의적 자기효능감, 영역 창의성 간의 구조적인 관계를 규명하고, 목표지향성과 창의적 자기효능감의 이중매개효과를 알아보는 데 있다. 중국 대학생 805명을 대상으로 하였으며, 영역 창의성은 학문, 과학, 예술 영역을 대상으로 하였다. 주요 연구결과는 다음과 같다. 첫째, 창의성장 마인드셋은 숙달목표지향성, 수행목표지향성, 창의적 자기효능감, 그리고 학문적, 과학적, 예술적 창의성에 직접적인 영향을 미치고, 숙달목표지향성을 매개로 학문, 예술적 창의성에 간접적 영향을, 창의적 자기효능감을 매개로 학문적, 과학적, 예술적 창의성에 간접적인 영향을 미치는 것으로 나타났다. 둘째, 창의고정 마인드셋은 학문, 과학적 창의성에만 직접적인 영향을 미치는 것으로 나타났다. 또한 창의고정 마인드셋은 숙달목표지향성을 매개로 학문적, 과학적, 예술적 창의성에 부적 영향을 미쳤고, 수행목표지향성을 매개로 과학적 창의성에 부적 영향, 예술적 창의성에는 정적으로 간접 효과가 나타났다. 셋째, 창의성 마인드셋과 영역 창의성 간의 관계에서 목표지향성과 창의적 자기효능감의 이중 매개효과는 숙달목표지향성과 자기효능감의 경로에서만 유의하였고, 수행목표지향성과 자기효능감의 경로는 유의하지 않았다. 본 연구를 통해 창의성의 변화신념을 갖는 것이 영역 창의성을 향상시키는 데 유익함을 확인하였다. 마지막으로 본 연구에 대한 의의와 후속 연구를 위한 제언을 하였다. This study examines the relationship between creative mindset and domain-specific creativity and the role of goal orientation and creative self-efficacy in doble-mediating the relation. The research data were collected from 805 Chinese university students. The results found that (1) the growth creative mindset had a direct effect on mastery goal orientation, performance goal orientation, creative self-efficacy, and domains of creativity (Scholarly, Scientific, Artistic), indirect effect on domains of creativity (Scholarly, Artistic) through mastery goal orientation, and an indirect effect on domains of creativity (Scholarly, Scientific, Artistic) through creative self-efficacy. (2) The fixed creative mindset had a direct effect on domains of creativity (Scholarly, Scientific) only. Also, the fixed creative mindset had a negative effect on domains of creativity (Scholarly, Scientific, Artistic) through mastery goal orientation and a negative effect on domain of creativity (Scientific) and positive effect on domain of creativity (Artistic) through performance goal orientation. (3) In the relationship between creativity mindset and domains of creativity, the doble-mediating effect of goal orientation and creative self-efficacy was significant only in the path of mastery goal orientation and self-efficacy, but not in the path of performance goal orientation and self-efficacy. Therefore, the growth creative mindset is beneficial to enhance domains of creativity. The significance of this study and suggestions for future research are discussed.

Knockdown of GCF2/LRRFIP1 by RNAi Causes Cell Growth Inhibition and Increased Apoptosis in Human Hepatoma HepG2 Cells

Li, Jing-Ping,Cao, Nai-Xia,Jiang, Ri-Ting,He, Shao-Jian,Huang, Tian-Ming,Wu, Bo,Chen, De-Feng,Ma, Ping,Chen, Li,Zhou, Su-Fang,Xie, Xiao-Xun,Luo, Guo-Rong Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.6

Background: GC-binding factor 2 (GCF2) is a transcriptional regulator that represses transcriptional activity of the epidermal growth factor receptor (EGFR) by binding to a specific GC-rich sequence in the EGFR gene promoter. In addition to this function, GCF2 has also been identified as a tumor-associated antigen and regarded as a potentially valuable serum biomarker for early human hepatocellular carcinoma (HCC) diagnosis. GCF2 is high expressed in most HCC tissues and cell lines including HepG2. This study focused on the influence of GCF2 on cell proliferation and apoptosis in HepG2 cells. Materials and Methods: GCF2 expression at both mRNA and protein levels in HepG2 cells was detected with reverse transcription (RT) PCR and Western blotting, respectively. RNA interference (RNAi) technology was used to knock down GCF2 mRNA and protein expression. Afterwards, cell viability was analyzed with a Cell Counting Kit-8 (CCK-8), and cell apoptosis and caspase 3 activity by flow cytometry and with a Caspase 3 Activity Kit, respectively. Results: Specific down-regulation of GCF2 expression caused cell growth inhibition, and increased apoptosis and caspase 3 activity in HepG2 cells. Conclusions: These primary results suggest that GCF2 may influence cell proliferation and apoptosis in HepG2 cells, and also provides a molecular basis for further investigation into the possible mechanism at proliferation and apoptosis in HCC.

Enhanced CO2/N2 separation performance in HP-Cu-BTCs by modifying the open-metal sites and porosity using added templates

Ping Yang,Rujin Zhou,Youhua Zhang,Shui Cao,Dan Zhang,Hongbing Ji,Linhai Duan,Xiuhong Meng 한국화학공학회 2023 Korean Journal of Chemical Engineering Vol.40 No.3

HP-Cu-BTCs (CTAB), HP-Cu-BTC(N,N), HP-Cu-BTC(SDBS) series with open metal coordination site Cu(I), cage window sites, tunable porosity, high specific surface area, cavity, etc., were synthesized using cationic surfactant (cetyltrimethylammonium bromide, neutral organic amine, and an anionic surfactant as templates, respectively, A variety of techniques were used to analyze the materials before and after CO2 cycle adsorption at 303K. A high BET specific surface area (1,194.06 m2/g) and total pore volume (0.63 cm3/g) were found in the synthesized HP-Cu-BTC(NN). The synthesized HP-Cu-BTC(N,N) not only has high CO2 adsorption capacity (7.4293 mmol/g) but also good selectivity (37.20) for adsorption separation of CO2/N2. Besides, FT-IR spectroscopy, CO2-TPD curves and adsorption kinetic curve demonstrated that the adsorption mechanism of synthesized HP-Cu-BTC(N,N) was mainly attributable to physisorption and it could be regenerated at relatively low temperature. The mesoporous structure not only improves the uptake capacity but also improves the diffusion and mass transfer of CO2. At the same time, the CO2-TPD showed that the HP-Cu-BTCs may have two major adsorption sites. One is to absorb CO2 molecules through van der Waals forces. The other is the electrostatic interaction of the open Cu sites with CO2. Therefore, the CO2/N2 adsorption selectivity of HP-Cu-BTC(N,N) is significantly higher than that of conventional Cu-BTC. After five consecutive adsorption/desorption cycles, the adsorbents retained an excellent adsorption property. Thus, it is a very good adsorbent for the CO2 capture.

Effect of PCL-b-PEG Oligomer Containing Ionic Elements on Phase Interfacial Properties and Aggregated Structure of PLA/PCL Blends

Ping Wang,Shang Gao,Xinliang Chen,Li Yang,Tian Cao,Bingyu Fan,Jin Liu,Xianhai Hu 한국고분자학회 2022 Macromolecular Research Vol.30 No.7

The polycaprolactone (PCL)-b-polyethylene glycol (PEG) oligomer (Oli) and its derivative containing ionic elements (ILs) were used as interfacial compatibilizers and regulators, and the polylactic acid (PLA)/PCL/Oli and PLA/PCL/ILs blends were prepared by solution blending. The effects of Oli and ILs on the phase interfacial properties, aggregated structure, crystallization and mechanical properties of PLA/PCL blends were systematically studied. The results show that the ILs with strong interfacial emulsification ability can improve the dispersion of PCL in PLA matrix, and enhance the two-phase interfacial adhesion. When the content of ILs is 5 %, ion clusters can form and alleviate the restricted crystallization of PCL, and promote the segment movement of PLA through the non-covalent bonding of ionic elements. So the crystallization ability of PLA and PCL improve simultaneously. ILs have a strong regulatory effect on the phase interfacial morphology and aggregated structure of PLA/PCL blends, and the PLA/PCL blends containing high content of 5 % ILs can significantly improve the mechanical properties of PLA/PCL blends.

ORiginal Article : The Expression of Programmed Death-1 in Circulating CD4+ and CD8+ T Cells during Hepatitis B Virus Infection Progression and Its Correlation with Clinical Baseline Characteristics

( Ping Xu ),( Yong Jing Chen ),( Hui Chen ),( Xiao Yan Zhu ),( Hua Feng Song ),( Li Juan Cao ),( Xue Feng Wang ) The Editorial Office of Gut and Liver 2014 Gut and Liver Vol.8 No.2

Background/Aims: Programmed death-1 (PD-1) expression was investigated in CD4+ and CD8+ T cells from hepatitis B virus (HBV)-infected patients at the chronic hepatitis B (CHB) infection, liver cirrhosis (LC), and hepatocellular carcinoma (HCC) stages. Methods: PD-1 expression in circulating CD4+ and CD8+ T cells was detected by flow cytometry. The correla-tions between PD-1 expression and HBV viral load, alanine aminotransaminase (ALT) levels and aspartate aminotrans-ferase (AST) levels were analyzed using GraphPad Prism 5.0. Results: PD-1 expression in CD4+ and CD8+ T cells was significantly increased in both the CHB group and advanced-stage group (LC plus HCC). In the CHB group, PD-1 expres-sion in both CD4+ and CD8+ T cells was positively correlated with the HBV viral load, ALT, and AST levels. However, in the LC plus HCC group, significant correlations between PD-1 expression and the clinical parameters were nearly absent. Conclusions: PD-1 expression in peripheral CD4+ and CD8+ T cells is dynamic, changes with HBV infection progression, and is related to HBV viral load and liver function, especially in CHB. PD-1 expression could be utilized as a potential clini-cal indicator to determine the extent of virus replication and liver injury. (Gut Liver 2014;8:186-195)

Comparison and Distribution of Phosphorus Fractions in Surface Horizons of Two Paddy Soil Chronosequences

Ping Zou,Jianrong Fu,Zhihong Cao,Jing Ye,Qiaogang Yu 한국토양비료학회 2014 한국토양비료학회 학술발표회 초록집 Vol.2014 No.6

Enhanced Reflectance of Cholesteric Liquid Crystal Device with Quantum Dots

Cao, Jin,Chen, Chao Ping,Bae, Byung Seong,Song, Jang-Kun,Kim, Dae Soo,Jhun, Chul Gyu Informa UK (TaylorFrancis) 2015 Molecular Crystals and Liquid Crystals Vol.613 No.1

<P>Cholesteric liquid crystal (CLC) has a helical structure with either of left-handedness or right-handedness. Due to the helical structure, the selective reflection occurs depending on the chrial pitch. However, the reflectance of the CLC layer is theoretically limited to 50% because only one of right- or left-handed circularly polarized light is reflected. In this paper, we demonstrate high reflectance of CLC layer with quantum dots for the color reflector application.</P>