Browsing by Author "Lin, Chia-Hui"

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Design and Structural Analysis of Novel Pharmacophores for Potent and Selective Peroxisome Proliferator-activated Receptor gamma Agonists
(2009-04-23)
Lin, Chia-Hui
;
Peng, Yi-Hui
;
Coumar, Mohane Selvaraj
;
Chittimalla, Santhosh Kumar
;
Liao, Chun-Chen
Utilizing medicinal chemistry design strategies Such as benzo splitting and ring expansion, we converted PPAR alpha/gamma dual agonist 1 to selective PPAR gamma agonists 19 and 20. Compounds 19 and 20 were 2- to 4-fold better than rosiglitazone at PPAR gamma receptor. with 80- to 100-fold PPAR gamma selectivity over PPAR alpha receptor. X-ray cocrystal studies in PPAR gamma and modeling studies in PPAR alpha give molecular insights for the improved PPAR gamma potency and selectivity for 19 when compared to 1.
Effects of different chromosome representations in developing genetic algorithms to solve DFJS scheduling problems
(2017-04)
Wu, Muh-Cherng
;
Lin, Chi-Shiuan
;
Lin, Chia-Hui
;
Chen, Chen-Fu
;
工業工程與管理學系
This paper attempts to compare the effect of using different chromosome representations while developing a genetic algorithm to solve a scheduling problem called DFJS (distributed flexible job shop scheduling) problem. The DFJS problem is strongly NP-hard; most recent prior studies develop various genetic algorithms (GAs) to solve the problems. These prior GAs are similar in the algorithmic flows, but are different in proposing different chromosome representations. Extending from this line, this research proposes a new chromosome representation (called Sop) and develops a genetic algorithm (called GA_OP) to solve the DFJS problem. Experiment results indicate that GA_OP outperforms all prior genetic algorithms. This research advocates the importance of developing appropriate chromosome representations while applying genetic algorithms (or other meta-heuristic algorithms) to solve a space search problem, in particular when the solution space is high-dimensional. (C) 2016 Elsevier Ltd. All rights reserved.
GADD45a and GADD45b Genes in Rheumatoid Arthritis and Systemic Lupus Erythematosus Patients
(2019-06-01)
Li, Ruei-Nian
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Lin, Yuan-Zhao
;
Pan, Ya-Chun
;
Lin, Chia-Hui
;
Tseng, Chia-Chun
Background: GADD45 genes are stress sensors in response to cellular stress response, activated signal pathways leading to the stimulation of inflammatory cytokines. This study is to examine the associations of GADD45a and GADD45b genes with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) patients. Methods: 230 patients of RA, 140 patients of SLE, and 191 healthy controls were enrolled. Genomic DNA was extracted from peripheral blood mononuclear cells and gene polymorphisms were genotyped by TaqMan assay. RNA expression was quantitated with real-time polymerase chain reaction. Results: The RNA expression of the GADD45b gene was significantly lower in RA patients than the control cases (p = 0.03). The odds ratio of GADD45a genotype -589 CC (rs581000) was significantly low (OR = 0.36, 95% CI, 0.15-0.87) in DR4-negative RA patients. The odds ratio of GADD45b genotype -712CT (rs3795024) in DR4-negative RA patients was 0.41 (95% CI, 0.18-0.95). In clinical manifestation, the odds ratio of GADD45b -712CT genotype with anti-RNP antibody was 4.14 (95% CI, 1.10-15.63) in SLE patients. GADD45a genotype -589GG+GC was associated with rheumatoid factor (RF) in SLE patients. Conclusions: Genotypes GADD45a -589CC and GADD45b -712CT were shown to be less susceptible to RA and related to the disease state in SLE patients.
Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis
(2019-09-01)
Tseng, Chia-Chun
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Lin, Yuan-Zhao
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Lin, Chia-Hui
;
Li, Ruei-Nian
;
Yen, Chang-Yi
Using next-generation sequencing to decipher methylome and transcriptome and underlying molecular mechanisms contributing to rheumatoid arthritis (RA) for improving future therapies, we performed methyl-seq and RNA-seq on peripheral blood mononuclear cells (PBMCs) from RA subjects and normal donors. Principal component analysis and hierarchical clustering revealed distinct methylation signatures in RA with methylation aberrations noted across chromosomes. Methylation alterations varied with CpG features and genic characteristics. Typically, CpG islands and CpG shores were hypermethylated and displayed the greatest methylation variance. Promoters were hypermethylated and enhancers/gene bodies were hypomethylated, with methylation variance associated with expression variance. RA genetically associated genes preferentially displayed differential methylation and differential expression or interacted with differentially methylated and differentially expressed genes. These differentially methylated and differentially expressed genes were enriched with several signaling pathways and disease categories. 10 genes (CD86, RAB20, XAF1, FOLR3, LTBR, KCNH8, DOK7, PDGFA, PITPNM2, CELSR1) with concomitantly differential methylation in enhancers/promoters/gene bodies and differential expression in B cells were validated. This integrated analysis of methylome and transcriptome identified novel epigenetic signatures associated with RA and highlighted the interaction between genetics and epigenetics in RA. These findings help our understanding of the pathogenesis of RA and advance epigenetic studies in regards to the disease.
Structural Basis for the Improved Potency of Peroxisome Proliferator-Activated Receptor (PPAR) Agonists
(2010-10-04)
Peng, Yi-Hui
;
Coumar, Mohane Selvaraj
;
Leou, Jiun-Shyang
;
Wu, Jian-Sung
;
Shiao, Hui-Yi
The need to develop safer and more effective antidiabetic drugs is essential owing to the growth worldwide of the diabetic population. Targeting the PPAR receptor is one strategy for the treatment of diabetes; the PPAR agonists rosiglitazone and pioglitazone are already on the market. Here we report the identification of a potent PPAR agonist, 15, whose PPAR gamma activation was more than 20 times better than that of rosiglitazone. Compound 15 was designed to incorporate an indole head with a carboxylic acid group, and 4-phenylbenzophenone tail to achieve a PPAR gamma EC(50) of 10 nm. Compound 15 showed the most potent PPAR gamma agonist activity among the compounds we investigated. To gain molecular insight into the improved potency of 15, a structural biology study and binding energy calculations were carried out. Superimposition of the X-ray structures of 15 and agonist 10 revealed that, even though they have the same indole head part, they adopt different conformations. The head part of 15 showed stronger interactions toward PPAR gamma; this could be due to the presence of the novel tail part 4-phenylbenzophenone, which could enhance the binding efficiency of 15 to PPAR gamma.
Structural Basis for the Improved Potency of Peroxisome Proliferator-Activated Receptor (PPAR) Agonists
(2010-10-04)
Peng, Yi-Hui
;
Coumar, Mohane Selvaraj
;
Leou, Jiun-Shyang
;
Wu, Jian-Sung
;
Shiao, Hui-Yi
The need to develop safer and more effective antidiabetic drugs is essential owing to the growth worldwide of the diabetic population. Targeting the PPAR receptor is one strategy for the treatment of diabetes; the PPAR agonists rosiglitazone and pioglitazone are already on the market. Here we report the identification of a potent PPAR agonist, 15, whose PPAR gamma activation was more than 20 times better than that of rosiglitazone. Compound 15 was designed to incorporate an indole head with a carboxylic acid group, and 4-phenylbenzophenone tail to achieve a PPAR gamma EC(50) of 10 nm. Compound 15 showed the most potent PPAR gamma agonist activity among the compounds we investigated. To gain molecular insight into the improved potency of 15, a structural biology study and binding energy calculations were carried out. Superimposition of the X-ray structures of 15 and agonist 10 revealed that, even though they have the same indole head part, they adopt different conformations. The head part of 15 showed stronger interactions toward PPAR gamma; this could be due to the presence of the novel tail part 4-phenylbenzophenone, which could enhance the binding efficiency of 15 to PPAR gamma.