• Asian Pacific Journal of Cancer Prevention
• /
• v.14 no.9
• /
• pp.5281-5286
• /
• 2013

Purpose: Prostate cancer caused by the abnormal disorderly growth of prostatic acinar cells is the most prevalent cancer of men in western countries. We aimed to screen out differentially expressed genes (DEGs) and explore small molecule drugs for prostate cancer. Materials and Methods: The GSE3824 gene expression profile of prostate cancer was downloaded from Gene Expression Omnibus database which including 21 normal samples and 18 prostate cancer cells. The DEGs were identified by Limma package in R language and gene ontology and pathway enrichment analyses were performed. In addition, potential regulatory microRNAs and the target sites of the transcription factors were screened out based on the molecular signature database. In addition, the DEGs were mapped to the connectivity map database to identify potential small molecule drugs. Results: A total of 6,588 genes were filtered as DEGs between normal and prostate cancer samples. Examples such as ITGB6, ITGB3, ITGAV and ITGA2 may induce prostate cancer through actions on the focal adhesion pathway. Furthermore, the transcription factor, SP1, and its target genes ARHGAP26 and USF1 were identified. The most significant microRNA, MIR-506, was screened and found to regulate genes including ITGB1 and ITGB3. Additionally, small molecules MS-275, 8-azaguanine and pyrvinium were discovered to have the potential to repair the disordered metabolic pathways, abd furthermore to remedy prostate cancer. Conclusions: The results of our analysis bear on the mechanism of prostate cancer and allow screening for small molecular drugs for this cancer. The findings have the potential for future use in the clinic for treatment of prostate cancer.

• Vacuum Magazine
• /
• v.2 no.1
• /
• pp.4-9
• /
• 2015

A nanopore is a very small hole that can be used as single-molecule detector. The detection principle is based on monitoring the ionic current reduced by passage of a molecule through the nanopore as a voltage is applied across the nanopore. Here, we introduce biological nanopores and solid-state nanopores. Then, research and current trend about nanopore-based DNA biosensor and protein analysis are reviewed.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.8
• /
• pp.3899-3903
• /
• 2012

B7-H3 is a newly discovered member of the B7/CD28 superfamily which functions as an important T-cell immune molecule. It has been reported recently that B7-H3 is highly expressed in many cancer cells, the data indicating that it may be a regulation factor contributing to tumor-resistance. In our study, we used bioinformatics to identify differentially expressed genes between colonic cancer cells and normal colonic cells, aiming to analyze mechanisms and identify sub-pathways closely related to progression, with the final aim of finding small molecule drugs which might interfere this progression. We found that ajmaline is one related factor which may enhance self-immunity in colon carcinoma therapy and B7-H3 plays important roles with regard to immunoreactions of colonic cancer cells. All the results indicate that H7-B3 is a favorable prognostic biomarker for colon carcinomas, providing novel information regarding likely targets for intervention.

• Molecules and Cells
• /
• v.46 no.1
• /
• pp.65-67
• /
• 2023

SMILES (simplified molecular-input line-entry system) information of small molecules parsed by one-hot array is passed to a convolutional neural network called black box. Outputs data representing a gene signature is then matched to the genetic signature of a disease to predict the appropriate small molecule. Efficacy of the predicted small molecules is examined by in vivo animal models. GSEA, gene set enrichment analysis.

• The Korean Journal of Applied Statistics
• /
• v.24 no.3
• /
• pp.495-503
• /
• 2011

When a patent of an innovative (brand-name) small-molecule drug expires, generic copies of the innovative drug may be marketed if their therapeutic equivalence to the innovative drug has been shown. The small-molecule drugs are considered therapeutically equivalent and can be used interchangeably if two drugs are shown to be pharmaceutically equivalent with identical active substance and bioequivalent with comparable pharmacokinetics in a crossover clinical trial. However, the therapeutic equivalence paradigm cannot be applied to biosimilars since the active ingredients of biosimilars are huge molecules with complex and heterogeneous structures, and these molecules are difficult to replicate in every detail. The European Medicine Agency(EMEA) has introduced a regulatory biosimilar pathway which mandates clinical trials to show therapeutic equivalence. In this paper, we discuss statistical considerations in the design and analysis of biosimilar cancer clinical trials.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.11
• /
• pp.3681-3685
• /
• 2012

We developed a simple and effective method for the SERS-based detection of protein-small molecule complexes and label-free proteins using avidin-induced silver aggregation. Upon excitation with light of the appropriate wavelength (633 and 532 nm), the aggregated silver nanoparticles generate a strong electric field that couples with the resonance of the molecules (atto610 and cytochrome c), increasing the characteristic signals of these molecules and resulting in sensitive detection. The detection limit of biotin with the proposed method is as low as 48 ng/mL. The most important aspect of this method is the induction of silver aggregation by a protein (avidin), which makes the silver more biocompatible. This technique is very useful for the detection of protein-small molecule complexes.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.24
• /
• pp.10847-10853
• /
• 2015

Background: Lapatinib, a dual tyrosine kinase inhibitor that interrupts the epidermal growth factor receptor (EGFR) and HER2/neu pathways, has been indicated to have significant efficacy in treating HER2-positive breast cancer. However, acquired drug resistance has become a very serious clinical problem that hampers the use of this agent. In this study, we aimed to screen small molecule drugs that might reverse lapatinib-resistance of breast cancer by exploring differentially expressed genes (DEGs) via a bioinformatics method. Materials and Methods: We downloaded the gene expression profile of BT474-J4 (acquired lapatinib-resistant) and BT474 (lapatinib-sensitive) cell lines from the Gene Expression Omnibus (GEO) database and selected differentially expressed genes (DEGs) using dChip software. Then, gene ontology and pathway enrichment analyses were performed with the DAVID database. Finally, a connectivity map was utilized for predicting potential chemicals that reverse lapatinib-resistance. Results: A total of 1, 657 DEGs were obtained. These DEGs were enriched in 10 pathways, including cell cycling, regulation of actin cytoskeleton and focal adhesion associate examples. In addition, several small molecules were screened as the potential therapeutic agents capable of overcoming lapatinib-resistance. Conclusions: The results of our analysis provided a novel strategy for investigating the mechanism of lapatinib-resistance and identifying potential small molecule drugs for breast cancer treatment.

• Bulletin of the Korean Chemical Society
• /
• v.3 no.2
• /
• pp.50-55
• /
• 1982

A study of small water clusters composed of two to seven molecules has been performed by using the revised empirical potential function for conformational analysis (REPFCA). Various structures of clusters have been investigated and the relative probability of cluster per molecule is discussed. In general, cyclic structures of water clusters are more favorable than open structures. It is found that cyclic pentamer is the most favorable unit structure in the water cluster.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.10 no.3
• /
• pp.212-217
• /
• 2005

Desorption/ionization on silicon mass spectrometry (DIOS-MS) is a relatively new laser desorption/ionization technique for mass spectrometry without employing an organic matrix. This present study was carried to survey the experimental factors to improve the efficiency of DIOS-MS through electrochemical etching condition in structure and morphological properties of the porous silicon. The porous structure of silicon structure and its properties are crucial for the better performance of DIOS-MS and they can be controlled by the suitable selection of electrochemical conditions. The fabrication of porous silicon and ion signals on DIOS-MS were examined as a function of silicon orientation, etching time, etchant, current flux, irradiation, pore size, and pore depth. We have also examined the effect of pre- and post-etching conditions for their effect on DIOS-MS. Finally, we could optimize the electrochemical conditions for the efficient performance of DIOS-MS in the analysis of small molecule such as amino acid, drug and peptides without any unknown noise or fragmentation.

• Journal of Photoscience
• /
• v.12 no.2
• /
• pp.87-93
• /
• 2005

A new assay technique to distinguish between pure compounds and the isomeric mixtures has been suggested using single molecule (SM) fluorescence detection technique. Since the number of emission spots in a fluorophorespread film prepared from a genuine dye solution was determined by experimental condition, the deviation of spot numbers from the expected values could be considered to be an indication of lower purity of the sample solution. The lower limit of sample concentration for this assay was determined to be $5{\times}10^{-10}$ M to show uniform number of expected spots within 10% uncertainties in our experimental condition. An individual fluorescence intensity distribution for a mixture of isomers having doubly different emissivities was simulated by adding distributions obtained from Cy3 and nile red (NR) independently. The result indicated that the mixture could be identified from the pure compounds through the difference in the number of Gaussian functions to fit the distribution. This new assay technique can be applied to the purity test for synthetic biofluorophores which are usually prepared in small quantities not enough for classical ensemble assays.