• 통합자연과학논문집
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• 제5권4호
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• pp.216-219
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• 2012

Structure-based drug design possibly benefit from in silico methods that precisely predict the binding affinity of small molecules to target macromolecules. There are many limitations arise from the difficulty of predicting the binding affinity of a small molecule to a biological target with the current scoring functions. There is thus a strong interest in novel methodologies based on MD simulations that claim predictions of greater accuracy than current scoring functions, helpful for a regular use designed for drug discovery in the pharmaceutical industry. Herein, we report a short review on free energy calculations using MMPBSA method a useful method in structure based drug discovery.

• International Journal of Industrial Entomology and Biomaterials
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• 제15권2호
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• pp.115-122
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• 2007

As the genome of B.mori is available in GenBank and the EST database of B.mori is expanding, identification of novel genes of B.mori is conceivable by data-mining techniques. We used the in silico cloning method to get the vacuolar-type $H^+-ATP$ synthetase (V-ATPase) c subunit (16 kDa proteolipid subunit) gene of B.mori and analysed with bioinformatics tools. The result was confirmed by RT-PCR and sequencing. The V-ATPase c subunit cDNA contains a 468 bp ORF. The ORF encoded a 155-residue protein that showed extensive homology with V-ATPase c subunits from other 15 species and contained four membrane-spanning helices. Tissue expression pattern analysis revealed that V-ATPase c expressed strongly in Malpighian tubules, not in fat body. This gene has been registered in GenBank under the accession number EU082222.

• 통합자연과학논문집
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• 제6권2호
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• pp.100-103
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• 2013

Using computational approaches we can dock small molecules into the structures of Macromolecular targets and then score their potential complementarity to binding sites is widely used in hit identification and lead optimization techniques. This review seeks to provide the application of docking in structure-based drug design (binding mode prediction, Lead Identification and Lead optimization), and also discussed how to manage errors in docking methodology in order to overcome certain limitations of docking and scoring algorithm.

• International Journal of Industrial Entomology and Biomaterials
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• 제14권2호
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• pp.69-74
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• 2007

As the genome of B. mori is available in GenBank and the EST database of B. mori is expanding, identification of novel genes of B. mori was conceivable by datamining techniques and bioinformatics tools. In this study, we used the in silico cloning method to get the 6-Phosphogluconolactonase (6PGL) gene of B. mori and analysed with bioinformatics tools. The result was confirmed by RT-PCR and prokaryotic expression. The 6PGL cDNA comtains a 702 bp ORF. The deduced protein has 233 amino acid residues, with the predicted molecular weight of 25946. 72 Da, isoelectric point of 5.41, and contains conserved NagB domains. This gene has been registered in GenBank under the accession number EF198104.

• Translational and Clinical Pharmacology
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• 제26권4호
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• pp.145-149
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• 2018

Cases of drug-induced QT prolongation and sudden cardiac deaths resulted in market withdrawal of many drugs and world-wide regulatory changes through accepting the ICH guidelines E14 and S7B. However, because the guidelines were not comprehensive enough to cover the electrophysiological changes by drug-induced cardiac ion channel blocking, CiPA was initiated by experts in governments and academia in the USA, Europe, and Japan in 2013. Five years have passed since the launch of the CiPA initiative that aimed to improve the current ICH guidelines. This report reviews the current achievements of the CiPA initiative and explores unresolved issues.

• Journal of Industrial and Engineering Chemistry
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• 제67권
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• pp.293-300
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• 2018

Lipocalins are diverse group of small extracellular proteins found in various organisms. In this study, members of 10 non-homologous lipocalin-ligand crystal complex structures were remodeled using rigid and flexible ligand modes to validate the prediction efficiency of molecular docking simulation. The modeled ligand conformations indicated a high prediction accuracy in rigid ligand mode using cluster based analysis for most cases whereas the flexible ligand mode required further considerations such as ligand binding energy and RMSD for some cases. This in silico study is expected to serve as a platform in the screening of novel ligands against lipocalin family of proteins.

• Journal of Microbiology and Biotechnology
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• 제17권8호
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• pp.1236-1241
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• 2007

Five fusion proteins between Z domains derived from Staphylococcal Protein A and Green Fluorescent Protein or Human Proinsulin were produced on the periplasm of Escherichia coli. The effects of the molecular weight and amino acid composition of the translocated peptide, culture medium composition, and growth phase of the bacterial culture were analyzed regarding the expression and periplasmic secretion of the recombinant proteins. It was found that secretion was not affected by the size of the translocated peptide (17-42 kDa) and that the highest periplasmic production values were obtained on the exponential phase of growth. Moreover, the highest periplasmic values were obtained in minimal medium, showing the relevance of the culture medium composition on secretion. In silico prediction analysis suggested that with respect to the five proteins used in this study, those that are prone to form ${\alpha}$-helix structures are more translocated to the periplasm.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
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• pp.192.2-193
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• 2003

Capsaicin, a pungent ingredient in chili pepper, is known to excite sensory neurons that mediate pain sensation. This effect of capsaicin is determined by unique receptors and the capsaicin receptor (transient receptor potential subfamily V, member 1 (TRPV1)) was cloned recently. TRPV1 contains six transmembrane domains and three ankyrin repeats at N-terminal. This characteristic architecture is common in other ion channel in TRPV families. (omitted)

• Journal of Microbiology and Biotechnology
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• 제22권1호
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• pp.46-49
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• 2012

The Vibrio vulnificus vuuA gene, of which expression is repressed by a complex of iron and ferric uptake regulator (Fur), was characterized to localize the Fur-binding site in its upstream regulatory region. In silico analysis suggested the presence of two possible Fur-binding sites; one is a classical Fur-box and the other is a previously reported distinct Fur-binding site. Site-directed mutagenesis and DNase I protection assays revealed the binding site for the iron-Fur complex, which includes an extended inverted repeat containing a homologous sequence to the classical Fur-box.

• Genomics & Informatics
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• 제12권4호
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• pp.171-180
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• 2014

Aberrant DNA methylation, as an epigenetic marker of cancer, influences tumor development and progression. We downloaded publicly available DNA methylation and gene expression datasets of matched cancer and normal pairs from the Cancer Genome Atlas Data Portal and performed a systematic computational analysis. This study has three aims to screen genes that show hypermethylation and downregulated patterns in colorectal cancers, to identify differentially methylated regions in one of these genes, SFRP1, and to test whether the SFRP genes affect survival or not. Our results show that 31 hypermethylated genes had a negative correlation with gene expression. Among them, SFRP1 had a differentially methylated pattern at each methylation site. We also show that SFRP1 may be a potential biomarker for colorectal cancer survival.