• YAKHAK HOEJI
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• v.51 no.6
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• pp.463-468
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• 2007

Chong Myung Tang is consisted of three medicinal herbs (Acori Graminei Rhizoma, Polygalae Radix and Hoelen cum Radix). It has been used as a medicine for the purpose of learning and memory improvement. In this paper, Chong Myung Tang was screened the biological activities for Alzheimer's disease. The extract (70% ethanol) of Acari Graminei Rhizoma (1 mg/ml) showed that acetylcholinesterase (AChE) and amyloid beta ($A{\beta}$) peptide aggregation inhibitory potency are 43.1% and 76.5%, respectively. The extract of Polygalae Radix showed inhibitory activity against $A{\beta}_{1-42}$ peptide aggregation (51.5%). To predict the drug-likeness, oral absorption ability; blood-brain barrier (BBB) penetraion rate, mutagenecity and carcinogenicity; in silico screening was performed against 16 compounds in the three medicinal herbs. According to the results, all compounds have appropriate chemical structures as medicines. The six compounds in Acori Graminei Rhizoma and the five compounds in Hoelen cum Radix showed excellent oral absorption rate and BBB penetration rate. The four compounds in Polygalae Radix showed excellent oral absorption rate, but their BBB penetration was presented low rate. And, the extract of Hoelen cum Radix didn't show AChE and $A{\beta}_{1-42}$ peptide aggregation inhibitory activities in vitro. Therefore, their activity in brain may be other mechanism. According to all of the results, in silico prediction technology is convenient and effective to determine biological active compounds in medicinal herbs.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2022.05a
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• pp.270-272
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• 2022

Safety is one of the factors that prevent clinical drugs from being distributed on the market. In the case of neurotoxicity, which is the main cause of safety problems caused by drug side effects, risk assessment of drugs and compounds is required in advance. Currently, experiments for testing drug safety are based on animal experimetns, which have the disadvantage of being time-consuming and expensive. Therefore in order to solve the above problem, a neurotoxic prediction model through an in silico experiment was suggested. In this study, the category of neurotoxicity was expanded using a unified medical language system and various related compound data were obtained based on an integrated database. The SMILES (Simplified Molecular Input Line Entry System) of the obtained compounds were converted into fingerprints and it is used as input of machine learning. The model finally predicts the presence or absence of neurotoxicity. The experiment proposed in this study can reduce the time and cost required for the in vivo experiment. Furthermore, it is expected to shorten the research period for new drug development and reduce the burden of suspension of development.

• Journal of Life Science
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• v.33 no.6
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• pp.490-497
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• 2023

Pregnant women may need to take medications to treat preexisting diseases or diseases that develop during pregnancy. However, some drugs may be fetotoxic and lead to, for example, teratogenicity and growth retardation. Predicting the fetotoxicity of drugs is thus important for the health of the mother and fetus. The fetotoxicity of many drugs has not been established because various challenges hinder the ability of researchers to determine their fetotoxicity. The need exists for in silico-based fetotoxicity assessment models, as they can modernize the testing paradigm, improve predictability, and reduce the use of animals and the costs of fetotoxicity testing. In this study, we collected data on the fetotoxicity of drugs and constructed fetotoxicity prediction models based on various machine learning algorithms. We optimized the models for more precise predictions by tuning the hyperparameters. We then performed quantitative performance evaluations. The results indicated that the constructed machine learning-based models had high performance (AUROC >0.85, AUPR >0.9) in fetotoxicity prediction. We also analyzed the feature importance of our model's predictions, which could be leveraged to identify the specific features of drugs that are strongly associated with fetotoxicity. The proposed model can be used to prescreen drugs and drug candidates at a lower cost and in less time. It provides a predictive score for fetotoxicity risk, which may be beneficial in the design of studies on fetotoxicity in human pregnancy.

• International Journal of Oral Biology
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• v.42 no.2
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• pp.63-70
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• 2017

Selecting an appropriate antigen with optimal immunogenicity and physicochemical properties is a pivotal factor to develop a protein based subunit vaccine. Despite rapid progress in modern molecular cloning and recombinant protein technology, there remains a huge challenge for purifying and using protein antigens rich in hydrophobic domains, such as membrane associated proteins. To overcome current limitations using hydrophobic proteins as vaccine antigens, we adopted in silico analyses which included bioinformatic prediction and sequence-based protein 3D structure modeling, to develop a novel periodontitis subunit vaccine against the outer membrane protein FomA of Fusobacterium nucleatum. To generate an optimal antigen candidate, we predicted hydrophilicity and B cell epitope parameter by querying to web-based databases, and designed a truncated FomA (tFomA) candidate with better solubility and preserved B cell epitopes. The truncated recombinant protein was engineered to expose epitopes on the surface through simulating amino acid sequence-based 3D folding in aqueous environment. The recombinant tFomA was further expressed and purified, and its immunological properties were evaluated. In the mice intranasal vaccination study, tFomA significantly induced antigen-specific IgG and sIgA responses in both systemic and oral-mucosal compartments, respectively. Our results testify that intelligent in silico designing of antigens provide amenable vaccine epitopes from hard-to-manufacture hydrophobic domain rich microbial antigens.

• The Journal of Internal Korean Medicine
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• v.27 no.4
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• pp.888-894
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• 2006

Objectives : For the purpose of developing new anti-HIV agents from natural sources, the extracts of Ricinus communis were tested for their inhibitory effects on essential enzymes reverse transcriptase (RT), protease and alpha-glucosidase. Inhibition activity of major compounds of Ricinus communis were predicted from quantitative structure activity relationships (QSAR) in silico. Methods and Results : In the anti-HIV-1 RT using enzyme-linked oligonucleotide sorbent assay (ELOSA) method, water and methanol extracts (100ug/ml) of Ricinus communis showed strong activity of 94.2% and 82.7%, respectively. In the HIV-1 protease and alpha-glucosidase inhibition assay, neither water nor methanol extracts of Ricinus communis inhibited the activity of the enzyme to cleave any substrates as oligopeptides and oligosaccharides. Conclusions : We found that for these samples it is possible that the inhibition of the RT in vitro is due to the secondary metabolites of Ricinus communis such as ricinine and quercetin. It would beof great interest to identify the compounds which are responsible for this inhibition, since all therapeutically useful agents up to date are RT inhibitors.

• Genomics & Informatics
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• v.19 no.1
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• pp.7.1-7.13
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• 2021

Levodopa (L-DOPA) therapy is normally practised to treat motor pattern associated with Parkinson disease (PD). Additionally, several inhibitory drugs such as Entacapone and Opicapone are also cosupplemented to protect peripheral inactivation of exogenous L-DOPA (~80%) that occurs due to metabolic activity of the enzyme catechol-O-methyltransferase (COMT). Although, both Entacapone and Opicapone have U.S. Food and Drug Administration approval but regular use of these drugs is associated with high risk of side effects. Thus, authors have focused on in silico discovery of phytochemicals and evaluation of their effectiveness against human soluble COMT using virtual screening, molecular docking, drug-like property prediction, generation of pharmacophoric property, and molecular dynamics simulation. Overall, study proposed, nine phytochemicals (withaphysalin D, withaphysalin N, withaferin A, withacnistin, withaphysalin C, withaphysalin O, withanolide B, withasomnine, and withaphysalin F) of plant Withania somnifera have strong binding efficiency against human COMT in comparison to both of the drugs i.e., Opicapone and Entacapone, thus may be used as putative bioenhancer in L-DOPA therapy. The present study needs further experimental validation to be used as an adjuvant in PD treatment.

• Journal of Industrial and Engineering Chemistry
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• v.67
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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.

• KSBB Journal
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• v.26 no.2
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• pp.131-138
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• 2011

Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.

• Toxicological Research
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• v.35 no.3
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• pp.257-270
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• 2019

Silver nanoparticles (AgNPs) have been widely used in a variety of applications in innovative development; consequently, people are more exposed to this particle. Growing concern about toxicity from AgNP exposure has attracted greater attention, while questions about nanosilver-responsive genes and consequences for human health remain unanswered. By considering early detection and prevention of nanotoxicology at the genetic level, this study aimed to identify 1) changes in gene expression levels that could be potential indicators for AgNP toxicity and 2) morphological phenotypes correlating to toxicity of HepG2 cells. To detect possible nanosilver-responsive genes in xenogenic targeted organs, a comprehensive systematic literature review of changes in gene expression in HepG2 cells after AgNP exposure and in silico method, connection up- and down-regulation expression analysis of microarrays (CU-DREAM), were performed. In addition, cells were extracted and processed for transmission electron microscopy to examine ultrastructural alterations. From the Gene Expression Omnibus (GEO) Series database, we selected genes that were up- and down-regulated in AgNPs, but not up- and down-regulated in silver ion exposed cells, as nanosilver-responsive genes. HepG2 cells in the AgNP-treated group showed distinct ultrastructural alterations. Our results suggested potential representative gene data after AgNPs exposure provide insight into assessment and prediction of toxicity from nanosilver exposure.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1343-1349
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• 2021

Cockroaches live in places where various pathogens exist and thus are more likely to use antimicrobial compounds to defend against pathogen intrusions. We previously performed an in silico analysis of the Periplaneta americana transcriptome and detected periplanetasin-5 using an in silico antimicrobial peptide prediction method. In this study, we investigated whether periplanetasin-5 has anticancer activity against the human leukemia cell line K562. Cell growth and survival of K562 cells treated with periplanetasin-5 were decreased in a dose-dependent manner. By using flow cytometric analysis, acridine orange/ethidium bromide (AO/EB) staining and DNA fragmentation, we found that periplanetasin-5 induced apoptotic and necrotic cell death in leukemia cells. In addition, these events were associated with increased levels of the pro-apoptotic proteins Fas and cytochrome c and reduced levels of the anti-apoptotic protein Bcl-2. Periplanetasin-5 induces the cleavage of pro-caspase-9, pro-caspase-8, pro-caspase-3, and poly (ADP-ribose) polymerase (PARP). The above data suggest that periplanetasin-5 induces apoptosis via both the intrinsic and extrinsic pathways. Moreover, caspase-related apoptosis was further confirmed by using the caspase inhibitor carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]-fluoromethylketone (Z-VAD-FMK), which reversed the periplanetasin-5-induced reduction in cell viability. In conclusion, periplanetasin-5 caused apoptosis in leukemia cells, suggesting its potential utility as an anticancer therapeutic agent.