• Journal of Plant Biotechnology
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• v.49 no.4
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• pp.316-324
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• 2022

Hair loss causes psychological stress due to its effect on appearance. Therefore, the global market for hair loss treatment products is rapidly growing. The present study demonstrated that ginseng berry-derived and sequence-modified peptides promoted the proliferation rate of dermal papilla (DP) cells and keratinocytes, in addition to having antioxidant properties. Moreover, the potential role of these ginseng berry peptides as TGF-β2 antagonists was confirmed through in silico computer docking. In addition to promoting the growth of ,the ginseng berry-derived peptides also promoted the proliferation of keratinocytes experimental Particularly, an unmodified ginseng berry-derived peptide (GB-1) and two peptides with sequence modifications (GB-2 and GB-3) decreased ROS generation and exhibited a protective effect on damaged HaCaT keratinocytes. Computer-aided peptide discovery was conducted to identify the potential interactions of important proteins with transforming growth factor-beta 2 (TGF-β2), a key protein that plays a crucial role in the human hair growth cycle. Our results demonstrated that MAGH, an amino acid sequence present in herbal supplements and plant-based natural compounds, can inhibit TGF-β2.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.14-14
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• 2020

In December 2019, the COVID-19 epidemic was discovered in Wuhan, China, and since has disseminated around the world impacting human health for millions. Herein, in-silico drug discovery approaches were utilized to identify potential candidates as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (M^pro) inhibitors. We investigated several databases including natural and natural-like products (>100,000 molecules), DrugBank database (10,036 drugs), major metabolites isolated from daily used spices (32 molecules), and current clinical drug candidates for the treatment of COVID-19 (18 drugs). All tested compounds were prepared and screened using molecular docking techniques. Based on the calculated docking scores, the top ones from each project under investigation were selected and subjected to molecular dynamics (MD) simulations followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Combined long MD simulations and MM-GBSA calculations revealed the potent compounds with prospective binding affinities against M^pro. Structural and energetic analyses over the simulated time demonstrated the high stabilities of the selected compounds. Our results showed that 4-bis([1,3]dioxolo)pyran-5-carboxamide derivatives (natural and natural-like products database), DB02388 and Cobicistat (DB09065) (DrugBank database), salvianolic acid A (spices secondary metabolites) and TMC-310911 (clinical-trial drugs database) exhibited high binding affinities with SARS-CoV-2 M^pro. In conclusion, these compounds are up-and-coming anti-COVID-19 drug candidates that warrant further detailed in vitro and in vivo experimental estimations.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.542-551
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• 2017

Small phytochemicals have been successfully adopted as antibacterial chemotherapies and are being increasingly viewed as potential antibiofilm agents. Some of these molecules are known to repress biofilm and toxin production by certain bacterial and yeast pathogens, but information is lacking with regard to the genes allied with biofilm formation. The present study was performed to investigate the inhibitory effect of burdock root extract (BRE) and of chlorogenic acid (CGA; a component of BRE) on clinical isolates of Klebsiella pneumoniae. BRE and CGA exhibited significant antibiofilm activity against K. pneumoniae without inflicting any harm to its planktonic counterparts. In vitro assays supported the ${\beta}$-lactamase inhibitory effect of CGA and BRE while in silico docking showed that CGA bound strongly with the active sites of sulfhydryl-variable-1 ${\beta}$-lactamase. Furthermore, the mRNA transcript levels of two biofilm-associated genes (type 3 fimbriae mrkD and trehalose-6-phosphate hydrolase treC) were significantly downregulated in CGA- and BRE-treated samples. In addition, CGA inhibited biofilm formation by Escherichia coli and Candida albicans without affecting their planktonic cell growth. These findings show that BRE and its component CGA have potential use in antibiofilm strategies against persistent K. pneumoniae infections.

• 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.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1051-1054
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• 2013

Closo-carborane has been considered as an efficient boron-carrier for boron neutron capture therapy (BNCT) and an attractive surrogate of lipophilic phenyl or cyclohexyl ring in drug design. Despite a great number of carborane-containing ligands have been synthesized and evaluated, molecular modeling studies of carborane ligands with macromolecules have been rarely reported. We herein describe a facile docking and scoring-function strategy of 16 carborane ligands with an estrogen receptor by using the commercial Gaussian, Chem3D Pro and Discovery Studio (DS) computational programs. Docked poses of the carborane ligands in silico exhibited similar binding modes to that of the crystal ligand in the active site of estrogen receptor. Score analysis of the best docked pose for each ligand indicated that the Ligscore1 and the Dockscore have a moderate correlation with in vitro biological activity. This is the first report on the scoring-correlation studies of carborane ligands with macromolecules. The integrated Gaussian-DS approach has a potential application for virtual screening, De novo design, and optimization of carborane ligands in medicinal chemistry.

• 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.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2147-2150
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• 2010

c-Jun N-terminal kinase 1 (JNK1) is involved in apoptosis, cell differentiation and proliferation. It has been reported that a flavonol, quercetin, induces cell apoptosis and JNK inhibition. In order to understand the interactions of quercetin and JNK1, we performed receptor-oriented pharmacophore based in silico screening and determined a binding model of human JNK1 and quercetin at the ATP binding site of JNK1. 5-OH of A-ring and carbonyl oxygen of C-ring of quercetin participated in hydrogen bonding interactions with backbone of E109 and M111. Additionally, 3'-OH of quercetin formed a hydrogen bond with backbone of I32. One hydrophobic interaction is related on the binding of quercetin to JNK1 with I32, N114, and V158. Based on this model, we conducted a docking study with other 8 flavonols to find possible flavonoids inhibitors of JNK1. We proposed that one flavonols, rhamnetin, can be a potent inhibitor of JNK and 5-OH of A-ring and 3'-OH of B-ring of flavonols are the essential features for JNK1 inhibition.

• Korean Journal of Microbiology
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• v.44 no.4
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• pp.333-338
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• 2008

Computational analysis of partial rpoB gene sequence (777 bp) was done in this study to identify B. anthracis and its closely related species B. cereus and B. thuringiensis. Sequence data including 17 B. anthracis strains, 9 B. cereus strains, and 7 B. thuringiensis strains were obtained by searching databases. Those sequences were aligned and used for other computational analysis. B. anthracis strains were identificated by in silico restriction enzyme digestion. B. cereus and B. thuringiensis were not segregated by this method. Those sequencing and BLAST search were required to distinguish the two. In actual identification tests, B. anthracis strains could be identified by PCR-RFLP, and B. cereus and B. thuringiensis strains were distinguished by BLAST search with reliable e-value. In this study fast and accurate method for identifying three Bacillus species, and flow chart of identification were developed.

• The Korean Journal of Physiology and Pharmacology
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• v.23 no.5
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• pp.295-303
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• 2019

A heart simulator, UT-Heart, is a finite element model of the human heart that can reproduce all the fundamental activities of the working heart, including propagation of excitation, contraction, and relaxation and generation of blood pressure and blood flow, based on the molecular aspects of the cardiac electrophysiology and excitation-contraction coupling. In this paper, we present a brief review of the practical use of UT-Heart. As an example, we focus on its application for predicting the effect of cardiac resynchronization therapy (CRT) and evaluating the proarrhythmic risk of drugs. Patient-specific, multiscale heart simulation successfully predicted the response to CRT by reproducing the complex pathophysiology of the heart. A proarrhythmic risk assessment system combining in vitro channel assays and in silico simulation of cardiac electrophysiology using UT-Heart successfully predicted drug-induced arrhythmogenic risk. The assessment system was found to be reliable and efficient. We also developed a comprehensive hazard map on the various combinations of ion channel inhibitors. This in silico electrocardiogram database (now freely available at http://ut-heart.com/) can facilitate proarrhythmic risk assessment without the need to perform computationally expensive heart simulation. Based on these results, we conclude that the heart simulator, UT-Heart, could be a useful tool in clinical medicine and drug discovery.

• Genomics & Informatics
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• v.14 no.4
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• pp.222-229
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• 2016

Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling. The vast amount of biological information generated by academic and industrial research groups is reflected in a rapidly growing body of scientific literature and expanding data resources. However, the genome, biological pathway, and related disease data are insufficient to explain the health benefits of kimchi because of the varied and heterogeneous data types. Therefore, we have constructed an appropriate semantic data model based on an integrated food knowledge database and analyzed the functional and biological processes associated with kimchi in silico. This complex semantic network of several entities and connections was generalized to answer complex questions, and we demonstrated how specific disease pathways are related to kimchi consumption.