• Journal of Institute of Control, Robotics and Systems
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• v.11 no.10
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• pp.823-829
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• 2005

We have newly constructed an in silico model of fermentative metabolism for Lactococcus lactis in order to analyze the characteristics of metabolite flux for dynamic network. A rigorous mathematical model for metabolic flux has been developed and simulation researches have been performed by using GEPASI program. In this simulation task, we were able to predict the whole flux distribution trend for lactate metabolism and analyze the flux ratio on the pyruvate branch point by using metabolic flux analysis(MFA). And we have studied flux control coefficients of key reaction steps in the model by using metabolic control analysis(MCA). The role of pyruvate branch seems to be essential for the secretion of lactate and other organic byproducts. Then we have made an effort to elucidate its metabolic regulation characteristics and key reaction steps, and find an optimal condition for the production of lactate.

• CELLMED
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• v.3 no.2
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• pp.12.1-12.4
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• 2013

Identification of target protein is an important procedure in the course of drug discovery. Because of complexity, action mechanisms of herbal medicine are rather obscure, unlike small-molecular drugs. Inverse docking simulation is a reverse use of molecular docking involving multiple target searches for known chemical structure. This methodology can be applied in the field of target fishing and toxicity prediction for herbal compounds as well as known drug molecules. The aim of this review is to introduce a series of in silico works for predicting potential drug targets and side-effects based on inverse docking simulations.

• The Korean Journal of Physiology and Pharmacology
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• v.20 no.1
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• pp.111-117
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• 2016

Vagal nerve activity has been known to play a crucial role in the induction and maintenance of atrial fibrillation (AF). However, it is unclear how the distribution and concentration of local acetylcholine (ACh) promotes AF. In this study, we investigated the effect of the spatial distribution and concentration of ACh on fibrillation patterns in an in silico human atrial model. A human atrial action potential model with an ACh-dependent $K^+$ current ($I_{KAch}$) was used to examine the effect of vagal activation. A simulation of cardiac wave dynamics was performed in a realistic 3D model of the atrium. A model of the ganglionated plexus (GP) and nerve was developed based on the "octopus hypothesis". The pattern of cardiac wave dynamics was examined by applying vagal activation to the GP areas or randomly. AF inducibility in the octopus hypothesis-based GP and nerve model was tested. The effect of the ACh concentration level was also examined. In the single cell simulation, an increase in the ACh concentration shortened $APD_{90}$ and increased the maximal slope of the restitution curve. In the 3D simulation, a random distribution of vagal activation promoted wavebreaks while ACh secretion limited to the GP areas did not induce a noticeable change in wave dynamics. The octopus hypothesis-based model of the GP and nerve exhibited AF inducibility at higher ACh concentrations. In conclusion, a 3D in silico model of the GP and parasympathetic nerve based on the octopus model exhibited higher AF inducibility with higher ACh concentrations.

• 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.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.793-794
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• 2005

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.390-390
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• 2005

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.672-673
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• 2005

• Biomolecules & Therapeutics
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• v.30 no.5
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• pp.427-434
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• 2022

The drug repurposing strategy has been applied to the development of emergency COVID-19 therapeutic medicines. Current drug repurposing approaches have been directed against RNA polymerases and viral proteases. Recently, we found that the inhibition of the interaction between the SARS-CoV-2 structural nucleocapsid (N) and spike (S) proteins decreased viral replication. In this study, drug repurposing candidates were screened by in silico molecular docking simulation with the SARS-CoV-2 structural N protein. In the ChEMBL database, 1994 FDA-approved drugs were selected for the in silico virtual screening against the N terminal domain (NTD) of the SARS-CoV-2 N protein. The tyrosine 109 residue in the NTD of the N protein was used as the center of the ligand binding grid for the docking simulation. In plaque forming assays performed with SARS-CoV-2 infected Vero E6 cells, atovaquone, abiraterone acetate, and digoxin exhibited a tendency to reduce the size of the viral plagues without affecting the plaque numbers. Abiraterone acetate significantly decreased the accumulation of viral particles in the cell culture supernatants in a concentration-dependent manner. In addition, abiraterone acetate significantly decreased the production of N protein and S protein in the SARS-CoV-2-infected Vero E6 cells. In conclusion, abiraterone acetate has therapeutic potential to inhibit the viral replication of SARS-CoV-2.

• The Korean Journal of Physiology and Pharmacology
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• v.23 no.1
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• pp.71-79
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• 2019

Body surface potential map, an electric potential distribution on the body torso surface, enables us to infer the electrical activities of the heart. Therefore, observing electric potential projected to the torso surface can be highly useful for diagnosing heart diseases such as coronary occlusion. The BSPM for the heart of a patient show a higher level of sensitivity than 12-lead ECG. Relevant research has been mostly based on clinical statistics obtained from patients, and, therefore, a simulation for a variety of pathological phenomena of the heart is required. In this study, by using computer simulation, a body surface potential map was implemented according to various occlusion locations (distal, mid, proximal occlusion) in the left anterior descending coronary artery. Electrophysiological characteristics of the body surface during the ST segment period were observed and analyzed based on an ST isointegral map. We developed an integrated system that takes into account the cellular to organ levels, and performed simulation regarding the electrophysiological phenomena of the heart that occur during the first 5 minutes (stage 1) and 10 minutes (stage 2) after commencement of coronary occlusion. Subsequently, we calculated the bipolar angle and amplitude of the ST isointegral map, and observed the correlation between the relevant characteristics and the location of coronary occlusion. In the result, in the ventricle model during the stage 1, a wider area of ischemia led to counterclockwise rotation of the bipolar angle; and, during the stage 2, the amplitude increased when the ischemia area exceeded a certain size.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.425-431
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• 2005

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.