• Journal of Korean Society for Atmospheric Environment
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• v.29 no.4
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• pp.459-476
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• 2013

Receptor models have been rapidly developed to manage the ambient air quality and to establish effective emission reduction strategies. The models are used to identify various emission sources and apportion quantitatively the ambient pollutant mass based on various measured physico-chemical properties of the air pollutants at the receptor site. Many types of receptor models have been applied to estimate source contributions since those provide fundamental information when establishing reasonable environmental policies in Korea and Foreign countries. In this paper, we will introduce the basic concept and principal of the receptor model, various types of existing models with discussing strong and weak points for each model, and performance procedure of PMF model as the most popular model in the world. Further the trends of receptor modeling studies in Korea and other countries were provided. Finally, the improvement directions of the modeling works for the national and local air quality management were suggested in this paper.

• Journal of Integrative Natural Science
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• v.10 no.3
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• pp.119-124
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• 2017

Glucagon-like peptide 2 receptor, a GPCR, binds with the glucagon-like peptide, GLP-2 and regulates various metabolic functions in the gastrointestinal tract. It plays an important role in the nutrient homeostasis related to nutrient assimilation by regulating mucosal epithelium. GLP-2 receptor affects the cellular response to external injury, by controlling the intestinal crypt cell proliferation. As they are therapeutically attractive towards diseases related with the gastrointestinal tract, it becomes essential to analyse their structural features to study the pathophysiology of the diseases. As the three dimensional structure of the protein is not available, in this study, we have performed the homology modelling of the receptor based on single- and multiple template modeling. The models were subjected to model validation and a reliable model based on the validation statistics was identified. The predicted model could be useful in studying the structural features of GLP-2 receptor and their role in various diseases related to them.

• Journal of Integrative Natural Science
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• v.10 no.1
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• pp.14-19
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• 2017

Neuromedin, a neuropeptide, which is involved in various functions that include contractile activity on smooth muscle, controlling the blood flow and ion transport in the intestine, increased blood pressure and regulation of adrenocortical function. It is involved in the pathophysiology of various immune mediated inflammatory diseases like asthma. In this study, we have performed protein-protein docking analysis of neuromedin U - neuromedin U receptor 1 complex. We have developed homology models of neuromedin U, and selected a reliable model using model validation. The model was docked with the receptor model, to analyse the crucial interactions of the complex. This study could be helpful as a tool in developing novel and potent drugs for the diseases related with neuromedin U receptor 1.

• Translational and Clinical Pharmacology
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• v.26 no.3
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• pp.115-117
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• 2018

This tutorial explains the basic principles of mechanistic ligand-receptor interaction model, which is an operational model of agonism. A growing number of agonist drugs, especially immune oncology drugs, is currently being developed. In this tutorial, time-dependent ordinary differential equation for simple $E_{max}$ operational model of agonism was derived step by step. The differential equation could be applied in a pharmacodynamic modeling software, such as NONMEM, for use in non-steady state experiments, in which experimental data are generated while the interaction between ligand and receptor changes over time. Making the most of the non-steady state experimental data would simplify the experimental processes, and furthermore allow us to identify more detailed kinetics of a potential drug. The operational model of agonism could be useful to predict the optimal dose for agonistic drugs from in vitro and in vivo animal pharmacology experiments at the very early phase of drug development.

• Environmental Sciences Bulletin of The Korean Environmental Sciences Society
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• v.4 no.2
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• pp.111-116
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• 2000

Transboundary air pollution has recently become an area of increasing scientific interest and political concern as countries are receiving air pollutants from their neighbors. In order to gain a better understanding of the long-range transport processes of air pollutants and the source-receptor relationships among neighboring countries, an atmospheric transport model coupled with a RAMS(Regional Atmospheric Modeling System) model was applied to the East Asia region during the entire month of January 1993. The scalar transport option of the RAMS model was used to calculate special atmospheric constituents such as trace gases or aerosols. The sulfate production in clouds and rainwater and its removal processes by dry and wet deposition were considered. The sulfate budget from source regions to receptor regions was estimated by analysing the source-receptor relationships. When a specific receptor site revealed a sulfate value higher than the sulfate concentration based on its own source origin, this was taken to indicate long-range transport from another source region. The contribution ratio from various source region was calculated. The contribution ratio of dry and wet deposition was higher on the main continent of the East region. Furthermore, the high deposition amounts were identified on the west coast of Korea and the East China Sea.

• Journal of Integrative Natural Science
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• v.6 no.1
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• pp.16-20
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• 2013

G-protein-coupled receptor (GPCR) superfamily is the largest known receptor family, characterized by seven transmembrane domains and considered to be an important drug target. In this study we focused on an orphan GPCR termed as GPR18. As there is no X-ray crystal structure has been reported for this receptor, we report on a homology model of GPR18. Template structure with high homology was used for modeling and ten models were developed. A model was selected and refined by energy minimization. The selected model was further validated using various parameters. Our results could be a starting point for further structure based drug design.

• Journal of Integrative Natural Science
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• v.10 no.3
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• pp.125-130
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• 2017

Glucagon like pepide-2, one of the GLPs, is involved in various metabolic functions in the gastrointestinal tract. It plays a major role in the regulation of mucosal epithelium and the intestinal crypt cell proliferation. Because of their therapeutic importance towards the diseases in the gastrointestinal tract, it becomes necessary to study their interaction with its receptor, GLP-2R. In this study, we have developed protein-protein docking complexes of GLP-2 - GLP-2 receptor. Homology models of GLP-2 are developed, and a reliable model out of the predicted models was selected after model validation. The model was bound with the receptor, to study the important interactions of the complex. This study could be useful in developing novel and potent drugs for the diseases related with GLP-2.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.2008-2014
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• 2011

Serotonin or 5-hydroxytryptamine subtype 2C ($5-HT_{2C}$) receptor belongs to class A amine subfamily of G-protein-coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (${\beta}$2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.

• Genomics & Informatics
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• v.19 no.1
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• pp.9.1-9.5
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• 2021

Mammalian olfactory receptors are a family of G protein-coupled receptors (GPCRs) that occupy a large part of the genome. In human genes, olfactory receptors account for more than 40% of all GPCRs. Several types of GPCR structures have been identified, but there is no single olfactory receptor whose structure has been determined experimentally to date. The aim of this study was to model the interactions between an olfactory receptor and its ligands at the molecular level to provide hints on the binding modes between the OR2W1 olfactory receptor and its agonists and inverse agonists. The results demonstrated the modes of ligand binding in a three-dimensional model of OR2W1 and showed a statistically significant difference in binding affinity to the olfactory receptor between agonists and inverse agonists.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.13-24
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• 2013

Dopamine agonists and antagonists and its receptor play a critical role in the information transfer in the nervous system, and dopamine receptor-ligands interactions are deeply related to Parkinson's disease, schizophrenia and some other mental diseases. However, the only experimental 3D structure available for dopamine receptors is human D3 dopamine receptor. Therefore, it is important to create model of subtype dopamine receptor-ligands interactions. We report here the 3D structures of the human D1 and D2 dopamine receptor predicted by using GalaxyTBM, and its predicted binding site determined by using GalaxyDock. The highly conserved Asp on TM 3 and Phe on TM 6 have critical role in ligand binding. Also, highly conserved serines on TM 5 are essential for binding agonists and some kinds of antagonists. We identify differences between binding sites of agonists and antagonists of human D1 and D2 dopamine receptor, and find the reasons of selective binding of antagonists.