• 통합자연과학논문집
• /
• 제10권2호
• /
• pp.74-77
• /
• 2017

Bradykinin receptor B2 (B2R) is a GPCR protein which binds with the inflammatory mediator hormone bradkynin. Kallidin, a decapeptide, also signals through this receptor. B2R is crucial in the cross-talk between renin-angiotensin system (RAS) and the kinin-kallikrein system (KKS) and in many processes including vasodilation, edema, smooth muscle spasm and pain fiber stimulation. Thus the structural study of the receptor becomes important. We have predicted the peptide structures of Bradykinin and Kallidin from their amino acid sequences and the structures were docked with the receptor structure. The results obtained from protein-protein docking could be helpful in studying the B2R structural features and in the pathophysiology in various diseases related to it.

• 통합자연과학논문집
• /
• 제9권4호
• /
• pp.234-240
• /
• 2016

Bradykinin receptor B2, a GPCR protein, binds with the inflammatory mediator hormone bradkynin. It plays an important role in cross-talk between the renin-angiotensin system (RAS) and the kinin-kallikrein system (KKS). Also, it is involved in many processes including vasodilation, edema, smooth muscle spasm and pain fiber stimulation. Hence, studuying the structural features of the receptor becomes important. But the unavailability of the three dimensional structure of the protein makes the analysis difficult. Hence we have performed the homology modelling of Bradykinin receptor B2 with 5 different templates. 25 different homology models were constructed. Two best models were selected based on the model validation. The developed models could be helpful in analysing the structural features of Bradykinin receptor B2 and in pathophysiology of various disorders related to them.

• 통합자연과학논문집
• /
• 제10권3호
• /
• pp.119-124
• /
• 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.

• Genomics & Informatics
• /
• 제19권1호
• /
• pp.9.1-9.5
• /
• 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.

• Genomics & Informatics
• /
• 제19권2호
• /
• pp.18.1-18.8
• /
• 2021

G protein–coupled receptors (GPCRs), including olfactory receptors, account for the largest group of genes in the human genome and occupy a very important position in signaling systems. Although olfactory receptors, which belong to the broader category of GPCRs, play an important role in monitoring the organism's surroundings, their actual three-dimensional structure has not yet been determined. Therefore, the specific details of the molecular interactions between the receptor and the ligand remain unclear. In this report, the interactions between human olfactory receptor 1A1 and its odorant molecules were simulated using computational methods, and we explored how the chemically simple odorant molecules activate the olfactory receptor.

• Bulletin of the Korean Chemical Society
• /
• 제34권11호
• /
• pp.3429-3443
• /
• 2013

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

• Translational and Clinical Pharmacology
• /
• 제26권3호
• /
• pp.115-117
• /
• 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
• /
• 제4권2호
• /
• pp.111-116
• /
• 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.

• EDISON SW 활용 경진대회 논문집
• /
• 제6회(2017년)
• /
• pp.46-53
• /
• 2017

알츠하이머병은 치매를 유발하는 가장 주된 원인 질환으로 환자들은 인지장애를 겪게 된다. 현재 치료약으로 사용되는 약으로는 acetylcholinesterase 저해재가 있지만 이 약들의 효과는 미비하다. 그래서 인지기능에 영향을 미친다고 알려진 신경전달물질인 GABA, Glutamate, acetylcholine의 수치를 조절 할 수 있는 $5-HT_6$ receptor antagonist가 현재 개발되고 있다. 현재 여러 antagonist들이 임상실험 되었고, 인지 능력향상에 효과를 보이고 있다. 그러나, $5-HT_6$ receptor의 구조가 밝혀지지 않아 아직 원자적 수준의 결합 분석이 이루어지지 않았으므로 이 부분에 대한 연구가 필요하다. 따라서 본 연구에서는 Homology modeling을 통해 receptor의 구조를 예측하고, 현재 임상실험 중인 antagonist들 중 7개를 docking을 통해 단백질과 리간드의 결합을 예측하였다. Edison에서 Galaxy TBM과 Galaxy Refine을 사용하여 Homology modeling 한 결과 GPCR의 전형적인 모델에 특징적으로 긴 cterminal을 가졌다는 것을 확인 할 수 있었다. 생성된 구조를 가지고 Edison의 Dock 프로그램으로 7개의 antagonist가 어떠한 결합을 하는지 분석하였다. 그 결과, binding pose에 공통적으로 Trp102, Asp106, Val107, Pro177, Phe188, Val189, Ala192, Phe284, Phe285, Asn288, Thr306, Tyr310이 관여하는 것을 docking을 통해 알 수 있었다. 특히, Phe285는 7개의 antagonist 중에 4개와의 interaction을 하고 있는 것을 관찰하였다. 이 연구를 통하여 $5-HT_6$에 효과적으로 결합하여 치료효과를 낼 수 있는 신약을 개발할 수 있다.

• Journal of Pharmaceutical Investigation
• /
• 제26권3호
• /
• pp.155-168
• /
• 1996

The active site of cyclooxygenase was modeled by complementary receptor-cavity mapping procedure using 3D structures of the non-steroidal antiinflammatory drugs (NSAIDs). A total of 50 NSAIDs were chosen as data ligands which compete the same site on the enzyme. Partial atomic charges were estimated, and the energetic differences for various conformations were calculated so as to meet the need for a most efficient overlapping of the probably-equivalent functional groups of the ligand molecules. The structure activity relationships of the NSAIDs, if available, were fully considered throughout the modeling. The overall shape of the model obtained is similar to a boot-without-bottom. Most of inner surface of the cavity appeared as hydrophobic; two polar counterparts except the carboxyl-binding position were found. By this model, some clear explanations could be given on the experimental observations which were not satisfiably understood yet.