• Genomics & Informatics
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• v.11 no.4
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• pp.224-229
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• 2013

Receptor for advanced glycation endproducts (RAGE) is a multi-ligand receptor that is able to bind several different ligands, including advanced glycation endproducts, high-mobility group protein (B)1 (HMGB1), S-100 calcium-binding protein, amyloid-${\beta}$-protein, Mac-1, and phosphatidylserine. Its interaction is engaged in critical cellular processes, such as inflammation, proliferation, apoptosis, autophagy, and migration, and dysregulation of RAGE and its ligands leads to the development of numerous human diseases. In this review, we summarize the signaling pathways regulated by RAGE and its ligands identified up to date and demonstrate the effects of hyper-activation of RAGE signals on human diseases, focused mainly on renal disorders. Finally, we propose that RAGE and its ligands are the potential targets for the diagnosis, monitoring, and treatment of numerous renal diseases.

• 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.

• 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.

• BMB Reports
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• v.31 no.5
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• pp.419-426
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• 1998

The nuclear hormone receptor superfamily currently includes approximately equal numbers of conventional receptors and orphan receptors, which do not have known ligands. Here, we review recent progress from this laboratory on three orphans, two of which are moving from orphan to conventional receptor status. Perhaps the most unusual is CAR, which is a constitutive transactivator in the absence of ligands but becomes transcriptionally inactive in the presence of its ligands, which are androgen metabolites. The response of CAR to its ligands is thus opposite to that of the conventional receptor paradigm. RIP14 (also known as FXR) is activated by both all-trans retinoic acid and a synthetic retinoid previously thought to specifically target the retinoic acid receptors (RARs), and thus appears to be a novel retinoid receptor. Finally, SHP is a novel orphan that lacks a DNA binding domain and interacts with a number of other receptor superfamily members. While it generally inhibits its targets, including CAR, the retinoid X receptor (RXR), and the estrogen receptor (ER), it stimulates transactivation by the orphan SF-1.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.4
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• pp.2371-2375
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• 2013

Breast cancer is one of the most common malignancies in women around the world. Among the various hormonal types of breast cancer, those that are estrogen receptor (ER) positive account for the majority. Among the estrogen related receptors, estrogen related receptor ${\alpha}$ is known to have a potential role in breast cancer and is one of the therapeutic target. Hence, prediction of novel ligands interact with estrogen related receptor alpha is therapeutically important. The present study, aims at prediction and analysis of ligands from the KEGG COMPOUND database (containing 10,739 entries) able to interact against estrogen receptor alpha using a similarity search and molecular docking approach.

• Genomics & Informatics
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• v.10 no.2
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• pp.128-132
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• 2012

To learn the differences between the structure-activity relationship and molecular vibration-activity relationship in the ligand-receptor interaction of the histamine receptor, 47 ligands of the histamine receptor were analyzed by structural similarity and molecular vibrational frequency patterns. The radial tree that was produced by clustering analysis of molecular vibrational frequency patterns shows its potential for the functional classification of histamine receptor ligands.

• YAKHAK HOEJI
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• v.58 no.1
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• pp.16-20
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• 2014

KR-31064 was developed for the strong angiotensin II receptor antagonist among the one of pyridyl imidazol series compounds. To investigate the receptor-ligand binding characteristics of this nonpeptide antagonist, binding experiments were deployed in various conditions and ex vivo contractile responses were tested toward the standard compound, losartan. Receptor binding experiments with radiolabeled angiotensin II, the $IC_{50}$ value for KR-31064 resulted 0.67 nM without any activities toward type 2 angiotensin II receptor. The comparative potency against losartan was more than 18 fold and the specific activity in type 1 angiotensin II receptor was more than 10,000 fold comparing to the type 2 receptor. Scatchard analysis of saturation binding data showed KR-31064 acted on the receptor in a competitive mode. KR-31064 inhibited the contractile response derived by angiotensin II ($pK_B$: 9.86) similar to that of losartan with decreased maximum signals. As a potent and specific type 1 angiotensin II receptor antagonist, KR-31064 may have possibilities for the development of diagnostic ligands that can be used as tools for various biochemical research experiments and non-invasive diagnostics.

• Biomolecules & Therapeutics
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• v.31 no.4
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• pp.359-369
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• 2023

Dependence receptors are a group of receptor proteins with shared characteristics of transducing two different signals within cells. They can transduce a positive signal of survival and differentiation in the presence of ligands. On the other hand, dependence receptors can transduce an apoptosis signal in the absence of ligands. The function of these receptors depends on the availability of their ligands. Several receptor tyrosine kinases (RTKs) have been reported as dependence receptors. When cells undergo apoptosis by dependence receptors, the intracellular domain of some RTKs is cleaved by the caspases. Among the RTKs that belong to dependence receptors, we focused on eight RTKs (RET, HER2, MET, ALK, TrkC, EphA4, EphB3, and c-KIT) that are cleaved by caspases. In this review, we describe the features of the receptors, their cleavage sites, and the fate of the cleaved products, as well as recent implications on them being used as potential therapeutics for cancer treatment.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.346.1-346.1
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• 2002

FXR (farnesoid X-activated receptor) is a member of nuclear steroid hormone receptor superfamily and especially a orphan receptor, which are able to control mevalonate pathway upon activation by binding of the specific ligands. We. have launched our study for development of FXR specific ligands getting on in lead discovery. A promising lead stilbene analog was obtained through the screening of a set of library compounds which was previously targeted for other nuclear receptors. And then synthetic modilication of the lead was perfoumde. In addition. fishing a new pharmacophore was fried by UNITT aearch. which brought new structural features.

• 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.