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1.  Structure-based prediction of subtype-selectivity of Histamine H3 receptor selective antagonists in clinical trials 
Histamine receptors (HRs) are excellent drug targets for the treatment of diseases such as schizophrenia, psychosis, depression, migraine, allergies, asthma ulcers, and hypertension. Among them, the human H3 Histamine receptor (hH3HR) antagonists have been proposed for specific therapeutic applications, including treatment of Alzheimer's disease, attention deficit hyperactivity disorder (ADHD), epilepsy, and obesity.1 However, many of these drug candidates cause undesired side effects through the cross-reactivity with other histamine receptor subtypes. In order to develop improved selectivity and activity for such treatments it would be useful to have the three dimensional structures for all four HRs. We report here the predicted structures of four HR subtypes (H1, H2, H3, and H4) using the GEnSeMBLE (GPCR Ensemble of Structures in Membrane BiLayer Environment) Monte Carlo protocol.2 sampling ~ 35 million combinations of helix packings to predict the 10 most stable packings for each of the four subtypes. Then we used these best 10 protein structures with the DarwinDock Monte Carlo protocol to sample ~ 50,000*20 poses to predict the optimum ligand-protein structures for various agonists and antagonists. We find that E2065.46 contributes most in binding H3 selective agonists (5, 6, 7) in agreement with experimental mutation studies. We also find that conserved E5.46/ S5.43 in both of hH3HR and hH4HR are involved in H3/ H4 subtype selectivity. In addition, we find that M3786.55 in hH3HR provides additional hydrophobic interactions different from hH4HR (the corresponding amino acid of T3236.55 in hH4HR) to provide additional subtype bias. From these studies we developed a pharmacophore model based on our predictions for known hH3HR selective antagonists in clinical study [ABT-239 1, GSK-189,254 2, PF-3654746 3, and BF2.649 (Tiprolisant) 4] that suggests critical selectivity directing elements are: the basic proton interacting with D1143.32, the spacer, the aromatic ring substituted with the hydrophilic or lipophilic groups interacting with lipophilic pockets in TMs 3-5-6 and the aliphatic ring located in TMs 2-3-7. These 3D structures for all four HRs should help guide the rational design of novel drugs for the subtype selective antagonists and agonists with reduced side effects.
PMCID: PMC3246544  PMID: 22035233
Membrane protein structure; binding; docking; modeling; receptor; ligand
2.  Conformational Changes Involved in G Protein-coupled Receptor Activation 
Trends in pharmacological sciences  2008;29(12):616-625.
Little is known about the nature of the conformational changes that convert G protein-coupled receptors (GPCRs), which bind diffusible ligands, from their resting into their active states. To gain structural insight into this process, various laboratories have used disulfide cross-linking strategies involving cysteine-substituted mutant GPCRs. Several recent disulfide cross-linking studies using the M3 muscarinic acetylcholine receptor as a model system have led to novel insights into the conformational changes associated with the activation of this prototypical class I GPCR. These structural changes are predicted to involve multiple receptor regions, primarily distinct segments of transmembrane helices III, VI, and VII, as well as helix 8. Given the high degree of structural homology found among most GPCRs, it is likely that these findings will be of considerable general relevance. A better understanding of the molecular mechanisms underlying GPCR activation may lead to novel strategies aimed at modulating GPCR function for therapeutic purposes.
PMCID: PMC3475190  PMID: 18838178
3.  Purification of Sulphate Leach Liquor of Spent Raneynickel Catalyst Containing Al and Ni by Solvent Extraction with Organophosphorus-Based Extractants 
The Scientific World Journal  2012;2012:286494.
Solvent extraction (SX) separation of Al from Ni sulphate leach liquor (LL) of spent Raneynickel catalyst containing 0.12 M Al and 1.448 M Ni using organophosphorus extractants has been investigated. Optimization of process conditions includes aqueous pH, extractant concentration, phase ratio, and stripping. Comparison of Al extraction efficiency with 0.45 M extractant concentration for TOPS 99, PC 88 A, and Cyanex 272 at an equilibrium pH of 2.23 was 81.8%, 98.6%, and 75%, respectively. The corresponding coextraction of Ni was 0.65, 0.6, and 0.9. Among the three extractants screened, PC 88A showed better extraction efficiency for Al at lower pH values than the others. Using 0.45 M PC 88 A, extraction isotherm was obtained at an aqueous-to-organic (A : O) phase ratio of 1 : 1–3 and O : A ratio of 1 : 1–5, which predicted possible separation of Al in 2 stages at A/O ratio of 2. Quantitative stripping was achieved by H2SO4.
PMCID: PMC3289934  PMID: 22505841
4.  Low Serum Testosterone Concentrations in Hospitalized Men with Poorly Controlled Type 2 Diabetes 
Endocrinology and Metabolism  2014;29(4):574-578.
Our aim was to examine whether serum testosterone concentrations are in fact low in hospitalized men with poorly controlled type 2 diabetes compared with healthy men. In this study, 79 men aged 40 years or older (41 healthy men and 38 men with type 2 diabetes) were included. Total testosterone and sex hormone-binding globulin levels were measured. The average duration of diagnosed diabetes was 10.8 years and the mean glycated hemoglobin value was 10.8%. Total testosterone concentrations were lower in men with type 2 diabetes than in healthy men, after adjusting for age and body mass index (3.83±0.32 ng/mL vs. 5.63±0.31 ng/mL, P<0.001). In conclusion, this study shows that serum testosterone concentrations are lower in hospitalized men with poorly controlled type 2 diabetes than in healthy men. Therefore, men with poorly controlled type 2 diabetes should undergo further assessment for hypogonadism.
PMCID: PMC4285042  PMID: 25325269
Testosterone; Diabetes mellitus, type 2; Hypogonadism
5.  Effects of patient‐tailored atorvastatin therapy on ameliorating the levels of atherogenic lipids and inflammation beyond lowering low‐density lipoprotein cholesterol in patients with type 2 diabetes 
Recently, patient‐tailored statin therapy was proven effective for achieving target low‐density lipoprotein (LDL) cholesterol levels. It is unclear, however, whether this therapeutic modality would be effective for atherogenic lipid profiles and inflammation in patients with type 2 diabetes.
Materials and Methods
The present study was an 8‐week, multicenter, single‐step titration trial of patient‐tailored atorvastatin therapy (10, 20 and 40 mg) according to baseline LDL cholesterol levels in 440 patients with type 2 diabetes. We measured the LDL particle size by polyacrylamide gel electrophoresis, and used high‐sensitivity C‐reactive protein (hsCRP) and adiponectin as surrogate markers of inflammation.
In the intention‐to‐treat analysis, 91% of the patients achieved their LDL cholesterol targets (<2.6 mmol/L) at week 8. There were significant reductions at week 8 in total cholesterol, triglycerides, non‐high‐density lipoprotein cholesterol (HDL) cholesterol, and the total cholesterol:HDL cholesterol ratio compared with the baseline values for all of the doses. The mean LDL particle size was significantly increased, and the small, dense LDL cholesterol levels were decreased in a dose‐dependent manner over the study period. In addition, the hsCRP levels were decreased in those high‐risk patients with baseline hsCRP levels over 3 mg/L (P < 0.001), and the adiponectin levels tended to increase with all of the doses (P = 0.004) at 8 weeks.
Patient‐tailored atorvastatin therapy based on LDL cholesterol at baseline was effective in ameliorating atherogenic LDL particle size and inflammation, in addition to achieving the target LDL cholesterol level without an undesirable effect on glycemic control in patients with type 2 diabetes. This trial was registered with (no. NCT01239849).
PMCID: PMC4025110  PMID: 24843697
Atorvastatin; Low‐density lipoprotein cholesterol; Type 2 diabetes mellitus
6.  Characterizing and Predicting the Functional and Conformational Diversity of Seven-Transmembrane Proteins 
Methods (San Diego, Calif.)  2011;55(4):405-414.
The activation of seven-transmembrane receptors (7TMRs) allows cells to sense their environment and convert extracellular signals (like hormone binding) into intracellular signals (through G protein-coupled and/or β arrestin-coupled pathways). A single 7TMR is capable of transducing a wide spectrum of physiological responses inside a cell by coupling to these pathways. This intracellular pleiotropic action is enabled by multiple conformations exhibited by these receptors. Developments in membrane protein structure determination technologies have led to a rapid increase in crystal structures for many 7TMRs. Majority of these receptors have been crystallized in their inactive conformation and, for some, one of the many active conformations has also been crystallized. Given the topological constraints of a lipid bilayer that results in a single fold of seven almost parallel TM helices connected by mostly unstructured loops, these structures exhibit a diversity of conformations not only across the receptors but also across the different functional forms for receptors with structures for one of the functionally active conformations. Here we present a method to characterize this conformational diversity in terms of TransMembrane Helix TOPology (TMHTOP) parameters (TMHTOP) and how to use these helix orientation parameters to predict functionally-distinct multiple conformations for these receptors. The TMHTOP parameters enable a quantification of the structural changes that underlie 7TM activation and also sheds a unique mechanistic light on the pleiotropic nature of these receptors. It provides a common language to describe the 7TMR activation mechanisms as well as differences across many receptors in terms of visually intuitive structural parameters. Protein structure prediction methods can use these parameters to describe 7TMR conformational ensembles, which coupled to experimental data can be used to develop testable hypotheses for the structural basis of 7TMR functions.
PMCID: PMC3286597  PMID: 22197575
G protein-coupled receptors; GPCRs; Conformational ensemble; Functional selectivity; Protein structure prediction; Transmembrane Helix Topology
7.  Prediction of the 3D structure for the rat urotensin II receptor and comparison of the antagonist binding sites and binding selectivity between human and rat from atomistic simulations 
ChemMedChem  2010;5(9):1594-1608.
Urotensin-II (U-II) has been shown to be the most potent mammalian vasoconstrictor known.[1, 2] Thus a U-II antagonist might be of therapeutic value in a number of cardiovascular disorders.[3] However, interspecies variability of several nonpeptidic ligands complicates the interpretation of in vivo studies of such antagonists in pre-clinical animal models of disease. Thus compound ACT058362 is a selective antagonist for human U-II receptor (hUT2R) with a reported Kd ~ 4 nM in a molecular binding assay, but it is reported to bind weakly to rat UT2R (rUT2R), with Kd ~ 1,500 nM.[4] In contrast, the arylsulphonamide SB706375 is a selective antagonist against both hUT2R (Kd: ~ 9 nM) and rUT2R (Kd: ~ 21 nM).[3] To understand the species selectivity of the UT2R, we investigated the binding site of ACT058362 and SB706375 complex with both hUT2R and rUT2R to explain the dramatic (~ 400-fold) lower affinity of ACT058362 for rUT2R and the similar (~10 nM) affinity of SB706375 for both UT2R. These studies.used MembStruk and MSCDock to predict the UT2R structure and the binding site for ACT058362 and SB706375. Based on binding energy, we found two binding modes each with D1303.32 as the crucial anchoring point. We predict that ACT058362 (an aryl-amine-aryl or ANA ligand) binds in the TM 3456 region while we predict that SB706375 (an aryl-aryl-amine or AAN ligand) binds in the TM 1237 region. These predicted sites explain the known differences in binding the ANA ligand to rat and human while explaining the similar binding of the AAN compound to rat and human. Moreover the predictions explain currently available SAR data. To further validate the predicted binding site of these ligands to hUT2R and rUT2R, we propose several mutations that would help define the structural origins of differential responses of UT2R among species potentially indicating novel UT2R antagonists with cross-species high affinity.
PMCID: PMC3517062  PMID: 20683923
docking; G protein-coupled receptors; Urotensin II; dynamics. MSCDock; MembStruk; MembScream
8.  A Case of Helicobacter cinaedi Bacteremia in an Asplenic Patient 
Annals of Laboratory Medicine  2012;32(6):433-437.
Helicobacter cinaedi is an enterohepatic species. It can cause bacteremia, gastroenteritis, and cellulitis, particularly in immunocompromised individuals, such as those with acquired immunodeficiency syndrome, malignancy, or alcoholism. There are no previous reports of H. cinaedi infection in Korea. A 71-yr-old man was admitted to the emergency room because of dyspnea on November 9, 2011. He had undergone splenectomy 3 yr ago because of immune hemolytic anemia. Chest plain radiography revealed bilateral pleural effusion. He developed fever on hospital day (HD) 21. Three sets of blood cultures were taken, and gram-negative spiral bacilli were detected in all aerobic vials. The isolate grew in tiny colonies on chocolate agar after 3-day incubation under microaerophilic conditions. This organism tested positive for catalase and oxidase, and negative for urease. The 16S rRNA gene sequence of this isolate exhibited 99.8% homology with the published sequence of H. cinaedi CCUG 18818T (GenBank accession no. ABQT01000054) and 98.5% homology with the sequence of Helicobacter bilis Hb1T (GenBank accession no. U18766). The patient was empirically treated with piperacillin/tazobactam and levofloxacin, and discharged with improvement on HD 31. To our knowledge, this is the first report of H. cinaedi bacteremia in an asplenic patient. Asplenia appears to be a risk factor for H. cinaedi bacteremia.
PMCID: PMC3486939  PMID: 23130344
Helicobacter cinaedi; 16s rRNA; asplenia
9.  Orthogonal activation of the reengineered A3 adenosine receptor (neoceptor) using tailored nucleoside agonists 
Journal of medicinal chemistry  2006;49(9):2689-2702.
An alternative approach to overcome the inherent lack of specificity of conventional agonist therapy can be the reengineering of the GPCRs and their agonists. A reengineered receptor (neoceptor) could be selectively activated by a modified agonist, but not by the endogenous agonist. Assisted by rhodopsin-based molecular modeling, we pinpointed mutations of the A3 adenosine receptor (AR) for selective affinity enhancement following complementary modifications of adenosine. Ribose modifications examined included, at 3′: amino, aminomethyl, azido, guanidino, ureido; and at 5′: uronamido, azidodeoxy. N6-variations included: 3-iodobenzyl, 5-chloro-2-methyloxybenzyl, and methyl. An N6-3-iodobenzyl-3′-ureido adenosine derivative 10 activated phospholipase C in COS-7 cells (EC50=0.18 μM) or phospholipase D in chick primary cardiomyocytes mediated by a mutant (H272E), but not the wild-type, A3AR. The affinity enhancements for 10 and the corresponding 3′-acetamidomethyl analogue 6 were >100-fold and >20-fold, respectively. 10 concentration-dependently protected cardiomyocytes transfected with the neoceptor against hypoxia. Unlike 10, adenosine activated the wild-type A3AR (EC50 of 1.0 μM), but had no effect on the H272E mutant A3AR (100 μM). Compound 10 was inactive at human A1, A2A, and A2BARs. The orthogonal pair comprising an engineered receptor and a modified agonist should be useful for elucidating signaling pathways and could be therapeutically applied to diseases following organ-targeted delivery of the neoceptor gene.
PMCID: PMC3471142  PMID: 16640329
10.  Modulation of adenosine receptor affinity and intrinsic efficacy in adenine nucleosides substituted at the 2-position 
Bioorganic & medicinal chemistry  2004;12(11):2995-3007.
We studied the structural determinants of binding affinity and efficacy of adenosine receptor (AR) agonists. Substituents at the 2-position of adenosine were combined with N6-substitutions known to enhance human A3AR affinity. Selectivity of binding of the analogues and their functional effects on cAMP production were studied using recombinant human A1, A2A, A2B, and A3ARs. Mainly sterically small substituents at the 2-position modulated both the affinity and intrinsic efficacy at all subtypes. The 2-cyano group decreased hA3AR affinity and efficacy in the cases of N6-(3-iodobenzyl) and N6-(trans-2-phenyl-1-cyclopropyl), for which a full A3AR agonist was converted into a selective antagonist; the 2-cyano-N6-methyl analogue was a full A3AR agonist. The combination of N6-benzyl and various 2-substitutions (chloro, trifluoromethyl, and cyano) resulted in reduced efficacy at the A1AR. The environment surrounding the 2-position within the putative A3AR binding site was explored using rhodopsin-based homology modeling and ligand docking.
PMCID: PMC3463103  PMID: 15142558
Purines; Cyclic AMP; Binding; Antagonists; Agonists; GPCR; Molecular modeling
11.  (N)-Methanocarba 2,N6-Disubstituted Adenine Nucleosides as Highly Potent and Selective A3 Adenosine Receptor Agonists 
Journal of medicinal chemistry  2005;48(6):1745-1758.
A series of ring-constrained (N)-methanocarba-5′-uronamide 2,N6-disubstituted adenine nucleosides have been synthesized via Mitsunobu condensation of the nucleobase precursor with a pseudosugar ring containing a 5′-ester functionality. Following appropriate functionalization of the adenine ring, the ester group was converted to the 5′-N-methylamide. The compounds, mainly 2-chloro substituted derivatives, were tested in both binding and functional assays at human adenosine receptors (ARs), and many were found to be highly potent and selective A3AR agonists. Selected compounds were compared in binding to the rat A3AR to assess their viability for testing in rat disease models. The N6-(3-chlorobenzyl) and N6-(3-bromobenzyl) analogues displayed Ki values at the human A3AR of 0.29 and 0.38 nM, respectively. Other subnanomolar affinities were observed for the following N6 derivatives: 2,5-dichlorobenzyl, 5-iodo-2-methoxybenzyl, trans-2-phenyl-1-cyclopropyl, and 2,2-diphenylethyl. Selectivity for the human A3AR in comparison to the A1AR was (fold): the N6-(2,2-diphenylethyl) analogue 34 (1900), the N6-(2,5-dimethoxybenzyl) analogue 26 (1200), the N6-(2,5-dichlorobenzyl) and N6-(2-phenyl-1-cyclopropyl) analogues 20 and 33 (1000), and the N6-(3-substituted benzyl) analogues 17, 18, 28, and 29 (700–900). Typically, even greater selectivity ratios were obtained in comparison with the A2A and A2BARs. The (N)-methanocarba-5′-uronamide analogues were full agonists at the A3AR, as indicated by the inhibition of forskolin-stimluated adenylate cyclase at a concentration of 10 µM. The N6-(2,2-diphenylethyl) derivative was an A3AR agonist in the (N)-methanocarba-5′-uronamide series, although it was an antagonist in the ribose series. Thus, many of the previously known groups that enhance A3AR affinity in the 9-riboside series, including those that reducing intrinsic efficacy, may be adapted to the (N)-methanocarba nucleoside series of full agonists.
PMCID: PMC3463111  PMID: 15771421
12.  Management of Type 2 Diabetes Mellitus in Older Adults 
Diabetes & Metabolism Journal  2012;36(5):336-344.
In the near future, the majority of patients with diabetes will be adults aged 65 or older. Unlike young adults with diabetes, elderly diabetic people may be affected by a variety of comorbid conditions such as depression, cognitive impairment, muscle weakness (sarcopenia), falls and fractures, and physical frailty. These geriatric syndromes should be considered in the establishment of treatment goals in older adults with diabetes. Although there are several guidelines for the management of diabetes, only a few are specifically designed for the elderly with diabetes. In this review, we present specific conditions of elderly diabetes which should be taken into account in the management of diabetes in older adults. We also present advantages and disadvantages of various glucose-lowering agents that should be considered when choosing a proper regimen for older adults with diabetes.
PMCID: PMC3486979  PMID: 23130317
Diabetes mellitus, type 2; Elderly diabetes; Geriatric syndrome; Sarcopenia
13.  Ratio of Waist-to-Calf Circumference and Carotid Atherosclerosis in Korean Patients With Type 2 Diabetes 
Diabetes Care  2011;34(9):2067-2071.
To investigate whether waist circumference (WC), calf circumference (CC), and waist-to-calf ratio (WCR) are associated with carotid atherosclerosis in patients with type 2 diabetes.
This was an observational study performed in 3,694 Korean patients with type 2 diabetes. Anthropometric measures and carotid ultrasound were performed on each subject. Carotid atherosclerosis was defined as having a clearly isolated focal plaque or mean carotid intima-media thickness (CIMT) ≥1.1 mm.
CIMT and the frequency of carotid atherosclerosis were higher with increasing WC quartiles and decreasing CC quartiles. There was an augmentative effect of CC and WC on the frequency of carotid atherosclerosis, which was dramatically higher in both the highest WC quartile and lowest CC quartile. However, except for the relationship between the quartile of CC with the frequency of carotid atherosclerosis in men, those associations disappeared after adjusting for potential confounders. In contrast, WCR was significantly related to CIMT (only in women) and carotid atherosclerosis, even after adjustment (adjusted odds ratio for carotid atherosclerosis for the highest quartile of WCR compared with the lowest quartile being 1.178 [95% CI 1.026–1.353] and 1.276 [1.053–1.545] in men and women, respectively).
A low CC and high WC seems to be associated with a carotid atherosclerotic burden in Korean diabetic patients. In particular, compared with each circumference, WCR is independently associated with carotid atherosclerosis. However, the cross-sectional nature of the study limits conclusions regarding the direction or causality. Further longitudinal study is warranted in this and other ethnic groups.
PMCID: PMC3161258  PMID: 21775758
14.  Allosteric Modulation of the Adenosine Family of Receptors 
Allosteric modulators for adenosine receptors (ARs) are of an increasing interest and may have potential therapeutic advantage over orthosteric ligands. Benzoylthiophene derivatives (including PD 81,723), 2-aminothiazolium salts, and related allosteric modulators of the A1 AR have been studied. The benzoylthiophene derivatives were demonstrated to be selective enhancers for the A1 AR, with little or no effect on other subtypes of ARs. Allosteric modulation of the A2A AR has also been reported. A3 allosteric enhancers may be predicted to be useful against ischemic conditions. We have recently characterized two classes of A3 AR allosteric modulators: 3-(2-pyridinyl)isoquinolines (e.g. VUF5455) and 1H-imidazo-[4,5-c]quinolin-4-amines (e.g. DU124183), which selectively decreased the agonist dissociation rate at the human A3AR but not at A1 and A2A ARs. DU124183 left-shifted the agonist conc.-response curve for inhibition of forskolin-stimulated cAMP accumulation in intact cells expressing the human A3AR with up to 30% potentiation of the maximal efficacy. The increased potency of A3 agonists was evident only in the presence of an A3 antagonist, since VUF5455 and DU124183 also antagonized, i.e. displaced binding at the orthosteric site, with Ki values of 1.68 and 0.82 μM, respectively. A3AR mutagenesis studies implicated F1825.43 and N2747.45 in the action of the enhancers and was interpreted using a rhodopsin-based A3AR molecular model, suggesting multiple binding modes. Amiloride analogues, SCH-202676 (N-(2,3-diphenyl-1,2,4-thiadiazol-5(2H)-ylidene)methanamine), and sodium ions were demonstrated to be common allosteric modulators for at least three subtypes (A1, A2A, and A3) of ARs.
PMCID: PMC3431557  PMID: 15974932
15.  Purine Receptors: GPCR Structure and Agonist Design 
Molecular interventions  2004;4(6):337-347.
An integrated approach to the study of drug-receptor interactions has been applied to adenosine receptors (ARs) and P2Y nucleotide receptors. This approach includes probing the receptor structure through site-directed mutagenesis and molecular modeling, in concert with altering the structure of the agonist ligands. Goals of this structural approach are to generate a testable hypothesis for location of the binding site and subsequently to enable the rational design of new agonists and antagonists. In this manner, receptor subtype selectivity has been increased, and agonists have been converted into partial agonists and antagonists. An approach to receptor engineering (neoceptors) has been explored, in which synthetic small molecule agonists (neoligands) are specifically tailored to activate only receptors in which the putative binding sites have been modified. This orthogonal approach to receptor activation, intended for eventual gene therapy, has been demonstrated for A3 and A2A ARs.
PMCID: PMC3418328  PMID: 15616163
16.  Predicted Structures of Agonist and Antagonist Bound Complexes of Adenosine A3 Receptor 
Proteins  2011;79(6):1878-1897.
We used the GEnSeMBLE Monte Carlo method to predict ensemble of the 20 best packings (helix rotations and tilts) based on the neutral total energy (E) from a vast number (10 trillion) of potential packings for each of the 4 subtypes of the adenosine G protein-coupled receptors (GPCRs), which are involved in many cytoprotective functions. We then used the DarwinDock Monte Carlo methods to predict the binding pose for the human A3 adenosine receptor (hAA3R) for subtype selective agonists and antagonists.
We find that all four A3 agonists stabilize the 15th lowest conformation of apo-hAA3R while also binding strongly to the 1st and 3rd. In contrast the four A3 antagonists stabilize the 2nd or 3rd lowest conformation. These results show that different ligands can stabilize different GPCR conformations, which will likely affect function, complicating the design of functionally unique ligands.
Interestingly all agonists lead to a trans χ1 angle for W6.48 that experiments on other GPCRs associate with G-protein activation while all 20 apo-AA3R conformations have a W6.48 gauche+ χ1 angle associated experimentally with inactive GPCRs for other systems. Thus docking calculations have identified critical ligand-GPCR structures involved with activation.
We find that the predicted binding site for selective agonist Cl-IB-MECA to the predicted structure of hAA3R shows favorable interactions to three subtype variable residues, I2536.58, V169EL2, and Q167EL2, while the predicted structure for hAA2AR shows weakened to the corresponding amino acids: T2566.58, E169EL2, and L167EL2, explaining the observed subtype selectivity.
PMCID: PMC3092833  PMID: 21488099
docking; GPCR; agonists; antagonist; membrane protein predicted structure; adenosine receptor
17.  Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors 
Subtype 2 Serotonin (5-Hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions.1 We report here the predicted structure of 5-HT2B and 5-HT2C receptor bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5-HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydropyrrolo[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist-bound and the antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region
PMCID: PMC3070210  PMID: 21299232
GPCR; Serotonin; Docking; Membrane protein structure; Molecular dynamics
18.  Serum TSH Level in Healthy Koreans and the Association of TSH with Serum Lipid Concentration and Metabolic Syndrome 
The proper treatment of subclinical hypothyroidism and the normal range of serum thyroid stimulating hormone (TSH) concentration are intensely debated. However, few reports have investigated TSH concentrations in Asian ethnic groups. Therefore, the present study was designed to define the TSH reference range in a Korean population and to investigate the metabolic significance of TSH concentration.
We enrolled patients who underwent medical examination at the CHA Bundang Medical Center. Anthropometric data were evaluated, and serum TSH, free T4, and lipid profiles were assayed.
A total of 7,270 subjects were included. Mean TSH concentration of the study population was 1.82 ± 0.95 mU/L, and we observed a sex-related difference in TSH concentration (male, 1.67 ± 0.87 mU/L; female, 2.02 ± 1.01 mU/L; p < 0.01). When the 2.5 and 97.5 percentiles were calculated, 95% TSH reference limits were 0.52-4.29 mU/L. TSH concentration was higher in elderly subjects, during winter, in postmenopausal women, and in obese males. Moreover, TSH showed significantly positive correlations with serum total cholesterol, triglyceride, and low density lipoprotein cholesterol regardless of sex, age, season, obesity, or menopausal status (all p < 0.01). Finally, TSH concentration was positively related to the prevalence of metabolic syndrome.
We demonstrated the association between TSH concentration within the normal reference range and serum lipid levels. TSH concentration varies according to sex, age, season, and body mass index (only in males). Moreover, high normal TSH levels were significantly associated with an increased prevalence of metabolic syndrome, which may be of importance when evaluating subjects with high normal TSH concentration.
PMCID: PMC3245392  PMID: 22205844
Thyroid function tests; Thyrotropin; Metabolic syndrome
19.  A Neoceptor Approach to Unraveling Microscopic Interactions between the Human A2A Adenosine Receptor and Its Agonists 
Chemistry & biology  2005;12(2):237-247.
Strategically mutated neoceptors, e.g., with anionic residues in TMs 3 and 7 intended for pairing with positively charged amine-modified nucleosides, were derived from the antiinflammatory A2A adenosine receptor (AR). Adenosine derivatives functionalized at the 5′, 2, and N6 positions were synthesized. The T88D mutation selectively enhanced the binding of the chain-length-optimized 5′-(2-aminoethyl)uronamide but not 5′-(2-hydroxyethyl)uronamide, suggesting a critical role of the positively charged amine. Combination of this modification with the N6-(2-methylbenzyl) group enhanced affinity at the Q89D- and N181D- but not the T88D-A2AAR. Amino groups placed near the 2- or N6-position only slightly affected the binding to mutant receptors. The 5′-hydrazide MRS3412 was 670-and 161-fold enhanced, in binding and functionally, respectively, at the Q89D-A2AAR compared to the wild-type. Thus, we identified and modeled pairs of A2AAR-derived neoceptor-neoligand, which are pharmacologically orthogonal with respect to the native species.
PMCID: PMC3122079  PMID: 15734651
20.  Evaluating intra- and inter-examiner reproducibility in histometric measurement: one-wall intrabony periodontal defects in beagle dogs 
Accurate and exact measurement is an important factor for generating meaningful results in any properly designed study. If all the participating examiners are able to yield similar results, it will be possible to evaluate the objective results of the study more easily and quickly. The purpose of this study was to evaluate the intra- and inter-examiner reproducibility of histometric measurements in the intrabony periodontal defect model.
One wall intrabony defects were surgically created at the distal aspect of the second and the medial aspect of the fourth mandibular premolars in the right and left jaw quadrants in twenty beagle dogs and the defect sites received the following β-tri calcium phosphate, growth differentiation factor-0, growth differentiation factor-100 and sham surgery. Histometric analysis was performed after 8 weeks. Histometric parameters were recorded and repeated at three months interval by three examiners. Intra- and inter-examiner reproducibility was assessed.
Most parameters of all the groups showed high intra- and inter-examiner reproducibility. Parameters including defect height, bone regeneration height, cementum regeneration height, and formation of junctional epithelium yielded inter-examiner correlation ≥ 0.9. The intra-examiner reproducibility showed a high result, over 0.9.
Histometric evaluation of the one-wall intra-alveolar periodontal defect model showed high reproducibility not only for a single given examiner but also among the three examiners.
PMCID: PMC2931305  PMID: 20827326
Alveolar bone loss; Histology; Reproducibility of result
21.  Rosiglitazone and fenofibrate improve insulin sensitivity of pre-diabetic OLETF rats by reducing malonyl-CoA levels in the liver and skeletal muscle 
Life sciences  2009;84(19-20):688-695.
Rosiglitazone and fenofibrate, specific agonists of the peroxisome proliferator activated receptors-γ (PPARγ) and -α (PPARα), respectively, improve insulin sensitivity in diabetic animals and in patients with type 2 diabetes. Here we investigated how pre-diabetic Otsuka Long–Evans Tokushima Fatty (OLETF) rats fed with normal and high-fat diets respond to these PPAR agonists.
Main methods
Pre-diabetic OLETF rats were subjected to high-fat or standard diets with or without rosiglitazone or fenofibrate for 2 weeks. The metabolism of the rats and the levels of malonyl-CoA and activities of malonyl-CoA decarboxylase (MCD), acetyl-CoA carboxylase (ACC), and AMP-activated protein kinase (AMPK) in metabolic tissues were assessed.
Key findings
Rosiglitazone and fenofibrate significantly improved insulin sensitivity and reduced the levels of plasma triglycerides and free fatty acids in OLETF rats fed with a high-fat diet. Fenofibrate particularly reduced the body weight, fat, and total cholesterol in high fat diet OLETF rats. The highly elevated malonyl-CoA levels in the skeletal muscle and liver of OLETF rat were significantly reduced by rosiglitazone or fenofibrate due to, in part, the increased MCD activities and expression. On the other hand, ACC activities were unchanged in skeletal muscle and decreased in liver in high fat diet group. AMPK activities were dramatically decreased in OLETF rats and not affected by these agonists.
These results demonstrate that treatment of pre-diabetic OLETF rats–particularly those fed a high-fat diet–with rosiglitazone and fenofibrate significantly improves insulin sensitivity and fatty acid metabolism by increasing the activity of MCD and reducing malonyl-CoA levels in the liver and skeletal muscle.
PMCID: PMC2905871  PMID: 19250943
PPARγ; PPARα agonists; Rosiglitazone; Fenofibrate; Malonyl-CoA; Malonyl-CoA decarboxylase; Acetyl-CoA carboxylase
22.  The Clinical Characteristics of the Newly Diagnosed Early Onset (< 40 Years Old) Diabetes in Outpatients' Clinic 
Korean Diabetes Journal  2010;34(2):119-125.
The prevalence of type 2 diabetes in young adults and adolescents has increased in the last decade according to the increasing obese population. The aim of this study was to examine the clinical characteristics of patients diagnosed with diabetes mellitus before the age of 40 years as compared with patients diagnosed at older ages.
This was a cross-sectional, retrospective study using data from 350 diabetic patients who were diagnosed with diabetes in an outpatient setting between January 2005 and December 2007. Patients were diagnosed according to the criteria set forth by the American Diabetes Association. We examined the clinical characteristics and laboratory data of the patients through review of medical records and compared the early-onset diabetic patients (< 40 years old) and the usual-onset diabetic patients (≥ 40 years old).
The frequency of early-onset diabetes and usual-onset diabetes were 31.1% (n=109) and 68.9% (n=241), respectively. The early-onset diabetic patients more often had a positive family history of diabetes; higher HbA1c, fasting glucose, and postprandial glucose levels; experienced typical symptoms more frequently; had microalbuminuria more frequently; and required insulin therapy as initial treatment more frequently as compared to usual-onset diabetic patients, and these differences were significant. Conversely, hypertension was significantly more common in the usual-onset diabetic patients.
It could be concluded that we should control early onset diabetes more strictly to prevent its complication because early onset diabetic patients represented more severe hyperglycemia and had more prevalent microalbuminuria.
PMCID: PMC2883350  PMID: 20548844
Diabetes mellitus; Early-onset; Outpatient
23.  Selective A3 Adenosine Receptor Antagonists Derived from Nucleosides Containing a Bicyclo[3.1.0]hexane Ring System 
Bioorganic & medicinal chemistry  2008;16(18):8546-8556.
We have prepared 5′-modified derivatives of adenosine and a corresponding (N)-methanocarba nucleoside series containing a bicyclo[3.1.0]hexane ring system in place of the ribose moiety. The compounds were examined in binding assays at three subtypes of adenosine receptors (ARs) and in functional assays at the A3 AR. The H-bonding ability of a group of 9-riboside derivatives containing a 5′-uronamide moiety was reduced by modification of the NH, however these derivatives did not display the desired activity as selective A3 AR antagonists, as occurs with 5′-N,N-dimethyluronamides. However, truncated (N)-methanocarba analogues lacking a 4′-hydroxymethyl group were highly potent and selective antagonists of the human A3 AR. The compounds were synthesized from D-ribose using a reductive free radical decarboxylation of a 5′-carboxy intermediate. A less efficient synthetic approach began with L-ribose, which was similar to the published synthesis of (N)-methanocarba A3AR agonists. Compounds 33b – 39b (N6-3-halobenzyl and related arylalkyl derivatives) were potent A3AR antagonists with binding Ki values of 0.7 − 1.4 nM. In a functional assay of [35S]GTPγS binding, 33b (3-iodobenzyl) completely inhibited stimulation by NECA with a KB of 8.9 nM. Thus, a highly potent and selective series of A3AR antagonists has been described.
PMCID: PMC2593936  PMID: 18752961
G protein-coupled receptor; purines; molecular modeling; structure activity relationship; radioligand binding; adenylate cyclase
24.  Conversion of A3 Adenosine Receptor Agonists into Selective Antagonists by Modification of the 5′-Ribofuran-uronamide Moiety 
The highly selective agonists of the A3 adenosine receptor (AR), Cl-IB-MECA (2-chloro-N6-(3-iodobenzyl)-5′-N-methylcarboxamidoadenosine) and its 4′-thio analogue, were successfully converted into selective antagonists simply by appending a second N-methyl group on the 5′-uronamide position. The 2-chloro-5′-(N,N-dimethyl)uronamido analogues bound to, but did not activate the human A3AR, with Ki values of 29 nM (4′-O) and 15 (4′-S) nM, showing >100-fold selectivity over A1, A2A, and A2BARs. Competitive antagonism was demonstrated by Schild analysis. The 2-(dimethylamino)-5′-(N,N-dimethyl)uronamido substitution also retained A3AR selectivity but lowered affinity.
PMCID: PMC1351218  PMID: 16289820
nucleoside; G protein-coupled receptor; adenylyl cyclase; molecular modeling; radioligand binding; AR, adenosine receptor; CGS21680, 2-[p-(2-carboxyethyl)phenylethylamino]-5′-N-ethylcarboxamido-adenosine; CHO, Chinese hamster ovary; Cl-IB-MECA, 2-chloro-N6-(3-iodobenzyl)-5′-N-methylcarboxamidoadenosine; CPA, N6-cyclopentyladenosine; DMEM, Dulbecco’s modified Eagle’s medium; I-AB-MECA, N6-(4-amino-3-iodobenzyl)-5′-N-methylcarboxamidoadenosine; NECA, 5′-N-ethylcarboxamidoadenosine; PIA, N6-(phenylisopropyl)adenosine; PTLC, preparative thin layer chromatography

Results 1-24 (24)