Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.4.1 (phosphodiesterase)
18,767 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

15-Deoxy-Delta12,14-PGJ2 (dPGJ2) is a bioactive metabolite of the J2 series that has been identified as a ligand for peroxisome proliferator-activated receptor gamma (PPARgamma) and has received attention for its potential antiinflammatory effects. Because neutrophils express cell-surface receptors for PGs, the effect of dPGJ2 was tested on an inflammatory response that should not require PPARgamma, the oxidative burst made by adherent human neutrophils. dPGJ2 inhibited adhesion-dependent H2O2 production with an IC50 of 1. 5 microM when neutrophils were stimulated with TNF, N-formylnorleucylleucylphenylalanine, or LPS. Inhibition by dPGJ2 occurred during the lag phase, before generation of peroxide, suggesting blockade of an early signaling step. Indeed, dPGJ2 blocked adhesion of neutrophils to fibrinogen in response to TNF or LPS with an IC50 of 3-5 micro+dPGJ2 was more potent at inhibiting the adhesion-dependent oxidative burst than several other PGs tested. Further, dPGJ2 did not appear to act through either the DP receptor or receptors for PGE2. PG receptors modulate cAMP levels, and the inhibition of adhesion and oxidative burst by dPGJ2 was enhanced in the presence of 3-isobutyl-1-methylxanthine, a cAMP phosphodiesterase inhibitor. A potent PPARgamma agonist (AD-5075) did not inhibit peroxide production or adhesion, nor did it change the IC50 for dPGJ2 inhibition. These studies suggest that dPGJ2 may interact with an unknown receptor on neutrophils, distinct from PPARgamma, to modulate the production of reactive oxygen intermediates.
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PMID:15-Deoxy-Delta12,1412,14-prostaglandin J2 inhibits the beta2 integrin-dependent oxidative burst: involvement of a mechanism distinct from peroxisome proliferator-activated receptor gamma ligation. 1057 Mar 10

Activation of phosphodiesterase (PDE) 3B reduces free fatty acid output from adipocytes. Induction of PDE3B gene expression by adipocyte differentiation could improve insulin resistance. To examine whether the PDE3B promoter is activated by this differentiation, the 5' flanking sequence of the mouse PDE3B gene was isolated. The transcription initiation site was determined to be located 195 bp upstream of the translation start site. No putative binding site for peroxisome proliferator-activated receptor gamma was found within 2 kb upstream of the transcription initiation site. This region had promoter activity, which was further activated on adipocyte differentiation in 3T3-L1 cells.
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PMID:Activation of mouse phosphodiesterase 3B gene promoter by adipocyte differentiation in 3T3-L1 cells. 1155 56

Current pharmacological regimens for hypertriglyceridemia and low high-density lipoprotein (HDL) are limited to the peroxisome proliferator-activated receptor (PPAR) alpha activating fibrates, niacin, and statins. This pilot study examined the impact of simultaneous stimulation of cyclic adenosine monophosphate with a beta-adrenergic agonist and PPARgamma with pioglitazone (PIO) on lipoprotein composition in moderately obese, healthy subjects. Subjects were treated with PIO (45 mg) to stimulate PPARgamma or a combination of ephedrine (25 mg TID), a beta-agonist, with caffeine (200 mg TID), a phosphodiesterase inhibitor (ephedrine plus caffeine), or both for 16 weeks. Lipoproteins were separated by gradient ultracentrifugation into very low-density lipoprotein (VLDL), intermediate-density lipoprotein, low-density lipoprotein (LDL), and 3 HDL (L, M, and D) subfractions. Apolipoproteins were measured by high-performance liquid chromatography. PIO alone reduced the core triglyceride (TG) content relative to cholesterol ester (CE) in VLDL (-40%), IDL (-25%), and HDL-M (-38%). Ephedrine plus caffeine alone reduced LDL CE (-13%), phospholipids (-9%), and apolipoprotein (apo) B (-13%); increased HDL-M LpA-I (HDL containing apoA-I without apoA-II, 28%), CE/TG (23%), and CE/apoA-I (8%) while reducing apoA-II (-10%); and increased HDL-L LpA-I (29%). Combination therapy reduced total plasma TG (-28%), LDL cholesterol (LDL-C, -10%), apoB (-16%), apoB/apoA-I ratio (-21%) while increasing HDL cholesterol (HDL-C, 21%), total plasma apoA-I (12%), LpA-I (43%), and apoC-I (26%). It also reduced VLDL total mass (-34%) and apoC-III (-39%), LDL CE (-13%), apoB (-13%), and total mass (-11%). Combination therapy increased HDL-L CE/TG (32%), apoC-I (30%), apoA-I (56%), and LpA-I (70%), as well as HDL-M CE (35%), phospholipids (24%), total mass (19%), apoC-I (25%), apoA-I (18%), and LpA-I (56%). In conclusion, simultaneous beta-adrenergic and PPARgamma activation produced beneficial effects on VLDL, LDL, HDL-L, and HDL-M. Perhaps the most important impact of combination therapy was dramatic increases in LpA-I and apoC-I in HDL-L and HDL-M, which were much greater than the sum of the monotherapies. Because LpA-I appears to be the most efficient mediator of reverse-cholesterol transport and a major negative risk factor for cardiovascular disease, this combination therapy may provide very effective treatment of atherosclerosis.
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PMID:Combining beta-adrenergic and peroxisome proliferator-activated receptor gamma stimulation improves lipoprotein composition in healthy moderately obese subjects. 1632 16

Protein-ligand docking programs have been used to efficiently discover novel ligands for target proteins from large-scale compound databases. However, better scoring methods are needed. Generally, scoring functions are optimized by means of various techniques that affect their fitness for reproducing X-ray structures and protein-ligand binding affinities. However, these scoring functions do not always work well for all target proteins. A scoring function should be optimized for a target protein to enhance enrichment for structure-based virtual screening. To address this problem, we propose the supervised scoring model (SSM), which takes into account the protein-ligand binding process using docked ligand conformations with supervised learning for optimizing scoring functions against a target protein. SSM employs a rough linear correlation between binding free energy and the root mean square deviation of a native ligand for predicting binding energy. We applied SSM to the FlexX scoring function, that is, F-Score, with five different target proteins: thymidine kinase (TK), estrogen receptor (ER), acetylcholine esterase (AChE), phosphodiesterase 5 (PDE5), and peroxisome proliferator-activated receptor gamma (PPARgamma). For these five proteins, SSM always enhanced enrichment better than F-Score, exhibiting superior performance that was particularly remarkable for TK, AChE, and PPARgamma. We also demonstrated that SSM is especially good at enhancing enrichments of the top ranks of screened compounds, which is useful in practical drug screening.
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PMID:Supervised scoring models with docked ligand conformations for structure-based virtual screening. 1768 4

The evaluation of ligand conformations is a crucial aspect of structure-based virtual screening, and scoring functions play significant roles in it. While consensus scoring (CS) generally improves enrichment by compensating for the deficiencies of each scoring function, the strategy of how individual scoring functions are selected remains a challenging task when few known active compounds are available. To address this problem, we propose feature selection-based consensus scoring (FSCS), which performs supervised feature selection with docked native ligand conformations to select complementary scoring functions. We evaluated the enrichments of five scoring functions (F-Score, D-Score, PMF, G-Score, and ChemScore), FSCS, and RCS (rank-by-rank consensus scoring) for four different target proteins: acetylcholine esterase (AChE), thrombin (thrombin), phosphodiesterase 5 (PDE5), and peroxisome proliferator-activated receptor gamma (PPARgamma). The results indicated that FSCS was able to select the complementary scoring functions and enhance ligand enrichments and that it outperformed RCS and the individual scoring functions for all target proteins. They also indicated that the performances of the single scoring functions were strongly dependent on the target protein. An especially favorable result with implications for practical drug screening is that FSCS performs well even if only one 3D structure of the protein-ligand complex is known. Moreover, we found that one can infer which scoring functions significantly enrich active compounds by using feature selection before actual docking and that the selected scoring functions are complementary.
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PMID:Consensus scoring with feature selection for structure-based virtual screening. 1822 6

Cilostazol and ligands of peroxisome proliferator-activated receptors (PPARs) have been effectively used to alleviate diabetic complications, but the common and tissue-specific expression patterns of PPARs in different tissues in diabetic patients and those treated with cilostazol have not been reported. Here, we aimed to assess the effects of diabetes and cilostazol on mRNA expression of PPARalpha and PPARgamma in the aorta, renal cortex, and retina of diabetic rats treated with cilostazol for 8 weeks. PPARalpha mRNA expression showed uniform downregulation in all these tissues in diabetic rats, and this effect was reversed by cilostazol treatment. Surprisingly, PPARgamma mRNA expression was reduced in the renal cortex and retina, yet increased in the aorta of diabetic rats, although cilostazol still reversed these changes. Interestingly, cilostazol, a well-known phosphodiesterase 3 inhibitor and cAMP elevator, augmented cAMP content only in the aorta, but showed no significant effects in the renal cortex of diabetic rats. In conclusion, mRNA expression of PPARs is tissue-specific in diabetes and may be differently affected by cilostazol, possibly because of its tissue-specific effects on cAMP content.
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PMID:Tissue-specific expression of PPAR mRNAs in diabetic rats and divergent effects of cilostazol. 1864 96

Differentiation of 3T3-L1 preadipocytes can be induced by a 2-d treatment with a factor "cocktail" (DIM) containing the synthetic glucocorticoid dexamethasone (dex), insulin, the phosphodiesterase inhibitor methylisobutylxanthine (IBMX) and fetal bovine serum (FBS). We temporally uncoupled the activities of the four DIM components and found that treatment with dex for 48 h followed by IBMX treatment for 48 h was sufficient for adipogenesis, whereas treatment with IBMX followed by dex failed to induce significant differentiation. Similar results were obtained with C3H10T1/2 and primary mesenchymal stem cells. The 3T3-L1 adipocytes differentiated by sequential treatment with dex and IBMX displayed insulin sensitivity equivalent to DIM adipocytes, but had lower sensitivity to ISO-stimulated lipolysis and reduced triglyceride content. The nondifferentiating IBMX-then-dex treatment produced transient expression of adipogenic transcriptional regulatory factors C/EBPbeta and C/EBPdelta, and little induction of terminal differentiation factors C/EBPalpha and PPARgamma. Moreover, the adipogenesis inhibitor preadipocyte factor-1 (Pref-1) was repressed by DIM or by dex-then-IBMX, but not by IBMX-then-dex treatment. We conclude that glucocorticoids drive preadipocytes to a novel intermediate cellular state, the dex-primed preadipocyte, during adipogenesis in cell culture, and that Pref-1 repression may be a cell fate determinant in preadipocytes.
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PMID:Glucocorticoid signaling defines a novel commitment state during adipogenesis in vitro. 1865 67

Cyclic nucleotide phosphodiesterases (PDEs) are important regulators of signal transduction processes mediated by cAMP and cGMP. One PDE family member, PDE3B, plays an important role in the regulation of a variety of metabolic processes such as lipolysis and insulin secretion. In this study, the cellular localization and the role of PDE3B in the regulation of triglyceride, cholesterol and glucose metabolism in hepatocytes were investigated. PDE3B was identified in caveolae, specific regions in the plasma membrane, and smooth endoplasmic reticulum. In caveolin-1 knock out mice, which lack caveolae, the amount of PDE3B protein and activity were reduced indicating a role of caveolin-1/caveolae in the stabilization of enzyme protein. Hepatocytes from PDE3B knock out mice displayed increased glucose, triglyceride and cholesterol levels, which was associated with increased expression of gluconeogenic and lipogenic genes/enzymes including, phosphoenolpyruvate carboxykinase, peroxisome proliferator-activated receptor gamma, sterol regulatory element-binding protein 1c and hydroxyl-3-methylglutaryl coenzyme A reductase. In conclusion, hepatocyte PDE3B is localized in caveolae and smooth endoplasmic reticulum and plays important roles in the regulation of glucose, triglyceride and cholesterol metabolism. Dysregulation of PDE3B could have a role in the development of fatty liver, a condition highly relevant in the context of type 2 diabetes.
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PMID:Phosphodiesterase 3B is localized in caveolae and smooth ER in mouse hepatocytes and is important in the regulation of glucose and lipid metabolism. 1926 49

Caffeine is consumed by most people in Europe and North America. As a risk factor for osteoporosis, caffeine has been reported to decrease bone mineral density, negatively influence calcium absorption and increase the risk of bone fracture in women. Except for the epidemiological observations and several studies which proved caffeine's unfavorable effects on osteoblast proliferation and impaired ability to form bone, little mechanism is known for the caffeine-induced osteoporosis. Since our unpublished studies showed that the precursor cells of osteoblasts, bone marrow-derived mesenchymal stem cells (BMSCs), were more sensitive than osteoblasts when exposed to the same dose of caffeine. We herein hypothesize that MSCs may be the primary target cells for caffeine-induced osteoporosis. It is well established that increasing cyclic 3',5'-adenosine monophosphate (cAMP) can regulate the expression of key genes involved in bone metabolism, including Cbfa1, PPARgamma, RANKL and OPG. We thereby propose the hypothesis that caffeine, a known inhibitor of cAMP phosphodiesterase, may affect bone metabolism by activating cAMP-dependent protein kinase A (PKA) pathway. In addition, considering the fact observed in epidemiology that caffeine's negative effects on bone only occurred in postmenopausal women and the inverse roles of caffeine and estrogen on bone metabolism, we postulate that caffeine may exert its undesirable influences on bone only in absence or low level of estrogen in vivo and estrogen may antagonize the adverse effect of caffeine on bone. Since several studies have demonstrated that estrogen may have ability to temper the biological effects of cAMP stimulators' roles on bone through cAMP to regulate some important genes' expression in bone metabolism. We assume that estrogen may block cAMP-dependent PKA pathway which is shared by caffeine, to exhibit its antagonistic roles.
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PMID:Reciprocal roles between caffeine and estrogen on bone via differently regulating cAMP/PKA pathway: the possible mechanism for caffeine-induced osteoporosis in women and estrogen's antagonistic effects. 1927 93

Airway inflammation, airway remodeling and airway hyperresponsiveness are the fundamental components of pathogenesis that lead to symptoms and lung function changes in asthma. Airway remodeling describes the structural changes to the airways in asthma. The remodeling process involves diverse pathological changes including epithelial metaplasia, subepithelial fibrosis, angiogenesis and smooth muscle thickening. Airway remodeling contributes to irreversible loss of lung function and airway hyperresponsiveness. Remodeling is associated with severe and persistent disease but can also occur early in the course of disease pathogenesis and does not resolve spontaneously. Current asthma therapies, for example corticosteroids, are successful in treating allergic inflammation, an important factor contributing to remodeling, but do not specifically target the remodeling process, and remodeling changes progress despite optimal control of inflammation. Moreover, airway remodeling is not eradicated or prevented despite widespread use of anti-inflammatory treatments. There is limited evidence for the effectiveness of leukotriene inhibitors, phosphodiesterase inhibitors, mast cell tryptase inhibitors, and peroxisome proliferator-activated receptor gamma agonists in the treatment or prevention of remodeling changes. The search for novel therapies that can specifically reverse or prevent airway remodeling is an active area of research. Treatments that may be useful in preventing airway remodeling include those that directly or indirectly target single or multiple components of the airway remodeling process. Identification of novel asthma genes may also allow disease targeting. A better understanding of airway remodeling in asthma will facilitate the development of new treatments for asthma beyond control of symptoms and inflammation.
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PMID:The effects of current therapies on airway remodeling in asthma and new possibilities for treatment and prevention. 2002 56


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