R than” a threshold (ranging from 1028 M to 1022 M, depending on the study the data originated from) were treated as “inactive”. For molecules with more than one independentlymeasured Ki value, the average was calculated. Cases with at least one “active” and one “inactive”, i.e. inconsistent, classification with respect to a particular receptor were discarded. The MedChemExpress 14636-12-5 selectivity ratio was calculated by dividing the respective Ki values of one ligand against two different receptor subtypes, and binned according to their ratio. The Ki-value of an inactive molecule was arbitrarily set to 1 M, except for cases where a molecule was inactive against both investigated subtypes, and was thus not considered further in the analysis. The choice of the numerical value for inactive compounds had no influence on the conclusions drawn, as we only compared data that had been obtained with the same settings.In Silico Screening for A1AR AntagonistsFigure 5. Chart 2. Molecules identified in this study. Binding affinity data at three AR subtypes are presented in Table 1. doi:10.1371/journal.pone.0049910.gIn Silico Screening for A1AR AntagonistsExperimental AssaysBinding affinity for three human AR (hAR) subtypes was measured using standard radioligand assays and membrane preparations from Chinese hamster ovary (CHO) cells [35] (A1 and A3) or human embryonic kidney (HEK) 293 cells (A2A) stably expressing a hAR subtype (Table 1). Receptor binding assays: [3H]8-Cyclopentyl-1,3-dipropylxanthine ([3H]DPCPX, 120 Ci/mmol) 23388095 and [125I]N6-(4-amino-3-iodobenzyl)adenosine-5′-N-methyluronamide ([125I]I-AB-MECA, 2200 Ci/ mmol) were purchased 1480666 from Perkin lmer Life and Analytical Science (Boston, MA). [3H](2-[p-(2-Carboxyethyl)phenyl-ethylamino]-5′-N-ethylcarboxamido-adenosine) ([3H]CGS21680, 39 Ci/ mmol) was purchased from American Radiolabeled Chemicals, Inc. (St. Louis, MO). Other pharmacological reagents were purchased from Tocris-R D Systems, Inc. (Minneapolis, MN). Test compounds were prepared as 5 mM stock solutions in DMSO and stored frozen. Cell Culture and Membrane Preparation: CHO cells stably expressing the recombinant hA1 and hA3ARs, and HEK-293 cells stably expressing the hA2AAR were cultured in Dulbecco’s modified Eagle medium (DMEM) and F12 (1:1) supplemented with 10 fetal bovine serum, 100 units/mL penicillin, 100 mg/mL streptomycin, and 2 mmol/mL glutamine. In addition, 800 mg/mL geneticin was added to the A2A media, while 500 mg/mL hygromycin was added to the A1 and A3 media. After harvesting, cells were homogenized and suspended in PBS. Cells were then centrifuged at 240 g for 5 min, and the pellet was resuspended in 50 mM Tris-HCl buffer (pH 7.5) containing 10 mM MgCl2. The suspension was homogenized and was then Naringin supplier ultra-centrifuged at 14,330 g for 30 min at 4uC. The resultant pellets were resuspended in Tris buffer and incubated with adenosine deaminase (3 units/mL) for 30 min at 37uC. The suspension was homogenized with an electric homogenizer for 10 sec, pipetted into 1 mL vials and then stored at -80uC until the binding experiments. The protein concentration was measured using the BCA Protein Assay Kit from Pierce Biotechnology, Inc. (Rockford, IL) [36]. Binding assays: Standard radioligand binding assays for A1, A2A, and A3ARs were used [37?9]. Into each tube in the binding assay was added 50 mL of increasing concentrations of the test ligand in Tris-HCl buffer (50 mM, pH 7.5) containing 10 mM MgCl2, 50 mL of the appropriate agonist radioligand.R than” a threshold (ranging from 1028 M to 1022 M, depending on the study the data originated from) were treated as “inactive”. For molecules with more than one independentlymeasured Ki value, the average was calculated. Cases with at least one “active” and one “inactive”, i.e. inconsistent, classification with respect to a particular receptor were discarded. The selectivity ratio was calculated by dividing the respective Ki values of one ligand against two different receptor subtypes, and binned according to their ratio. The Ki-value of an inactive molecule was arbitrarily set to 1 M, except for cases where a molecule was inactive against both investigated subtypes, and was thus not considered further in the analysis. The choice of the numerical value for inactive compounds had no influence on the conclusions drawn, as we only compared data that had been obtained with the same settings.In Silico Screening for A1AR AntagonistsFigure 5. Chart 2. Molecules identified in this study. Binding affinity data at three AR subtypes are presented in Table 1. doi:10.1371/journal.pone.0049910.gIn Silico Screening for A1AR AntagonistsExperimental AssaysBinding affinity for three human AR (hAR) subtypes was measured using standard radioligand assays and membrane preparations from Chinese hamster ovary (CHO) cells [35] (A1 and A3) or human embryonic kidney (HEK) 293 cells (A2A) stably expressing a hAR subtype (Table 1). Receptor binding assays: [3H]8-Cyclopentyl-1,3-dipropylxanthine ([3H]DPCPX, 120 Ci/mmol) 23388095 and [125I]N6-(4-amino-3-iodobenzyl)adenosine-5′-N-methyluronamide ([125I]I-AB-MECA, 2200 Ci/ mmol) were purchased 1480666 from Perkin lmer Life and Analytical Science (Boston, MA). [3H](2-[p-(2-Carboxyethyl)phenyl-ethylamino]-5′-N-ethylcarboxamido-adenosine) ([3H]CGS21680, 39 Ci/ mmol) was purchased from American Radiolabeled Chemicals, Inc. (St. Louis, MO). Other pharmacological reagents were purchased from Tocris-R D Systems, Inc. (Minneapolis, MN). Test compounds were prepared as 5 mM stock solutions in DMSO and stored frozen. Cell Culture and Membrane Preparation: CHO cells stably expressing the recombinant hA1 and hA3ARs, and HEK-293 cells stably expressing the hA2AAR were cultured in Dulbecco’s modified Eagle medium (DMEM) and F12 (1:1) supplemented with 10 fetal bovine serum, 100 units/mL penicillin, 100 mg/mL streptomycin, and 2 mmol/mL glutamine. In addition, 800 mg/mL geneticin was added to the A2A media, while 500 mg/mL hygromycin was added to the A1 and A3 media. After harvesting, cells were homogenized and suspended in PBS. Cells were then centrifuged at 240 g for 5 min, and the pellet was resuspended in 50 mM Tris-HCl buffer (pH 7.5) containing 10 mM MgCl2. The suspension was homogenized and was then ultra-centrifuged at 14,330 g for 30 min at 4uC. The resultant pellets were resuspended in Tris buffer and incubated with adenosine deaminase (3 units/mL) for 30 min at 37uC. The suspension was homogenized with an electric homogenizer for 10 sec, pipetted into 1 mL vials and then stored at -80uC until the binding experiments. The protein concentration was measured using the BCA Protein Assay Kit from Pierce Biotechnology, Inc. (Rockford, IL) [36]. Binding assays: Standard radioligand binding assays for A1, A2A, and A3ARs were used [37?9]. Into each tube in the binding assay was added 50 mL of increasing concentrations of the test ligand in Tris-HCl buffer (50 mM, pH 7.5) containing 10 mM MgCl2, 50 mL of the appropriate agonist radioligand.
