- Thurairatnam, S; Lim, S; Barker, RH; Choi-Sledeski, YM; Hirth, BH; Jiang, J; Macor, JE; Makino, E; Maniar, S; Musick, K; Pribish, JR; Munson, M Brain Penetrable Inhibitors of Ceramide Galactosyltransferase for the Treatment of Lysosomal Storage Disorders. ACS Med Chem Lett 11: 2010-2016 (2020)
- Milliken, BT; Melegari, L; Smith, GL; Grohn, K; Wolfe, AJ; Moody, K; Bou-Abdallah, F; Doyle, RP Fenretinide binding to the lysosomal protein saposin D alters ceramide solubilization and hydrolysis. RSC Med Chem 11: 1048-1052 (2020)
- Skácel, J; Slusher, BS; Tsukamoto, T Small Molecule Inhibitors Targeting Biosynthesis of Ceramide, the Central Hub of the Sphingolipid Network. J Med Chem 64: 279-297 (2021)
- Yasuda, T; Ueura, D; Nakagomi, M; Hanashima, S; Peter Slotte, J; Murata, M Design, synthesis of ceramide 1-phosphate analogs and their affinity for cytosolic phospholipase A2 as evidenced by surface plasmon resonance. Bioorg Med Chem Lett 107:
- ChEMBL_2057398 (CHEMBL4712399) Inhibition of human acid ceramidase using N-lauroyl ceramide incubated for 1 hr by LC/MS analysis
- ChEMBL_2164214 (CHEMBL5049075) Inhibition of human GCS using C8-ceramide and UDP-glucose as substrate incubated for 1 hr by RapidFire mass spectrometry
- ChEMBL_2164220 (CHEMBL5049081) Inhibition of mouse GCS using C8-ceramide and UDP-glucose as substrate incubated for 1 hr by RapidFire mass spectrometry
- ChEMBL_2238979 (CHEMBL5152875) Inhibition of human GCS using C8-ceramide and UDP-glucose as substrate incubated for 1 hrs by Rapidfire mass spectrometric analysis
- ChEMBL_2238985 (CHEMBL5152881) Inhibition of mouse GCS using C8-ceramide and UDP-glucose as substrate incubated for 1 hrs by Rapidfire mass spectrometric analysis
- ChEMBL_2348349 Inhibition of GCS in human A-375 cell golgi body preparations using ceramide and UDP-glucose as substrate by UDP-Glo based luminometric analysis
- ChEMBL_852173 (CHEMBL2157594) Inhibition of recombinant human nCDase expressed in Sf9 cells using fluorescently-labeled acyl-NBD-C12-ceramide as substrate after 2 hrs by fluorescence assay
- ChEMBL_947532 (CHEMBL2339238) Inhibition of alkaline ceramidase 2 in human HL-60 cells using 3H]C16-ceramide as substrate after 1 hr by liquid scintillation counting analysis
- ChEMBL_1932329 (CHEMBL4477981) Inhibition of SPT1 in human MCF7 cells assessed as suppression of 14C-serine incorporation into ceramide incubated for 2 hrs in presence of 4-HPR
- ChEBML_1686210 Inhibition of purified SMS2 (unknown origin) pre-incubated for 5 mins followed by DMPC and C6-NBD-ceramide addition and measured after 30 mins by HPLC method
- ChEMBL_1764945 (CHEMBL4200192) Inhibition of human SMS2 using C6-NBD-ceramide and DMPC as substrate preincubated for 5 mins followed by substrate addition and measured after 30 mins by HPLC analysis
- ChEMBL_1764948 (CHEMBL4200195) Inhibition of human SMS1 using C6-NBD-ceramide and DMPC as substrate preincubated for 5 mins followed by substrate addition and measured after 30 mins by HPLC analysis
- ChEMBL_1897476 (CHEMBL4399511) Inhibition of SMS1 in MEF cells using C6-NBD-ceramide as substrate preincubated for 1 hr followed by substrate addition and measured after 1 hr by HPLC analysis
- ChEMBL_1897477 (CHEMBL4399512) Inhibition of SMS2 in MEF cells using C6-NBD-ceramide as substrate preincubated for 1 hr followed by substrate addition and measured after 1 hr by HPLC analysis
- ChEMBL_1723998 (CHEMBL4139276) Inhibition of human SMS2 expressed in HEK293T cells using C2-ceramide as substrate preincubated for 60 mins followed by substrate addition measured after 30 mins by RapidFire/mass spectrometry assay
- ChEMBL_1724010 (CHEMBL4139288) Inhibition of full length C-terminal FLAG tagged human SMS2 expressed in HEK293 cell membranes using DMPC-d72 and C17-ceramide as substrate after 15 mins by RapidFire/mass spectrometry assay
- ChEMBL_2266215 Inhibition of Glucosylceramide synthase (unknown origin) using C6-ceramide and UDP-glucose as substrate preincubated for 30 mins followed by substrate addition and measured after 2 hrs by UDP-Glo luminometer analysis
- ChEMBL_1910275 (CHEMBL4412721) Inhibition of purified SMS2 (unknown origin) using C6-NBD-Ceramide and DMPC as substrates preincubated for 5 mins followed by substrate addition and measured after 30 mins by TLC or HPLC method
- ChEMBL_1910276 (CHEMBL4412722) Inhibition of purified SMS1 (unknown origin) using C6-NBD-Ceramide and DMPC as substrates preincubated for 5 mins followed by substrate addition and measured after 30 mins by TLC or HPLC method
- ChEMBL_1897470 (CHEMBL4399505) Inhibition of SMS1 (unknown origin) stably expressed in mouse ZS cells using C6-NBD-ceramide as substrate preincubated for 30 mins followed by substrate addition and measured after 3 hrs by HPLC analysis
- ChEMBL_1897471 (CHEMBL4399506) Inhibition of SMS2 (unknown origin) stably expressed in mouse ZS cells using C6-NBD-ceramide as substrate preincubated for 30 mins followed by substrate addition and measured after 3 hrs by HPLC analysis
- ChEMBL_2381449 Inhibition of GCS activity in human A-375 cells using C6 ceramide as substrate pre-incubated for 30 mins followed by substrate addition and measured after 20 hrs by UDP-Glo based luminometric analysis
- ChEMBL_1465154 (CHEMBL3405855) Binding affinity to histidine-tagged human recombinant COL4A3ABP containing CERT START domain pre-incubated for 30 mins before biotinylated ceramide probe addition and measured after 18 hrs post probe addition by TR-FRET binding assay
- ChEMBL_2223201 (CHEMBL5136535) Inhibition of GCS in human A-375 cells using C6-ceramide and UDP-glucose as substrate preincubated for 30 mins followed by substrate addition measured after 20 hrs by UDP-Glo glucosylceramide synthase based luminometer analysis
- ChEMBL_1897472 (CHEMBL4399507) Noncompetitive inhibition of SMS1 (unknown origin) stably expressed in mouse ZS cells using 5 to 50 uM C6-NBD-ceramide as substrate preincubated for 30 mins followed by substrate addition and measured after 3 hrs by HPLC analysis
- ChEMBL_1897473 (CHEMBL4399508) Noncompetitive inhibition of SMS2 (unknown origin) stably expressed in mouse ZS cells using 5 to 50 uM C6-NBD-ceramide as substrate preincubated for 30 mins followed by substrate addition and measured after 3 hrs by HPLC analysis
- ChEMBL_1910274 (CHEMBL4412720) Inhibition of SMS2 (unknown origin) over-expressed in H5 insect cell lysate using C6-NBD-Ceramide and DMPC as substrates preincubated for 30 mins followed by substrate addition and measured after 2 hrs by TLC or HPLC method
- ChEMBL_1994371 (CHEMBL4628266) Inhibition of human recombinant C-terminal FLAG-tagged SMS2 expressed in Freestyle293 cell membrane using C14-phosphatidylcholineD72 and C17-ceramide pre-incubated for 60 mins followed by incubation with substrate for 30 mins measured by RapidFire/MS assay
- ChEMBL_1994372 (CHEMBL4628267) Inhibition of mouse recombinant C-terminal FLAG-tagged SMS2 expressed in mammalian expression system using C14-phosphatidylcholineD72 and C17-ceramide pre-incubated for 60 mins followed by incubation with substrate for 30 mins measured by RapidFire/MS assay
- ChEMBL_1994373 (CHEMBL4628268) Inhibition of human recombinant C-terminal FLAG-tagged SMS1 expressed in mammalian expression system using C14-phosphatidylcholineD72 and C17-ceramide pre-incubated for 60 mins followed by incubation with substrate for 30 mins measured by RapidFire/MS assay
- ChEMBL_1724007 (CHEMBL4139285) Inhibition of full length C-terminal FLAG tagged human SMS1 expressed in HEK293 cell membranes using DMPC-d72 and C17-ceramide as substrate preincubated for 60 mins followed by substrate addition measured after 30 mins by RapidFire/mass spectrometry assay
- ChEMBL_1724008 (CHEMBL4139286) Inhibition of full length C-terminal FLAG tagged human SMS2 expressed in HEK293 cell membranes using DMPC-d72 and C17-ceramide as substrate preincubated for 60 mins followed by substrate addition measured after 30 mins by RapidFire/mass spectrometry assay
- ChEMBL_1724011 (CHEMBL4139289) Inhibition of full length C-terminal FLAG tagged human SMS2 expressed in HEK293 cell membranes using DMPC-d72 and C17-ceramide as substrate preincubated for 60 mins followed by substrate addition measured after 15 mins by RapidFire/mass spectrometry assay
- ChEMBL_2354156 Inhibition of GCS in human A-375 cell golgi body using C6-ceramide and UDP-glucose as substrate assessed as reduction in UDP production preincubated for 30 mins followed by substrate addition and measured after 20 hrs by UDP-Glo luminometer analysis
- Scintillation Proximity Assay SphK activity was measured by a scintillation proximity assay as previously described [1], the disclosure of which is incorporated herein. Briefly, recombinant SphK1 or SphK2 were expressed in Sf9 insect cells, crude homogenates were prepared and incubated in 96 well FlashPlates (Perkin-Elmer) in a buffer containing D-erythro-sphingosine and γ-[33P]ATP. The [33P]S1P product, which adheres to the plate wall, was quantified by scintillation counting. To assay ceramide kinase or diacylglycerol kinases, the recombinant proteins were incubated with γ-[32P]ATP and substrate (C6 ceramide or 1-Ohexadecyl-2-acetyl-sn-glycerol, respectively) and the lipid product, after recovery by organic extraction, was resolved by thin layer chromatography, detected by autoradiography, and quantified by liquid scintillation counting. These assays were performed with and without a fixed concentration of inhibitor and its effect on KM and Vmax determined.
- Glucosylceramide Synthase Assay To determine glucosylceramide synthase inhibition, substrates at 2× of their Km (fluorescent ceramide and UDP-glucose, 3 μM and 4 μM respectively) and microsomes (1:50 dilution) are combined 1:1 and incubated at room temperature for 1 hour in the dark on a plate shaker. The reaction is stopped by the addition of 150 μL of 100 μM C8-ceramide in 50% aq. isopropanol; 10 μL of the final mix is analyzed on HPLC (with fluorescence detector). The mobile phase is 1% formic acid added to 81% methanol/19% water with flow rate 0.5 mL/min. Fluorescence is detected with λex=470 nm and λem=530 nm. Under these conditions, NBD-C6-GluCer had a retention time of about 1.7 min and NBD-C6-Cer elutes from the column after about 2.1 min. Both peaks are separated from each other and the baseline and were integrated automatically by the HPLC software. The percent conversion of substrate to product is used as the readout for inhibitor testing.
- Activity Assays The ability of the sphingo sine analogs presented herein to kill Pseudomonas aeruginosa in vitro, and based on the data shown below, concluded that the SPH analogs presented herein are highly efficient in killing bacteria. Compounds 791598 and 791577 were used as activity assay control references. To determine whether the sphingosine analogs presented herein can be metabolized by ceramide synthases (CerS natural sphingosine is a substrate for CerS), their N-acylation using 14C labeled CoA as a substrate was examined. The results confirmed that neither 791995 nor 791996 could be N-acylated, demonstrating that these SPH analogs are not substrates for CerS, and indicating that there is no concern that N-acylation might be an off-target effect (raw data and results not shown).
- Enzymatic Assay Protein concentration was determined using BCA assay kit. Sixty micrograms of MDCK cell lysate was incubated with various concentrations of a compound described herein from 0.001 μM−10 μM, respectively, or as indicated in Table 2, in 100 mM Tris buffer (pH 7.5) containing 10 mM MgCl2, 1 mM dithiothreitol, 1 mM EGTA, 2 mM NAD, 100 μM UDP-glucose, 10 μM C6-NBD-Ceramide (Matreya LLC, Pleasant Gap, Pa.), 35 μM dioleoylphosphatidylcholine and 5 μM sulfatide (Sigma) in a final reaction volume of 100 μL at 37° C. for 1 hour. 0.1% DMSO was used as mock treatment or control. The reaction was terminated by adding 100 μL acetonitrile solution and subjected to LC/MS analysis.
- GCS Enzymatic Assay This assay was modified based on the study by Larsen et al. (J. Lipid Res. 2011, 53, 282). Madin-Darby canine kidney (MDCK) cell lysate was prepared using M-PER Mammalian Protein Extraction Reagent (Thermal Scientific) in the presence of a protease inhibitor cocktail (Roche). Protein concentration was determined using BCA assay kit (Pierce). Sixty micrograms of MDCK cell lysate was incubated with various concentrations of a compound described herein from 0.001 μM-10 μM, respectively, or as indicated in Table 2, in 100 mM Tris buffer (pH 7.5) containing 10 mM MgCl2, 1 mM dithiothreitol, 1 mM EGTA, 2 mM NAD, 100 μM UDP-glucose, 10 μM C6-NBD-Ceramide (Matreya LLC, Pleasant Gap, Pa.), 35 μM dioleoylphosphatidylcholine and 5 μM sulfatide (Sigma) in a final reaction volume of 100 μL at 37° C. for 1 hour. 0.1% DMSO was used as mock treatment or control. The reaction was terminated by adding 100 μL acetonitrile solution and subjected to LC/MS analysis.The quantitative analysis of NBD-Ceramide and glucosylceramide was performed on a Shimadzu ultra-fast liquid chromatography (Shimadzu, Japan) coupled with API 4000 triple quadrupole mass spectrometer (Applied Biosystems, Concord, Ontario, Canada). Sample separation was conducted on a Waters Xbridge BEH130 C18, 100 mm×4.6 mm i.d, 3.5 μm (Milford, Mass., USA). The mobile phase consisted of water and acetonitrile supplemented with 0.1% formic acid (v/v). The flow rate was 1.0 mL/min. The initial mobile phase was 20% acetonitrile and was ramped in a linear fashion to 50% acetonitrile in 0.4 min. From 0.4 to 1.5 min, the gradient was ramped to 98% acetonitrile, and then was held at 100% until 8.0 min. Acetonitrile was reset to 20% in 1.5 min, and maintained until 10.0 min. The total run time was 10.0 min. The MS/MS detection was performed in ESI positive mode. The mass transition of NBD-Ceramide was m/z 576.36→558.40 under the collision energy of 15 V, and the mass transition of glucosylceramide was m/z 738.35-558.40 under 21V collision energy. The cell lysate was diluted with equal volume of acetonitrile. Aliquots of 50 μL diluted samples were added to 1.5 mL tubes, and 100 μL of acetonitrile containing internal standard (100 ng/mL tolbutamide) were added for protein precipitation. The mixture were vortexed and then centrifuged at 13000 rpm for 10 min. 70 μL of supernatant were mixed with 140 μL of H2O and the final solution were injected for LC/MS/MS analysis and IC50's and/or percent inhibitions calculated.
- Enzymatic Assay r-AC protein samples were pre-incubated with various concentrations of test compounds or vehicle control in 100 mM NaH2PO4/citrate buffer pH 4.5, 0.1% Nonidet P-40, 3 mM DTT for 30 min at 37° C. Samples were incubated with 100 μM N-lauroyl ceramide (Nu-Chek Prep, Elysian, Minn.) at 37° for 30 min. The reaction was stopped by addition of a mixture of chloroform/methanol (2:1 vol/vol) containing 1 nmol of heptadecanoic acid (HDA; NuChek Prep). The organic phases were collected, dried under nitrogen, and analyzed by LC/MS in the negative-ion mode using heptadecanoic acid (HDA) as internal standard (m/z=199 for lauric acid, m/z=269 for HDA). HDA was eluted on an XDB Eclipse C18 column isocratically at 2.2 mL/min for 1 min with a solvent mixture of 95% methanol and 5% water, both containing 0.25% acetic acid, and 5 mM ammonium acetate. The column temperature was 50° C.
- Acid Ceramidase Activity Assay A hAC protein preparation (10 μg) was preincubated with inhibitors (final DMSO concentration 1%) in assay buffer (100 mM sodium phosphate, 0.1% Nonidet P-40, 150 mM NaCl, 3 mM DTT, 100 mM sodium citrate, pH 4.5) for 30 min at 37° C. Reactions were started by the addition of 50 μM N-lauroyl ceramide (Nu-Chek Prep, Elysian, Minn.) and carried on for 30 min at 37° C. Reactions were stopped by addition of a mixture of chloroform/methanol (2:1, vol/vol) containing 1 nmol 11-lauroleic acid (NuChek Prep). The organic phases were collected, dried under nitrogen and analyzed by UPLC/MS (Acquity, Waters) in the negative-ion mode monitoring the reaction product (lauric acid, m/z=199) using 11-lauroleic acid as internal standard.Lipids were eluted on an Acquity UPLC BEH C18 column (50 mm length, 2.1 mm i.d., 1.7 μm pore size, Waters) column at 0.5 mL-min−1 for 1.5 min with a gradient of acetonitrile (CH3CN) and water, both containing 0.25% acetic acid and 5 mM ammonium acetat
- UDP-Glo Glucosylceramide Synthase Biochemical Assay Using Promega's UDP-Glo™ Glycosyltransferase assay kit (Promega Corporation, Madison, WI, USA (Promega)), GCS activity was indirectly measured by detecting the amount of UDP produced. An aliquot of GCS enzyme (1.5 μg crude golgi preparation, total protein) and titrated test compound were aliquoted to each well and incubated for 30 minutes at room temperature. Substrate mixture was prepared by mixing C6 ceramide (Avanti Polar Lipids, Alabaster, AL USA (Avanti)) (micelles prepared at 0.6 mM in 0.6 mM DOPC) and UDP-glucose (20 μ.M; Promega), at concentrations equivalent to 2×Km, in assay buffer (25 mM HEPES (pH 7.5), 50 mM KCl, 5 mM MgCl2). An equivalent volume of substrate mixture was then added to each well. Following a 20 h incubation at room temperature to allow for GCS turnover of substrate, an equal volume of UDP detection reagent (Promega) was added to each well and incubated for an additional 75 minutes at room temperature to simultaneously convert the accumulated UDP product into ATP and generate light in a luciferase reaction.
- UDP-Glo™ Glucosylceramide Synthase Biochemical Assay Using Promega's UDP-Glo™ Glycosyltransferase assay kit (Promega Corporation, Madison, WI, USA (Promega)), GCS activity was indirectly measured by detecting the amount of UDP produced. An aliquot of GCS enzyme (1.5 μg crude golgi preparation, total protein) and titrated test compound were aliquoted to each well and incubated for 30 minutes at room temperature. Substrate mixture was prepared by mixing C6 ceramide (Avanti Polar Lipids, Alabaster, AL USA (Avanti)) (micelles prepared at 0.6 mM in 0.6 mM DOPC) and UDP-glucose (20 μM; Promega), at concentrations equivalent to 2×Km, in assay buffer (25 mM HEPES (pH 7.5), 50 mM KCl, 5 mM MgCl2). An equivalent volume of substrate mixture was then added to each well. Following a 20 h incubation at room temperature to allow for GCS turnover of substrate, an equal volume of UDP detection reagent (Promega) was added to each well and incubated for an additional 75 minutes at room temperature to simultaneously convert the accumulated UDP product into ATP and generate light in a luciferase reaction.
- UDP-Glo Glucosylceramide Synthase Biochemical Assay Using Promega's UDP-Glo Glycosyltransferase assay kit (Promega Corporation, Madison, WI, USA (Promega)), GCS activity was indirectly measured by detecting the amount of UDP produced. An aliquot of GCS enzyme (1.5 μg crude golgi preparation, total protein) and titrated test compound were aliquoted to each well and incubated for 30 minutes at room temperature. Substrate mixture was prepared by mixing C6 ceramide (Avanti Polar Lipids, Alabaster, AL USA (Avanti)) (micelles prepared at 0.6 mM in 0.6 mM DOPC) and UDP-glucose (20 μM; Promega), at concentrations equivalent to 2 Km, in assay buffer (25 mM HEPES (pH 7.5), 50 mM KCl, 5 mM MgCl2). An equivalent volume of substrate mixture was then added to each well. Following a 20 h incubation at room temperature to allow for GCS turnover of substrate, an equal volume of UDP detection reagent (Promega) was added to each well and incubated for an additional 75 minutes at room temperature to simultaneously convert the accumulated UDP product into ATP and generate light in a luciferase reaction. The generated light was detected using a luminometer.
- UDP-Glo Glucosylceramide Synthase Biochemical Assay Using Promega's UDP-Glo Glycosyltransferase assay kit (Promega Corporation, Madison, WI, USA (Promega)), GCS activity was indirectly measured by detecting the amount of UDP produced. An aliquot of GCS enzyme (1.5 μg crude golgi preparation, total protein) and titrated test compound were aliquoted to each well and incubated for 30 minutes at room temperature. Substrate mixture was prepared by mixing C6 ceramide (Avanti Polar Lipids, Alabaster, AL USA (Avanti)) (micelles prepared at 0.6 mM in 0.6 mM DOPC) and UDP-glucose (20 μM; Promega), at concentrations equivalent to 2×Km, in assay buffer (25 mM HEPES (pH 7.5), 50 mM KCl, 5 mM MgCl2). An equivalent volume of substrate mixture was then added to each well. Following a 20 h incubation at room temperature to allow for GCS turnover of substrate, an equal volume of UDP detection reagent (Promega) was added to each well and incubated for an additional 75 minutes at room temperature to simultaneously convert the accumulated UDP product into ATP and generate light in a luciferase reaction. The generated light was detected using a luminometer.
- Fluorescence Based Assay The fluorescence based assay to monitor the activity of human nSMase2 in the presence or absence of potential inhibitors has been described recently. Figuera-Losada, et al. Lysate of cells expressing recombinant nSMase2 is used to catalyze the hydrolysis of sphingomyelin (SM) to ceramide and phosphorylcholine. Phosphorylcholine undergoes dephosphorylation in a reaction catalyzed by alkaline phosphatase (4 U/mL) to produce choline which in turn is oxidized by choline oxidase (0.1 U/mL) to betaine and hydrogen peroxide (H2O2). Hydrogen peroxide is made to react with Amplex red (50 μM) in the presence of horseradish peroxidase (HRP, 1 U/mL) to generate the fluorescent molecule resorufin. Generation of fluorescence is monitored by measuring relative florescence units (RFU) with excitation at 530 nm and emission at 590 nm. Extent of fluorescence is directly proportional to the extent of SM hydrolysis. Substrate stock solution is prepared in 2% Triton X-100 and sonicated for 1 min. Reactions are carried out for 1 h at 37° C. in 100 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Triton X-100. This assay has been optimized in 384-well format (50 μL total volume per well) under conditions where nSMase2-catalyzed hydrolysis of SM is linear with respect to nSMase2 concentration, time of incubation and SM concentration (FIGS. 3A-3C). The assay has high reliability (Z′=0.8-0.9). It is used for compound screening, IC50 determinations and mode of inhibition studies
- UDP-Glo Glucosylceramide Synthase Biochemical Assay Using Promega's UDP-Glo™ Glycosyltransferase assay kit (Promega Corporation, Madison, WI, USA (Promega)), GCS activity was indirectly measured by detecting the amount of UDP produced. An aliquot of GCS enzyme (1.5 μg crude golgi preparation, total protein) and titrated test compound were aliquoted to each well and incubated for 30 minutes at room temperature. Substrate mixture was prepared by mixing C6 ceramide (Avanti Polar Lipids, Alabaster, AL USA (Avanti)) (micelles prepared at 0.6 mM in 0.6 mM DOPC) and UDP-glucose (20 μM; Promega), at concentrations equivalent to 2×Km, in assay buffer (25 mM HEPES (pH 7.5), 50 mM KCl, 5 mM MgCl2). An equivalent volume of substrate mixture was then added to each well. Following a 20 h incubation at room temperature to allow for GCS turnover of substrate, an equal volume of UDP detection reagent (Promega) was added to each well and incubated for an additional 75 minutes at room temperature to simultaneously convert the accumulated UDP product into ATP and generate light in a luciferase reaction. The generated light was detected using a luminometer.Random luminescence values (RLUs) were normalized to mean “min” and “max” effects, as determined on each plate. “Min” was defined as the mean of the values of the wells treated with vehicle (DMSO) and which represent 0% inhibition; “max” was defined as the mean of the values of the wells treated with a reference inhibitor and which represent the 100% effect.
- Evaluation of Inhibitory Activities Against GCS (1) MaterialsA549 cells (ATCC, CCL-185)NBD C6-ceramide (Thermo Fisher, N1154)UDP-glucose (Sigma, U4625)Potassium chloride (Sigma, P9333)UltraPure™ 0.5 M EDTA (Invitrogen, 15575-038)BCA protein assay kit (Thermo Fisher, 23227)Ibiglustat (Shanghai Systeam Biochem Co., ltd, Genz-682452)HEPES (sigma, H3375)Protease/phosphatase inhibitor cocktail (CST, 5872s)DMEM (GIBCO, 11995-065)FBS (GIBCO, 16000-044)Antibiotic-Antimycotic (100×) (GIBCO, 15240-112)200 mM L-glutamine (GIBCO, 25030081)PBS (GIBCO, 10010-023)0.25% Trypsin-EDTA (GIBCO, 25200-056)Dimethyl sulfoxide (Sigma, 34869)2-propanol, HPLC grade (Burdick & Jackson, AH323-4)Hexane, HPLC grade (Burdick & Jackson, AH216-4)Chloroform (Sigma, C2432)Methanol (Merck, 1.06009.1011)(2) Protocol<1> Preparation of Cell LysatesA549 cells (ATCC, CCL-185) were cultured in a DMEM medium supplemented with 10% fetal bovine serum (FBS), 1× antibiotic-antimycotic, and 1×L-glutamine, in an incubator at 37° C. and 5% CO2. After the cells attached to the culture dish were washed with phosphate buffered saline (PBS), the cells were scraped off with a cell scraper and then centrifuged (4000 rpm, 3 min, 4° C.) to collect the cells in a 50 ml tube. The cell pellets were suspended in a lysis buffer (50 mM HEPES, pH 7.3, containing 1× the protease/phosphatase inhibitor cocktail), lysed by sonication, and then the lysate was centrifuged (13000 rpm, 10 min, 4° C.). The obtained supernatant was used for the quantitative analysis of proteins. The amount of proteins was measured using the BCA protein assay kit, using bovine serum albumin as a standard.
- Des1 Activity Assays Jurkat clone E6-1 cells were grown and then seeded at 106 cells/mL in a 96-well plate (400 μL in each well. The cells were administered 100 μL of cell culture media containing 50-μM NBD-C6-dihydroceramide (Des1 substrate), affording a final concentration of substrate of 10 μM. The cells were incubated with substrate at 4° C. for 30 minutes. Following the incubation at 4° C., the cell suspension was centrifuged at 1200 rpm for 3 minutes, and the cell pellet is resuspended in 400 μL of fresh media containing various concentrations of either fenretinide (known Des1 inhibitor control compound) or test article. The final concentrations of control compound and test compounds were tested in a range from 0-10 μM. The cells and compounds were incubated at 37° C. for 3 hours. Following the 3-hour incubation, the plate was centrifuged at 2500 g for 3 minutes at 4° C., followed by collection and transfer of 200 μL of the supernatant to a new 96-well plate with 300 μL of methanol an containing appropriate internal standards for liquid chromatography/tandem mass spectroscopy (LC/MS/MS) analysis (internal standard: 500 nM labetalol and 100 nM alprazolam). The samples were vortexed for 2 minutes followed by centrifugation at 3,220 g for 20 minutes. Following centrifugation, 200 μL of the supernatant was transferred to a new 96-well plate for LC-MS/MS analysis to determine the amount of NBD-C6-ceramide (Des1 product) produced. The assay was typically performed in duplicate. A reduction of at least 30% compared to vehicle control (0 μM test article) is indicative of an active compound, and a reduction of 75% compared to vehicle control is preferred.
- LC-MS Based In Vitro Assay hAC protein preparation (10 μg) was preincubated with inhibitors (final DMSO concentration 1%) in assay buffer (100 mM sodium phosphate, 0.1% Nonidet P-40, 150 mM NaCl, 3 mM DTT, 100 mM sodium citrate, pH 4.5) for 30 min at 37° C. Reactions were started by the addition of 50 μM N-lauroyl ceramide (Nu-Chek Prep, Elysian, Minn.) and carried on for 30 min at 37° C. Reactions were stopped by addition of a mixture of chloroform/methanol (2:1) containing 1 nmol 11-lauroleic acid (NuChek Prep). The organic phases were collected, dried under nitrogen and analyzed by UPLC/MS (Acquity, Waters). In the negative-ion mode monitoring the reaction product (lauric acid, m/z=199) using 11-lauroleic acid as internal standard.Lipids were eluted on an Acquity UPLC BEH C18 column (50×2.1 mmID, particle size 1.7 μm), column flow at 0.5 mL/min for 1.5 min with a gradient of acetonitrile and water, both containing 0.25% acetic acid and 5 mM ammonium acetate (70% to 100% acetonitrile in 0.5 min, 100% acetonitrile for 0.5 min, 70% acetonitrile for 0.4 min). The column temperature was 40° C. Electrospray ionization (ESI) was in the negative mode, capillary voltage was 1 kV and cone voltage was 50 V. N2 was used as drying gas at a flow rate of 500 L/h and at a temperature of 400° C.The [M-H]− ion was monitored in the selected-ion monitoring mode (m/z values: lauric acid 199, 11-lauroleic acid 197.35). Calibration curves were generated with authentic lauric acid (Nu Check Prep). Inhibition of AC activity was calculated as reduction of lauric acid in the samples compared to vehicle controls. IC50 values were calculated by non-linear regression analysis of log [concentration]/inhibition curves using GraphPad Prism 5 (GraphPad Software Inc., CA-USA) applying a standard slope curve fitting.
- UDP-Glo Glucosylceramide Synthase Biochemical Assay Using Promega s UDP-Glo Glycosyltransferase assay kit (Promega Corporation, Madison, WI, USA (Promega)), GCS activity was indirectly measured by detecting the amount of UDP produced. An aliquot of GCS enzyme (1.5 µg crude golgi preparation, total protein) and titrated test compound were aliquoted to each well and incubated for 30 minutes at room temperature. Substrate mixture was prepared by mixing C6 ceramide (Avanti Polar Lipids, Alabaster, AL USA (Avanti)) (micelles prepared at 0.6 mM in 0.6 mM DOPC) and UDP-glucose (20 µM; Promega), at concentrations equivalent to 2x Km, in assay buffer (25 mM HEPES (pH 7.5), 50 mM KCl, 5 mM MgCl2). An equivalent volume of substrate mixture was then added to each well. Following a 20 h incubation at room temperature to allow for GCS turnover of substrate, an equal volume of UDP detection reagent (Promega) was added to each well and incubated for an additional 75 minutes at room temperature to simultaneously convert the accumulated UDP product into ATP and generate light in a luciferase reaction. The generated light was detected using a luminometer. Random luminescence values (RLUs) were normalized to mean min and max effects, as determined on each plate. Min was defined as the mean of the values of the wells treated with vehicle (DMSO) and which represent 0% inhibition; max was defined as the mean of the values of the wells treated with a reference inhibitor and which represent the 100% effect. Values for %Emax and EC50 were determined by best-fitting the normalized data to a curve in Activity Base along a four-parameter logistic nonlinear regression (4PL) model (based on the Levenberg-Marquardt algorithm and defined by the equation below):where: n is 4PMin (bottom of the curve); m is 4PMax (top of the curve); i is IP (inflection point of curve); and p is slope. See Levenberg, K., A Method for the Solution of Certain Problems in Least Squares , Quart. Appl. Math.2, (1944), pp 164 168 and Marquardt, D., An Algorithm for Least Squares Estimation on Nonlinear Parameters , SIAM J. Appl. Math.11, (1963) pp 431 441.