- Tao, L; Xie, J; Wang, Y; Wang, S; Wu, S; Wang, Q; Ding, H Protective effects of aloe-emodin on scopolamine-induced memory impairment in mice and H2O2-induced cytotoxicity in PC12 cells. Bioorg Med Chem Lett 24: 5385-9 (2015)
- Yao, D; Wang, J; Wang, G; Jiang, Y; Shang, L; Zhao, Y; Huang, J; Yang, S; Wang, J; Yu, Y Design, synthesis and biological evaluation of coumarin derivatives as novel acetylcholinesterase inhibitors that attenuate H2O2-induced apoptosis in SH-SY5Y cells. Bioorg Chem 68: 112-123 (2016)
- PubChem, PC Concentration Response Redox Cycling H2O2 Generation assay to characterize small molecule inhibitors identified in the Polo box domain (PBD) of Plk1 Primary HTS. PubChem Bioassay (2007)
- PubChem, PC Concentration Response Redox Cycling H2O2 Generation assay, 1 mM DTT, to characterize small molecule inhibitors identified in the Polo box domain (PBD) of Plk1 Primary HTS. PubChem Bioassay (2007)
- ChEMBL_658093 (CHEMBL1249158) Inhibition of NOX4 expressed in HEK293 FS cells assessed as H2O2 production by H2O2/Tyr/LPO assay
- ChEMBL_2446262 Inhibition of human neutrophil MPO using H2O2 as substrate
- ChEMBL_1811673 (CHEMBL4311133) Inhibition of MPO (unknown origin) using H2O2 as substrate
- ChEMBL_1930531 (CHEMBL4433782) Inhibition of PARP1 in human HeLa cells assessed as reduction in H2O2-induced PAR formation incubated for 30 mins followed by H2O2 addition for 15 mins by immunocytochemistry analysis
- ChEMBL_695894 (CHEMBL1640946) Inhibition of recombinant MPO mediated LDL oxidation using MPO/Cl-/H2O2 system
- ChEMBL_819836 (CHEMBL2034450) Inhibition of human DAO measuring H2O2 production by Resorufin/Amplex Red assay
- ChEMBL_1285750 (CHEMBL3107874) Inhibition of PARP-1-mediated PARylation in H2O2-induced human HeLa cells preincubated for 3 hrs followed by H2O2 addition measured after 5 mins by Draq5 staining-based fluorescence assay
- ChEMBL_1510424 (CHEMBL3607349) Inhibition of PARP1 in human HeLa cells assessed as reduction of H2O2-induced PAR formation preincubated for 30 mins followed by H2O2 addition measured after 15 mins by immunocytochemical analysis
- ChEMBL_1636849 (CHEMBL3879747) Inhibition of human ASK1 expressed in HEK293 cells assessed as inhibition of H2O2-induced JNK phosphorylation preincubated for 30 mins followed by H2O2 addition measured after 30 mins by ELISA
- ChEMBL_1829870 (CHEMBL4329744) Inhibition of human PMN leukocytes MPO peroxidation activity using H2O2 as substrate preincubated for 10 mins followed by H2O2 addition and measured for 15 mins by amplex red reagent based assay
- ChEMBL_1811674 (CHEMBL4311134) Inhibition of MPO in human neutrophils using H2O2 as substrate measured after 5 mins
- ChEMBL_2316113 Inhibition of human MPO peroxidase activity incubated in presence of H2O2 by amplex red assay
- ChEMBL_819840 (CHEMBL2034554) Inhibition of human SSAO/VAP1 measuring H2O2 production by Kitz and Wilson plot analysis
- Diamine Oxidase (DAO) Selectivity Assay Promega ROS-Glo H2O2 Assay Kit, 50 ml. Cat No. G8821.
- ChEMBL_1829869 (CHEMBL4329743) Inhibition of human PMN leukocytes MPO chlorination activity using H2O2 as substrate preincubated for 10 mins followed by H2O2 addition and measured for 15 mins in presence of NaCl by aminophenyl fluorescein based assay
- ChEMBL_1829876 (CHEMBL4329750) Inhibition of human TPO assessed as reduction in H2O2 catalyzed 3,5-iodo tyrosine formation from 3-iodotyrosine and potassium iodide preincubated for 10 mins followed by tyrosine/potassium bromide/H2O2 addition measured after 15 mins
- ChEMBL_1829877 (CHEMBL4329751) Inhibition of human LPO assessed as reduction in H2O2 catalyzed 3,5-iodo tyrosine formation from 3-iodotyrosine and potassium iodide preincubated for 10 mins followed by tyrosine/potassium bromide/H2O2 addition measured after 15 mins
- ChEMBL_2504837 Inhibition of human MPO using H2O2 as substrate measured after 15 mins by chemiluminescence based assay
- ChEMBL_819788 (CHEMBL2034300) Inhibition of human recombinant SSAO/VAP1 assessed as H2O2 production by Resorufin/Amplex Red assay
- ChEMBL_819789 (CHEMBL2034301) Inhibition of human recombinant MAO-A assessed as H2O2 production by Resorufin/Amplex Red assay
- ChEMBL_819835 (CHEMBL2034449) Inhibition of human recombinant MAO-B assessed as H2O2 production by Resorufin/Amplex Red assay
- ChEMBL_819837 (CHEMBL2034551) Inhibition of SSAO/VAP1 in mouse adipocytes measuring H2O2 production by Resorufin/Amplex Red assay
- ChEMBL_874212 (CHEMBL2187944) Inhibition of human recombinant MAOA assessed as H2O2 production by Amplex Red reagent-based assay
- ChEMBL_874213 (CHEMBL2187945) Inhibition of human recombinant MAOB assessed as H2O2 production by Amplex Red reagent-based assay
- ChEMBL_887692 (CHEMBL2217301) Inhibition of PI3Kdelta assessed as inhibition of H2O2-induced AKT phosphorylation by cell-based assay
- ChEMBL_1367249 Inhibition of human recombinant MAO-A assessed as H2O2 production using p-tyramine substrate by fluorimetric method
- ChEMBL_2024726 (CHEMBL4678539) Inhibition of PARP-1 in human HeLa cells incubated for 18 hrs in presence of H2O2
- ChEMBL_2193773 (CHEMBL5106133) Inhibition of human MAO-A assessed as inhibition of H2O2 production using p-tyramine as substrate
- ChEMBL_2193774 (CHEMBL5106134) Inhibition of human MAO-B assessed as inhibition of H2O2 production using p-tyramine as substrate
- ChEMBL_2217367 (CHEMBL5130499) Inhibition of MPO (unknown origin) measured after 15 mins in presence of H2O2 by chemiluminescence assay
- ChEMBL_863186 (CHEMBL2175910) Inhibition of human Hao2-mediated oxidation of 2-hydroxyoctanoic acid assessed as proportionate release of H2O2
- ChEMBL_863190 (CHEMBL2175914) Inhibition of rat Hao2-mediated oxidation of 2-hydroxyoctanoic acid assessed as proportionate release of H2O2
- ChEMBL_1719894 (CHEMBL4134894) Inhibition of human FLAG-tagged TRPM2 expressed in HEK293 cells assessed as reduction in H2O2-induced intracellular calcium flux pretreated for 30 secs followed by H2O2 addition measured for 120 secs by Fluo4-AM dye based fluorescence assay
- ChEMBL_1367301 (CHEMBL866116) Inhibition of human recombinant MAO-B assessed as H2O2 production using p-tyramine substrate by fluorimetric method
- ChEMBL_1829875 (CHEMBL4329749) Inhibition of human EPX bromination activity assessed as reduction in H2O2 catalyzed 3-bromo tyrosine formation from tyrosine and potassium bromide preincubated for 10 mins followed by tyrosine/potassium bromide/H2O2 addition measured after 15 mins by RP-UPLC analysis
- ChEMBL_1471258 (CHEMBL3418557) Inhibition of human MAO-A using p-tyramine as substrate assessed as H2O2 production by amplex red assay
- ChEMBL_1471259 (CHEMBL3418558) Inhibition of human MAO-B using p-tyramine as substrate assessed as H2O2 production by amplex red assay
- ChEMBL_1664243 (CHEMBL4013924) Inhibition of bovine milk LPO assessed as reduction in NaOSCN production in presence of H2O2/NaSCN after 5 mins
- ChEMBL_1811675 (CHEMBL4311135) Inhibition of MPO in human neutrophils using H2O2 as substrate measured after 1 hr by fluorescence based HPLC analysis
- ChEMBL_2217369 (CHEMBL5130501) Inhibition of MPO in human HL-60 cells measured after 15 mins in presence of H2O2 by chemiluminescence assay
- ChEMBL_862123 (CHEMBL2174308) Inhibition of recombinant human myeloperoxidase assessed as taurine chloramine production after 5 mins by spectrophotometry in presence of H2O2
- ChEMBL_1286152 (CHEMBL3107009) Inhibition of PARP-1 in human HeLa cells assessed as decrease of H2O2-induced PARylation after 3 hrs by fluorescence assay
- ChEMBL_1448561 (CHEMBL3379837) Inhibition of human MAOA expressed in baculovirus-infected BTI insect cells assessed as H2O2 production by resorufin dye based fluorimetric method
- ChEMBL_1448562 (CHEMBL3379838) Inhibition of human MAOB expressed in baculovirus-infected BTI insect cells assessed as H2O2 production by resorufin dye based fluorimetric method
- ChEMBL_1462042 (CHEMBL3396577) Inhibition of human recombinant MAO-B using p-tyramine as substrate assessed as H2O2 production after 15 mins by fluorescence assay
- ChEMBL_1462053 (CHEMBL3396588) Inhibition of human recombinant MAO-A using p-tyramine as substrate assessed as H2O2 production after 15 mins by fluorescence assay
- ChEMBL_979078 (CHEMBL2421337) Inhibition of human recombinant MAO-B using benzylamine hydrochloride as substrate assessed as H2O2 synthesis after 1 hr by fluorescence assay
- ChEMBL_1444097 (CHEMBL3377805) Inhibition of human recombinant MAOA expressed in BTI-TN-5B1-4 cells using p-tyramine substrate assessed as reduction in H2O2 production
- ChEMBL_1444099 (CHEMBL3377807) Inhibition of human recombinant MAOB expressed in BTI-TN-5B1-4 cells using p-tyramine substrate assessed as reduction in H2O2 production
- ChEMBL_1526127 (CHEMBL3636511) Irreversible inhibition of MPO in LPS-stimulated human whole blood after 4 hrs by Amplex Red/H2O2-based fluorescence plate reader analysis
- ChEMBL_2075953 (CHEMBL4731487) Inhibition of JAK3 in mouse BaF3 cells assessed as reduction in cell viability in presence of 0.1 mM H2O2 by MTT assay
- ChEMBL_1584959 (CHEMBL3819983) Inhibition of GST-tagged LSD1 (2 to 852 residues) (unknown origin) using H3K4me2 substrate assessed as reduction in H2O2 production by fluorescence assay
- ChEMBL_1628935 (CHEMBL3871561) Inhibition of MPO chlorination activity (unknown origin) assessed as taurine chloramine formation after 5 mins in presence of H2O2/Cl- by HTS method
- ChEMBL_1664239 (CHEMBL4013920) Inhibition of recombinant MPO (unknown origin) assessed as reduction in LDL oxidation in presence of H2O2 and HCl after 5 mins by ELISA
- ChEMBL_1667719 (CHEMBL4017607) Inhibition of human LSD1 assessed as reduction in H2O2 production using pLys4Met H3 peptide as substrate by peroxidase coupled UV-visible spectrophotometric method
- ChEMBL_2437004 Inhibition of LPO (unknown origin)-mediated L-tyrosine nitration incubated for 20 mins in presence of H2O2 and sodium nitrite by RP-HPLC analysis
- ChEMBL_2466571 Inhibition of recombinant PRDX1 (unknown origin) using H2O2 as substrate preincubated for 0.5 hrs followed by substrate addition by TRX-TrxR-NADPH coupling assay
- ChEMBL_2466583 Inhibition of recombinant PRDX2 (unknown origin) using H2O2 as substrate preincubated for 0.5 hrs followed by substrate addition by TRX-TrxR-NADPH coupling assay
- ChEMBL_2466584 Inhibition of recombinant PRDX3 (unknown origin) using H2O2 as substrate preincubated for 0.5 hrs followed by substrate addition by TRX-TrxR-NADPH coupling assay
- ChEMBL_2466585 Inhibition of recombinant PRDX4 (unknown origin) using H2O2 as substrate preincubated for 0.5 hrs followed by substrate addition by TRX-TrxR-NADPH coupling assay
- ChEMBL_2466586 Inhibition of recombinant PRDX5 (unknown origin) using H2O2 as substrate preincubated for 0.5 hrs followed by substrate addition by TRX-TrxR-NADPH coupling assay
- ChEMBL_2466587 Inhibition of recombinant PRDX6 (unknown origin) using H2O2 as substrate preincubated for 0.5 hrs followed by substrate addition by TRX-TrxR-NADPH coupling assay
- ChEMBL_769921 (CHEMBL1832105) Inhibition of human recombinant DAAO expressed in Escherichia coli assessed as H2O2 production from D-serine degradation after 30 mins by fluorescence assay
- ChEMBL_968273 (CHEMBL2399754) Inhibition of human recombinant DAAO expressed in HEK293 cell lysate assessed as D-Serine conversion to H2O2 after 20 mins by spectrophotometric analysis
- ChEBML_1692777 Inhibition of human recombinant MAOA assessed as reduction in H2O2 production from p-tyramine incubated for 15 mins by Amplex red reagent based fluorimetric method
- ChEBML_1692779 Inhibition of human recombinant MAOB assessed as reduction in H2O2 production from p-tyramine incubated for 15 mins by Amplex red reagent based fluorimetric method
- ChEMBL_1621074 (CHEMBL3863357) Inhibition of recombinant human MAO-B using p-tyramine as substrate assessed as decrease in H2O2 production incubated for 15 mins by fluorimetric method
- ChEMBL_1621075 (CHEMBL3863358) Inhibition of recombinant human MAO-A using p-tyramine as substrate assessed as decrease in H2O2 production incubated for 15 mins by fluorimetric method
- ChEMBL_2048400 (CHEMBL4703099) Inhibition of recombinant human MPO incubated for 10 mins in presence of 240 mM NaCl and 10 uM H2O2 by aminophenyl fluorescein based assay
- ChEMBL_2238750 (CHEMBL5152646) Inhibition of porcine kidney DAAO using D-serine as substrate assessed as H2O2 formation by amplex red and peroxidase-coupled continuous fluorescence spectrophotometric analysis
- ChEMBL_739585 (CHEMBL1763411) Inhibition of human recombinant MAO-A expressed in BTI-TN-5B1-4 cells assessed as H2O2 production using para-tyramine substrate by fluorimetric method
- ChEMBL_739586 (CHEMBL1763412) Inhibition of human recombinant MAO-B expressed in BTI-TN-5B1-4 cells assessed as H2O2 production using para-tyramine substrate by fluorimetric method
- ChEBML_1664234 Inhibition of recombinant MPO (unknown origin) assessed as reduction in taurine chloramine production preincubated with enzyme and taurine followed by H2O2 addition measured after 5 mins
- ChEMBL_1522271 (CHEMBL3630540) Inhibition of recombinant human MAOA using p-tyramine as substrate assessed as H2O2 production preincubated for 15 mins followed by substrate addition by fluorometric analysis
- ChEMBL_1522272 (CHEMBL3630541) Inhibition of recombinant human MAOB using p-tyramine as substrate assessed as H2O2 production preincubated for 15 mins followed by substrate addition by fluorometric analysis
- ChEMBL_1891572 (CHEMBL4393399) Activation of human ERbeta assessed as induction of transcriptional activation incubated for 24 hrs in presence of 50 uM H2O2 by luciferase reporter gene assay
- ChEMBL_1891573 (CHEMBL4393400) Activation of human ERbeta assessed as induction of transcriptional activation incubated for 24 hrs in presence of 100 uM H2O2 by luciferase reporter gene assay
- ChEMBL_830732 (CHEMBL2061719) Inhibition of PARP1 in H202-stimulated human C41 cells incubated for 30 mins prior to H2O2-treatment measured after 10 mins by FITC-based immunostaining
- ChEMBL_1465838 (CHEMBL3406143) Inhibition of human recombinant LSD1 assessed as effect on H2O2 production incubated for 30 mins using methylated peptide substrate, Amplex red reagent and peroxidase by fluorimetry
- ChEMBL_1475314 (CHEMBL3425211) Inhibition of human recombinant LSD1 expressed in Escherichia coli using H3-H4 peptide as substrate assessed as H2O2 produced after 15 mins by amplex red assay
- ChEMBL_1664234 (CHEMBL4013915) Inhibition of recombinant MPO (unknown origin) assessed as reduction in taurine chloramine production preincubated with enzyme and taurine followed by H2O2 addition measured after 5 mins
- ChEMBL_1664255 (CHEMBL4013936) Inhibition of MPO in human neutrophils assessed as reduction in HOCl production preincubated for 30 mins followed by H2O2 addition by APF staining based flow cytometry
- ChEMBL_2217370 (CHEMBL5130502) Inhibition of human recombinant TPO (1 to 839 residues) expressed in baculovirus-infected insect cells measured after 15 mins in presence of H2O2 by chemiluminescence assay
- ChEMBL_1738669 (CHEMBL4154419) Inhibition of human TRPM2 expressed in HEK293 cells assessed as reduction in H2O2-induced intracellular calcium flux after 30 mins by Fluo4-AM dye based fluorescence assay
- ChEMBL_1738671 (CHEMBL4154421) Inhibition of human TRPM8 expressed in HEK293 cells assessed as reduction in H2O2-induced intracellular calcium flux after 30 mins by Fluo4-AM dye based fluorescence assay
- ChEMBL_979033 (CHEMBL2421086) Inhibition of human recombinant microsomal MAO-B expressed in baculovirus-infected insect BTI-TN-5B1-4 cells assessed as p-tyramine conversion to H2O2 by fluorescence assay
- ChEMBL_979034 (CHEMBL2421087) Inhibition of human recombinant microsomal MAO-A expressed in baculovirus-infected insect BTI-TN-5B1-4 cells assessed as p-tyramine conversion to H2O2 by fluorescence assay
- ChEMBL_1349995 (CHEMBL3270421) Inhibition of human recombinant MAO-A expressed in baculovirus infected insect cell microsomes assessed as p-tyramine conversion to resorufin and H2O2 after 15 mins by fluorimetric assay
- ChEMBL_1349997 (CHEMBL3270423) Inhibition of human recombinant MAO-B expressed in baculovirus infected insect cell microsomes assessed as p-tyramine conversion to resorufin and H2O2 after 15 mins by fluorimetric assay
- ChEMBL_1808896 (CHEMBL4308255) Inhibition of MAO-B in mouse brain assessed as reduction in H2O2 production incubated for 30 mins using benzylamine as substrate by Amplex red reagent based fluorescence assay
- ChEMBL_1884279 (CHEMBL4385861) Inhibition of human recombinant nSMase expressed in HEK293 cells using sphingomyelin as substrate by alkaline phosphatase, choline oxidase and horseradish peroxidase dependent H2O2 detection based fluorescence coupled assay
- Myeloperoxidase Assay Assays were performed at 22 °C with 2 nM MPO and 10 μM hydrogen peroxide (H2O2) in 20 mM NaH2PO4 buffer, pH 6.5 containing 140 mM NaCl, 10 mM taurine, and 1 mM L-tyrosine. Inhibitor compounds were preincubated with MPO for 15 min prior to the addition of H2O2, and the accumulation of taurine chloramine was determined after 1 min.
- ChEMBL_2311262 Inhibition of recombinant IL4I1 (unknown origin) assessed as reduction in H2O2 production preincubated for 4 hrs followed by Phe/Tyr/Trp addition measured after 120 mins by fluorescence based analysis
- ChEMBL_963635 (CHEMBL2395154) Inhibition of electric eel AChE preincubated for 30 mins prior to horseradish peroxidase, H2O2 and DETAPAC addition measured for 20 mins under ROS condition by Muraoka and Miura method
- ChEMBL_2078746 (CHEMBL4734537) Inhibition of electric eel AChE using acetylthiocholine iodide as substrate preincubated for 5 mins followed by substrate addition and measured after 1 min in presence of H2O2 by Ellman's method
- ChEMBL_770956 (CHEMBL1838195) Inhibition of recombinant human HDAC3/N-CoR2 using Boc-L-Lys(epsilon-trifluoroacetyl)-AMC as substrate by two-step fluorogenic assay in presence of 0.2 mM H2O2 (Rvb = 0.018 uM)
- ChEMBL_770957 (CHEMBL1838196) Inhibition of recombinant human HDAC3/N-CoR2 using Boc-L-Lys(epsilon-trifluoroacetyl)-AMC as substrate by two-step fluorogenic assay in presence of 0.4 mM H2O2 (Rvb = 0.018 uM)
- ChEMBL_770958 (CHEMBL1838197) Inhibition of recombinant human HDAC3/N-CoR2 using Boc-L-Lys(epsilon-trifluoroacetyl)-AMC as substrate by two-step fluorogenic assay in presence of 1 mM H2O2 (Rvb = 0.018 uM)
- ChEMBL_987411 (CHEMBL2438476) Competitive reversible inhibition of human recombinant MAO-B expressed in baculovirus infected BT1 insect cells using p-tyramine as substrate assessed as H2O2 production after 15 mins by fluorimetric analysis
- ChEMBL_987412 (CHEMBL2438477) Competitive reversible inhibition of human recombinant MAO-A expressed in baculovirus infected BT1 insect cells using p-tyramine as substrate assessed as H2O2 production after 15 mins by fluorimetric analysis
- Control Assay Assay controls. To rule out interference with either Nox2 or Nox4 luminescence assays, two approaches are used. In one, xanthine oxidase replaces the Nox2 enzymatic system as the source of ROS in the Nox2/LO12 assay. Xanthine is added to initiate the reaction and LO12 luminescence is recorded. In the other, exogenous H2O2 is supplied in place of the Nox4 expressing H2O2-generating cells and luminescence is recorded.
- ChEMBL_1563756 (CHEMBL3784057) Inhibition of recombinant human MAO-A using p-tyramine as substrate assessed as H2O2 production preincubated for 15 mins followed by substrate addition measured for 15 mins by amplex red assay
- ChEMBL_1563757 (CHEMBL3784058) Inhibition of recombinant human MAO-B using p-tyramine as substrate assessed as H2O2 production preincubated for 15 mins followed by substrate addition measured for 15 mins by amplex red assay
- ChEMBL_1796385 (CHEMBL4268502) Inhibition of human recombinant MAOB expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production by amplex red-based fluorescence assay
- ChEMBL_1690275 (CHEMBL4040845) Noncompetitive inhibition of human recombinant microsomal MAOB expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production by Lineweaver-Burk plot analysis
- ChEMBL_1796381 (CHEMBL4268498) Reversible competitive inhibition of human recombinant microsomal MAOA expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production by Dixon plot analysis
- ChEMBL_1796384 (CHEMBL4268501) Inhibition of human recombinant microsomal MAOA expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production by amplex red-based fluorescence assay
- ChEMBL_1796395 (CHEMBL4268512) Reversible competitive inhibition of human recombinant microsomal MAOB expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production by Dixon plot analysis
- In Vitro Assays of Nox Inhibiting Activity Reactive oxygen produced in whole cells or in membrane preparation of Nox1, Nox3, Nox4, Nox5 and xanthine oxidase and glucose oxidase were determined using Amplex Red as detection probe of formed H2O2. Amplex Red (10-acetyl-3,7-dihydroxyphenoxazine) in combination with HRP and co-factors reacts with H2O2 in a 1:1 stoichiometry to form a highly fluorescent resorufin excitated at 544 nm producing emission at 590 nm.
- ChEMBL_1434484 (CHEMBL3388870) Inhibition of human recombinant KDM1A/CoREST expressed in Escherichia coli assessed as reduction in H2O2 release using synthetic mono-methylated H3-K4 peptide (21 amino acids) substrate by horseradish peroxidase coupled enzyme assay
- ChEMBL_1462036 (CHEMBL3396571) Inhibition of human recombinant MAO-A using p-tyramine as substrate assessed as production of H2O2 incubated for 15 mins prior to substrate addition measured after 20 mins by microplate fluorescence reader analysis
- ChEMBL_1462037 (CHEMBL3396572) Inhibition of human recombinant MAO-B using p-tyramine as substrate assessed as production of H2O2 incubated for 15 mins prior to substrate addition measured after 20 mins by microplate fluorescence reader analysis
- ChEMBL_1912355 (CHEMBL4414938) Inhibition of ITK in human Jurkat cells assessed as reduction in PLCgamma1 phosphorylation at Y783 residues preincubated for 2 hrs followed by H2O2 addition and measured after 10 mins by Western blot analysis
- ChEBML_1690270 Inhibition of human recombinant microsomal MAOB expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production after 15 mins by amplex red-based fluorescence assay
- ChEBML_1690271 Inhibition of human recombinant microsomal MAOA expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production after 15 mins by amplex red-based fluorescence assay
- ChEMBL_1932452 (CHEMBL4478104) Inhibition of human microsomal MAO-B expressed in recombinant baculovirus infected insect BTI-TN-5B1-4 cells assessed as reduction in H2O2 production using p-tyramine as substrate after 15 mins by fluorescence assay
- ChEMBL_1932473 (CHEMBL4478125) Inhibition of human microsomal MAO-A expressed in recombinant baculovirus infected insect BTI-TN-5B1-4 cells assessed as reduction in H2O2 production using p-tyramine as substrate after 15 mins by fluorescence assay
- ChEMBL_873890 (CHEMBL2184301) Inhibition of human recombinant N-terminal histidine tagged LSD1 expressed in Escherichia coli BL21 (DE3) assessed as production of H2O2 using H3K4me2 H3K4me2 (1 to 21 amino acid residues) as substrate by chemiluminescence assay
- ChEMBL_1288156 (CHEMBL3110659) Inhibition of human recombinant LSD1 using di-methylated H3-K4 peptide as substrate assessed as release of H2O2 preincubated for 15 mins followed by substrate addition measured after 1 hr by peroxide/peroxidase-coupled assay
- ChEMBL_1390859 (CHEMBL3391327) Inhibition of full length human NOX2 transfected in COS 22 cells assessed as inhibition of Phorbol 12-myristate 13-acetate-stimulated ROS generation by measuring H2O2 production by fluorescence assay in presence of superoxide dismutase
- ChEMBL_1390861 (CHEMBL3391329) Inhibition of full length human NOX4 transfected in COS 22 cells assessed as inhibition of Phorbol 12-myristate 13-acetate-stimulated ROS generation by measuring H2O2 production by fluorescence assay in presence of superoxide dismutase
- ChEMBL_1690270 (CHEMBL4040840) Inhibition of human recombinant microsomal MAOB expressed in baculovirus infected BTI-TN-5B1- 4 cells using p-tyramine as substrate assessed as decrease in H2O2 production after 15 mins by amplex red-based fluorescence assay
- ChEMBL_1677666 (CHEMBL4027809) Inhibition of CrtN in Staphylococcus aureus Newman after 12 resistant development passages under 0.15% v/v H2O2 assessed as reduction in staphyloxanthin levels under IC90 level after 48 hrs by spectrophotometric method-based pigment inhibition assay
- ChEMBL_1932460 (CHEMBL4478112) Competitive inhibition of human microsomal MAO-B expressed in recombinant baculovirus infected insect BTI-TN-5B1-4 cells assessed as reduction in H2O2 production using p-tyramine as substrate after 15 mins by Dixon plot method
- ChEMBL_1981863 (CHEMBL4615125) Inhibition of human recombinant full-length nSMase expressed in HEK293 cells using sphingomyelin as substrate measured after 1 hr by alkaline phosphatase, choline oxidase and horseradish peroxidase dependent H2O2 detection-coupled amplex reagent based fluorescence assay
- ChEMBL_2362820 Inhibition of NOX2 (unknown origin) transfected in COS cells assessed as reduction in PMA-stimulated H2O2 production preincubated for 15 mins followed by PMA stimulation and measured for 1 hr by amplex red dye based fluorescence analysis
- ChEBML_1701355 Inhibition of recombinant human LOXL3 assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1932461 (CHEMBL4478113) Non-competitive inhibition of human microsomal MAO-B expressed in recombinant baculovirus infected insect BTI-TN-5B1-4 cells assessed as reduction in H2O2 production using p-tyramine as substrate after 15 mins by Dixon plot method
- ChEMBL_2103814 (CHEMBL4812317) Inhibition of C-terminal hexaHis-tagged TPO (unknown origin) expressed in Trichoplusia ni insect cells using 3-iodo tyrosine as substrate preincubated for 10 mins followed by substrate and H2O2 addition and further incubated for 15 mins
- ChEMBL_2118497 (CHEMBL4827563) Inhibition of recombinant human MAO-A expressed in baculovirus infected BTI cells assessed as inhibition of H2O2 production using kynuramine as substrate preincubated for 5 mins followed by substrate addition by Amplex Red reagent based fluorescence analysis
- ChEMBL_2118498 (CHEMBL4827564) Inhibition of recombinant human MAO-B expressed in baculovirus infected BTI cells assessed as inhibition of H2O2 production using kynuramine as substrate preincubated for 5 mins followed by substrate addition by Amplex Red reagent based fluorescence analysis
- ChEMBL_1349395 (CHEMBL3269985) Inhibition of human recombinant MAO-A expressed in baculovirus-infected BTI-TN-5B1-4 cell microsomes assessed as decrease in H2O2 production using p-tyramine as substrate preincubated for 15 mins by Amplex Red reagent based fluorimetric method
- ChEMBL_1349396 (CHEMBL3269986) Inhibition of human recombinant MAO-B expressed in baculovirus-infected BTI-TN-5B1-4 cell microsomes assessed as decrease in H2O2 production using p-tyramine as substrate preincubated for 15 mins by Amplex Red reagent based fluorimetric method
- ChEMBL_1701355 (CHEMBL4052337) Inhibition of recombinant human LOXL3 assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_2362821 Inhibition of NOX5 (unknown origin) transfected in HEK cells assessed as reduction in PMA/ionomycin-stimulated H2O2 production preincubated for 15 mins followed by PMA /ionomycin stimulation and measured for 1 hr by amplex red dye based fluorescence analysis
- ChEBML_1662056 Inhibition of recombinant human MAO-B expressed in baculovirus infected BTI insect cells assessed as reduction in H2O2 production using p-tyramine as substrate pretreated for 30 mins followed by substrate addition after 30 mins by Amplex red reagent based assay
- ChEBML_1701348 Inhibition of human LOXL2 expressed in CHO cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 15 mins followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEBML_1701368 Inhibition of rat LOXL2 expressed in CHO cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1564915 (CHEMBL3782872) Inhibition of human recombinant KDM1A/CoREST expressed in Escherichia coli using mono-methylated H3-K4 peptide as substrate assessed as H2O2 release preincubated for 15 mins followed by substrate addition measured for 12 mins by fluorescence-based microplate reader analysis
- ChEMBL_1634250 (CHEMBL3877042) Inhibition of human LSD1 assessed as reduction in H2O2 production using H3K4me2 (1 to 20 residues) peptide as substrate preincubated for 10 mins followed by substrate addition measured after 30 mins in presence of DTT by peroxidase coupled enzyme assay
- ChEMBL_1634251 (CHEMBL3877043) Inhibition of human LSD1 assessed as reduction in H2O2 production using H3K4me2 (1 to 20 residues) peptide as substrate preincubated for 10 mins followed by substrate addition measured after 30 mins in absence of DTT by peroxidase coupled enzyme assay
- ChEMBL_1634252 (CHEMBL3877044) Inhibition of human LSD1 assessed as reduction in H2O2 production using H3K4me2 (1 to 20 residues) peptide as substrate preincubated for 10 mins followed by substrate addition measured after 30 mins in presence of TCEP by peroxidase coupled enzyme assay
- ChEMBL_1662056 (CHEMBL4011737) Inhibition of recombinant human MAO-B expressed in baculovirus infected BTI insect cells assessed as reduction in H2O2 production using p-tyramine as substrate pretreated for 30 mins followed by substrate addition after 30 mins by Amplex red reagent based assay
- ChEMBL_1662057 (CHEMBL4011738) Inhibition of recombinant human MAO-A expressed in baculovirus infected BTI insect cells assessed as reduction in H2O2 production using p-tyramine as substrate pretreated for 30 mins followed by substrate addition after 30 mins by Amplex red reagent based assay
- ChEMBL_1667720 (CHEMBL4017608) Inhibition of human LSD1 (172 to 833 residues) assessed as reduction in H2O2 production using H3K4me2 (1 to 20 residues) peptide as substrate preincubated for 10 mins followed by substrate addition measured after 30 mins by peroxidase coupled enzyme assay
- ChEMBL_1701347 (CHEMBL4052329) Inhibition of human LOXL2 expressed in CHO cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1701348 (CHEMBL4052330) Inhibition of human LOXL2 expressed in CHO cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 15 mins followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1853663 (CHEMBL4354287) Inhibition of human recombinant MAO-A expressed in baculovirus infected BTI-TN-5B1-4 insect cells assessed as decrease in H2O2 production using p-tyramine as substrate incubated for 20 mins by horse-radish peroxidase/amplex red-based fluorescence method
- ChEMBL_1853664 (CHEMBL4354288) Inhibition of human recombinant MAO-B expressed in baculovirus infected BTI-TN-5B1-4 insect cells assessed as decrease in H2O2 production using p-tyramine as substrate incubated for 20 mins by horse-radish peroxidase/amplex red-based fluorescence method
- ChEMBL_956866 (CHEMBL2378113) Inhibition of human recombinant microsomal MAO-B expressed in baculovirus infected BTI-TN-5B1-4 cells using p-tyramine as substrate assessed as production of H2O2 incubated for 15 mins followed by substrate addition measured over 15 mins by fluorimetric analysis
- ChEMBL_956867 (CHEMBL2378114) Inhibition of human recombinant microsomal MAO-A expressed in baculovirus infected BTI-TN-5B1-4 cells using p-tyramine as substrate assessed as production of H2O2 incubated for 15 mins followed by substrate addition measured over 15 mins by fluorimetric analysis
- ChEBML_1701363 Inhibition of recombinant mouse LOXL2 expressed in mouse whole blood assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1558467 (CHEMBL3773502) Inhibition of recombinant human microsomal MAO-A expressed in baculovirus-infected insect cells using p-tyramine as substrate assessed as H2O2 production pretreated for 15 mins followed by addition of Amplex Red, horseradish peroxidase and substrate measured for 15 mins by fluorimetric method
- ChEMBL_1558469 (CHEMBL3773504) Inhibition of recombinant human microsomal MAO-B expressed in baculovirus-infected insect cells using p-tyramine as substrate assessed as H2O2 production pretreated for 15 mins followed by addition of Amplex Red, horseradish peroxidase and substrate measured for 15 mins by fluorimetric method
- ChEMBL_1648484 (CHEMBL3997540) Inhibition of full length recombinant human LOXL2 expressed in CHO cells assessed as reduction in H2O2 production using DAP as substrate preincubated for 15 mins followed by substrate addition measured every 2 minutes for 50 minutes by Amplex red dye based fluorescence assay
- ChEMBL_1648485 (CHEMBL3997541) Inhibition of full length recombinant human LOXL2 expressed in CHO cells assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 hrs followed by substrate addition measured every 2 minutes for 50 minutes by Amplex red dye based fluorescence assay
- ChEMBL_1701352 (CHEMBL4052334) Inhibition of recombinant human LOXL2 expressed in human whole blood assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_2088318 (CHEMBL4769581) Inhibition of human recombinant microsomal MAO-B expressed in baculovirus-infected BTI-TN-5B1-4 cells assessed as inhibition of H2O2 production using p-tyramine as substrate preincubated for 15 mins followed by substrate addition by Amplex Red reagent based fluorescence analysis
- ChEMBL_2088326 (CHEMBL4769589) Inhibition of human recombinant microsomal MAO-A expressed in baculovirus-infected BTI-TN-5B1-4 cells assessed as inhibition of H2O2 production using p-tyramine as substrate preincubated for 15 mins followed by substrate addition by Amplex Red reagent based fluorescence analysis
- ChEMBL_2283920 Inhibition of C-terminal 6-His tagged recombinant human IL4I1 (Gln22 to His567 residues) expressed in CHO cells using Phe/Tyr/Trp as substrate assessed as inhibition of H2O2 production measured after 240 mins by Amplex red and horseradish peroxidase based fluorescence assay
- ChEBML_1701351 Inhibition of human LOX expressed in HEK cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition in presence of 0.1% BSA measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1576943 (CHEMBL3806786) Inhibition of human recombinant microsomal MAO-B expressed in baculovirus infected BTI-TN-5B1-4 cells using p-tyramine as substrate assessed as reduction in H2O2 production preincubated for 15 mins followed by substrate addition measured for 15 mins Amplex red dye based fluorimetric method
- ChEMBL_1576945 (CHEMBL3806788) Inhibition of human recombinant microsomal MAO-A expressed in baculovirus infected BTI-TN-5B1-4 cells using p-tyramine as substrate assessed as reduction in H2O2 production preincubated for 15 mins followed by substrate addition measured for 15 mins Amplex red dye based fluorimetric method
- ChEMBL_1648492 (CHEMBL3997548) Inhibition of recombinant human C-terminal His10-tagged LOXL3 (1 to 753 residues) assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 hrs followed by substrate addition measured every 2 minutes for 50 minutes by Amplex red dye based fluorescence assay
- ChEMBL_1758278 (CHEMBL4193286) Inhibition of human recombinant MAO-A expressed in baculovirus infected BTI-TN5B1-4 cells using p-tyramine as substrate assessed as reduction in H2O2 production preincubated for 15 mins followed by substrate addition measured after 15 mins by Amplex red dye based fluorescence assay
- ChEMBL_1758279 (CHEMBL4193287) Inhibition of human recombinant MAO-B expressed in baculovirus infected BTI-TN5B1-4 cells using p-tyramine as substrate assessed as reduction in H2O2 production preincubated for 15 mins followed by substrate addition measured after 15 mins by Amplex red dye based fluorescence assay
- ChEMBL_1648489 (CHEMBL3997545) Inhibition of full length recombinant human LOXL2 expressed in CHO cells spiked into human whole blood assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 followed by substrate addition measured every 90 secs for 45 mins by Amplex red dye based fluorescence assay
- ChEMBL_1648490 (CHEMBL3997546) Inhibition of full length recombinant human LOXL2 expressed in CHO cells assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 hrs followed by substrate addition measured every 2 minutes for 50 minutes in presence of BSA by Amplex red dye based fluorescence assay
- ChEMBL_1648491 (CHEMBL3997547) Inhibition of full length recombinant human LOX expressed in HEK cells assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 hrs followed by substrate addition measured every 2 minutes for 50 minutes in presence of BSA by Amplex red dye based fluorescence assay
- ChEMBL_1648493 (CHEMBL3997549) Inhibition of full length recombinant mouse LOXL2 expressed in CHO cells assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 hrs followed by substrate addition measured every 2 minutes for 50 minutes in presence of BSA by Amplex red dye based fluorescence assay
- ChEMBL_1648494 (CHEMBL3997550) Inhibition of full length recombinant rat LOXL2 expressed in CHO cells assessed as reduction in H2O2 production using DAP as substrate preincubated for 2 hrs followed by substrate addition measured every 2 minutes for 50 minutes in presence of BSA by Amplex red dye based fluorescence assay
- ChEMBL_1701350 (CHEMBL4052332) Inhibition of human LOXL2 expressed in CHO cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition in presence of 0.1% BSA measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_1701351 (CHEMBL4052333) Inhibition of human LOX expressed in HEK cells assessed as reduction of H2O2 production from oxidative deamination of DAP preincubated for 2 hrs followed by substrate addition in presence of 0.1% BSA measured every 2 mins for 1 hr by amplex red reagent-based fluorescence assay
- ChEMBL_2019856 (CHEMBL4673669) Antagonist activity at mouse GOAT expressed in baculovirus infected sf9 insect cell membrane using ghrelin(1 to 5) pentapeptide as substrate preincubated for 5 mins followed by Palmitoyl-CoA and n-octynoyl-CoA addition and measured after 5 mins by amplex red/H2O2 reagent-based fluorescence method
- EPX Bromination Assay EPX bromination activity was measured in 100 mM KPi (pH 7.4) by monitoring the H2O2 catalyzed formation of 3-bromo tyrosine from tyrosine and potassium bromide. A 50 μl mixture of 0.6 μM EPX (Lee Biosolutions Cat. #342-60) was added to 100 nL inhibitor in 100% DMSO in a 384 well REMP plate. Enzyme and compound were preincubated for ten minutes at room temperature.After the ten minute preincubation of enzyme and inhibitor, 25 μL of a mixture containing 400 μM tyrosine and 1200 μM potassium bromide was added to the plate containing enzyme and inhibitor, followed by the addition of 25 μl of 20 μM H2O2. The reaction was allowed to proceed for 15 minutes, at which time it was quenched with 10 μL of 20% TCA. The final concentrations of all components were 0.3 μM EPX, 100 μM tyrosine, 400 μM potassium bromide, 5 μM H2O2, 0.1% DMSO, 2.0% TCA.
- EPX Bromination Assay EPX bromination activity was measured in 100 mM KPi (pH 7.4) by monitoring the H2O2 catalyzed formation of 3-bromo tyrosine from tyrosine and potassium bromide. A 50 μl mixture of 0.6 μM EPX (Lee Biosolutions Cat. #342-60) was added to 100 nL inhibitor in 100% DMSO in a 384 well REMP plate. Enzyme and compound were preincubated for ten minutes at room temperature.After the ten minute preincubation of enzyme and inhibitor, 25 μL of a mixture containing 400 μM tyrosine and 1200 μM potassium bromide was added to the plate containing enzyme and inhibitor, followed by the addition of 25 μl of 20 μM H2O2. The reaction was allowed to proceed for 15 minutes, at which time it was quenched with 10 μL of 20% TCA. The final concentrations of all components were 0.3 μM EPX, 100 μM tyrosine, 400 μM potassium bromide, 5 μM H2O2, 0.1% DMSO, 2.0% TCA.
- Inhibition Assay The DAAO inhibitory activity was measured by assaying the amount of hydrogen peroxide (H2O2) produced by reacting DAAO protein with flavin adenine dinucleotide (FAD) and D-alanine. The amount of H2O2 was determined by measuring the fluorescence generated on conversion of Amplex red (manufactured by Invitrogen Co.) into resorufin by the reaction of H2O2 with horseradish peroxidase (HRP). 4 uL of 4% dimethyl sulfoxide (DMSO) buffer (50 mM sodium phosphate (pH 7.5), 0.02% CHAPS) solution of the test compound was added to 384-well black, low volume plate, a mixed solution (4 uL) of recombinant human DAAO protein (15 nM), which had been expressed in Escherichia coli and purified, and 18 uM FAD was added, and the mixture was incubated at room temperature for 15 min. After incubation, a mixed buffer (4 uL) of 2.25 mM D-alanine, 1.5 U/mL HRP and 150 uM Amplex red was added, the mixture was incubated at room temperature for 30 min.
- MPO Activity Assay Assay mixtures (100 µL) contained 50 mM NaPi (pH 7.4), 150 mM NaCl, 1 mM DTPA, 2% DMSO, the indicated concentrations of H2O2, and Amplex Red. The reactions were initiated by the addition of 100 pM MPO. The fluorescent changes were measured at 530 (excitation) and 580 nm (emission).
- Concentration Response Redox Cycling H2O2 Generation assay to characterize small molecule inhibitors identified in the Polo box domain (PBD) of Plk1 Primary HTS. List of compounds to be tested: Compounds that met the active criterion of Z-score is
- POX Assay POX reactions were conducted in 2 ml of filtered and degassed 50 mM Tris-HCl, pH 8.0, containing 50 mM NaCl, 0.1 mM H2O2, 4.5 mM guaiacol, and the indicated concentrations of heme essentially as described previously [Yuan et al., Proc. Natl. Acad. Sci. USA., 103:6142-6147; Mbonye et al., J. Biol. Chem., 281:35770-35778].
- Concentration Response Redox Cycling H2O2 Generation assay, 1 mM DTT, to characterize small molecule inhibitors identified in the Polo box domain (PBD) of Plk1 Primary HTS. List of compounds to be tested: Compounds that met the active criterion of Z-score is
- DAAO Inhibitory Activity Assay The DAAO inhibitory activity was measured by assaying the amount of hydrogen peroxide (H2O2) produced by reacting DAAO protein with flavin adenine dinucleotide (FAD) and D-alanine. The amount of H2O2 was determined by measuring the fluorescence generated on conversion of Amplex red (manufactured by Invitrogen Co.) into resorufin by the reaction of H2O2 with horseradish peroxidase (HRP). 4 μL of 4% dimethyl sulfoxide (DMSO) buffer (50 mM sodium phosphate (pH 7.5), 0.02% CHAPS) solution of the test compound was added to 384-well black, low volume plate, a mixed solution (4 μL) of recombinant human DAAO protein (15 nM), which had been expressed in Escherichia coli and purified, and 18 μM FAD was added, and the mixture was incubated at room temperature for 15 min. After incubation, a mixed buffer (4 μL) of 2.25 mM D-alanine, 1.5 U/mL HRP and 150 μM Amplex red was added, the mixture was incubated at room temperature for 30 min, and the fluorescence (excitation wavelength 530 nm, fluorescence wavelength 590 nm) was measured using an Envision plate reader (manufactured by Perkin Elmer Co.). To cross-check the artificial inhibition of Amplex red conversion or the HRP activity inhibition of the test compound, the fluorescence was also measured under the conditions of 30 μM H2O2 addition in the absence of DAAO. Taking the fluorescence value in the absence of the test compound as 100% and the fluorescence value in the absence of DAAO as 0%, the DAAO activity was regarded to have been inhibited when the fluorescence value decreased by 50% in the presence of the test compound, and the concentration of the test compound at that time was taken as the IC50 value (nM).
- Biochemical Assay Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of various concentrations of inhibitor (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in triplicate. After leaving the enzyme interacting with the inhibitor, 12.5 μM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 1 hour at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 30 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor.
- MPO Peroxidation Assay (Amplex Red Assay) MPO peroxidation activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Amplex Red (Invitrogen Cat. #A12222) which can be oxidized to the highly fluorescent resorufin. Amplex Red is oxidized by the peroxidase action of MPO to resorufin. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 40 nM H2O2 (Sigma #349887) to 100 nL inhibitor in 100% DMSO in a 384 well Perkin Elmer Optiplate. Enzyme and compound were preincubated for ten minutes at room temperature.After the ten minute preincubation, 25 μL of an Amplex Red mixture containing 200 μM Amplex Red and 10 mM H2O2 was added to the plate. Kinetic determinations were carried out immediately on a Perkin Elmer Envision (15 minute kinetic read, Ex: 535 nm, Em: 590 nm).
- Activity Assay The MetAP-2 activity is determined by coupling enzymatic reactions. The tripeptide Met-Arg-Ser (MAS) is employed as substrate. The methionine liberated is firstly converted into Metox and H2O2 by L-aminooxidase (AAO). In the second step, the peroxidase (POD) with the aid of the H2O2 catalyses the oxidation of the leukodye dianisidine to dianisidineox, the increase of which is detected photometrically at 450 nm. MetAP-2 activity can be recorded continuously as kinetics. The reaction scheme illustrates that one mol of dianisidineox is formed per mol of methionene. The MetAP-2 enzyme activity can therefore be calculated directly as absorption per time unit. Qualification of the MetAP-2 activity (mol of Met/time unit) is possible with the aid of the dianisidineox extinction coefficient. The change in extinction per time unit is depicted graphically and a slope calculation is carried out in the visually linear region of the reaction.
- Enzyme Assay The functional activity of compounds inhibiting the DAAO enzyme was determined by utilizing the co-product of the catalysis of D-Serine, H2O2 which can be quantitatively measured using the Amplex Red (Invitrogen) detection. Amplex Red reagent is a colorless substrate that reacts with hydrogen peroxide (H2O2) with a 1:1 stoichiometry in the presence of hydrogen peroxide to produce highly fluorescent resorufin (excitation/emission maxima=570/585 nm). The changes in fluorescence were monitored by a fluorescence plate reader, Envision (Perkin Elmer) and increases in DAAO activity were readily detected upon addition of D-Serine and suppression of this response observed with the application of test compounds.Human DAAO enzyme was supplied by the Takeda Pharmaceutical Company (Osaka) and each batch was tested and used at concentrations giving comparable levels of activity. The Km of D-Serine was measured for each enzyme batch to maintain consistency; this Km was used in subsequent assays.
- Fluorimetric Assay The activities of recombinant hMAO-A and hMAO-B were determined using p-tyramine as common substrate and calculated as 0.18 +/- 0.01 nmol/mg/min (n = 3) and 0.12 +/- 0.02 nmol/mg/min (n = 3), respectively. The interactions of the synthesized compounds with hMAO isoforms were determined by a fluorimetric method described previously. The production of H2O2 catalyzed by MAO isoforms was detected using a non-fluorescent Amplex-Red reagent which reacts with H2O2 in the presence of horseradish peroxidase to produce the fluorescent product resorufin. The reaction was started by the addition of 200 uM Amplex Red reagent, 1 U/mL horseradish peroxidase, and p-tyramine (concentration range 0.1 to 1 mM). Control experiments were carried out using reference inhibitors (Selegiline and Moclobemide). The possible capacity of compounds to modify the fluorescence generated in the reaction mixture due to non-enzymatic inhibition was determined by adding these compounds to solutions containing only the Amplex Red reagent in sodium phosphate buffer.
- Biological Assay Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of at least eight 3-fold serial dilutions of the respective test compound (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in duplicate. After leaving the enzyme interacting with the inhibitor, KM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 30 minutes at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 5 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Ampiex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor.
- IL4I1 Enzymatic Assay nterleukin 4 inducible protein 1 (IL4I1) is an L-amino oxidase that catalyzes the oxidation of aromatic residues (Phe, Trp and Tyr): L-amino acid+H2O+O2→2-oxo acid+NH3+H2O2. Equal molar of H2O2 and the corresponding alpha-ketoacid are produced when IL4I1 and substrate are added. In this assay, the hydrogen peroxide generated by IL4I1 are then detected through a coupled reaction with Amplex Red (10-acetyl-3,7-dihydroxyphenoxazine) and Horse Peroxidase (HRP) to produce Resorufin product that could be detected in the form of fluorescence signals. The assessment of the inhibitory effect of small molecules (EC50) on IL4I1 is measured by the effectiveness of the compounds to inhibit the production of H2O2.Using this assay, the potency (EC50) of each compound was determined from a ten-point (1:3 serial dilution; top compound concentration of 10000 nM) titration curve using the following outlined procedure. To each well of a black flat-bottom Greiner (Cat #781076) 384 well-plate, 25 nL of compound (0.1% DMSO in final assay volume of 25 μL) was dispensed, followed by the addition of 12.5 μL of 1× assay buffer (50 mM Hepes 7.0 and 0.005% Tween20 (Sigma, Cat #P8341; low peroxide grade)) containing 2 nM of recombinant IL4I1 (R&D Systems, Cat #5684-AO-020). Plates were placed in an ambient temperature humidified chamber for a four-hour pre-incubation with compound. Subsequently, each reaction was initiated by the addition of 12.5 μL 1× assay buffer containing 2 mM of each aromatic amino acids (Phe/Tyr/Trp), 0.1 mM Amplex Red and 2 U/mL of HRP. The final reaction in each well of 25 μL consists of 1 nM of IL4I1, 1 mM of each residues (Phe, Tyr and Trp), 0.05 mM Amplex Red and 1 U/mL of HRP. It should be noted that the concentrations of Amplex Red and HRP used here are in excess such that the conversion of H2O2 to Resorufin product occurs instantaneously and non-rate limiting.
- Biochemical Inhibition Activity Assay The biochemical inhibition activity of the synthesized compounds on LSD1 was measured. The activity measurement was performed using LSD1 fluorescence analysis kit (available from BPS Bioscience Co., Ltd., Catalog No: 50106). This analysis kit is designed to measure activity of LSD1 enzyme. H2O2 generated upon demethylation of Lys4 moiety of histone H3 by LSD1 is reacted with HRP/Amplex Red reagent to form fluorescent Resorufin, which is measured by this kit, thereby confirming demethylation.
- Cell Based Assay As a means of assessing PI3K δ activation in response to stimuli, the phosphorylation status of the protein, Akt, a downstream product of PI3Kδ, signaling was determined.U937 cells, obtained from a human, leukemic, monocyte lymphoma cell line, were differentiated to macrophage-type cells by incubation with PMA (100 ng/mL) for 48 to 72 hr. Cells were then pre-incubated with either the test compound or vehicle for 2 hr and were then stimulated briefly by exposure to H2O2 (10 mM, 5-7 min) and the reaction stopped by replacing the media with 4% formaldehyde solution. Endogenous peroxide activity and formaldehyde were inactivated by incubating with quenching buffer (0.1% sodium azide, 1% H2O2 in PBS with 0.1% Triton X-100) for 20 min. The cells were washed with buffer (PBS containing 0.1% Triton X-100) and were incubated with blocking solution (1% BSA in PBS) for 1 hr and were then re-washed with buffer and incubated overnight with either anti-pAkt antibody or anti-pan-Akt antibody.
- LSD1 Assay The compounds of the invention can be tested for their ability to inhibit LSD1. The ability of the compounds of the invention to inhibit LSD1 can be tested as follows. Human recombinant LSD1 protein was purchased from BPS Bioscience Inc. In order to monitor LSD1 enzymatic activity and/or its inhibition rate by our inhibitor(s) of interest, di-methylated H3-K4 peptide (Millipore) was chosen as a substrate. The demethylase activity was estimated, under aerobic conditions, by measuring the release of H2O2 produced during the catalytic process, using the Amplex Red peroxide/peroxidase-coupled assay kit (Invitrogen).Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of various concentrations of inhibitor (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in triplicate. After leaving the enzyme interacting with the inhibitor, 12.5 μM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 1 hour at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 30 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor.The maximum demethylase activity of LSD1 was obtained in the absence of inhibitor and corrected for background fluorescence in the absence of LSD1. The Ki (IC50) of each inhibitor was estimated at half of the maximum activity.
- Biological Assays-Inhibition of LSD1 Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of at least eight 3-fold serial dilutions of the respective inhibitor (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in duplicate. After leaving the enzyme interacting with the inhibitor, KM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 30 minutes at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 5 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor.The maximum demethylase activity of LSD1 was obtained in the absence of inhibitor and corrected for background fluorescence in the absence of LSD1. The IC50 value of each inhibitor was calculated with GraphPad Prism Software.
- Biological Assay The compounds of the invention can be tested for their ability to inhibit LSD1. The ability of the compounds of the invention to inhibit LSD1 can be tested as follows. Human recombinant LSD1 protein was purchased from BPS Bioscience Inc (catalog reference number 50100: human recombinant LSD1, GenBank accession no. NM_015013, amino acids 158-end with N-terminal GST tag, MW: 103 kDa). In order to monitor LSD1 enzymatic activity and/or its inhibition rate by our inhibitor(s) of interest, di-methylated H3-K4 peptide (Anaspec) was chosen as a substrate. The demethylase activity was estimated, under aerobic conditions, by measuring the release of H2O2 produced during the catalytic process, using the Amplex Red hydrogen peroxide/peroxidase assay kit (Invitrogen).Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of at least eight 3-fold serial dilutions of the respective inhibitor (e.g., from 0 to 75 uM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in duplicate. After leaving the enzyme interacting with the inhibitor, KM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 30 minutes at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 5 extra minutes at room temperature in the dark. A 1 uM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor. The maximum demethylase activity of LSD1 was obtained in the absence of inhibitor and corrected for background fluorescence in the absence of LSD1. The IC50 value of each inhibitor was calculated with GraphPad Prism Software.
- Biological Assay The compounds of the invention can be tested for their ability to inhibit LSD1. The ability of the compounds of the invention to inhibit LSD1 can be tested as follows. Human recombinant LSD1 protein was purchased from BPS Bioscience Inc (catalog reference number 50100: human recombinant LSD1, GenBank accession no. NM_015013, amino acids 158-end with N-terminal GST tag, MW: 103 kDa). In order to monitor LSD1 enzymatic activity and/or its inhibition rate by our inhibitor(s) of interest, di-methylated H3-K4 peptide (Anaspec) was chosen as a substrate. The demethylase activity was estimated, under aerobic conditions, by measuring the release of H2O2 produced during the catalytic process, using the Amplex Red hydrogen peroxide/peroxidase assay kit (Invitrogen).Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of at least eight 3-fold serial dilutions of the respective test compound (e.g., from 0 to 75 uM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in duplicate. After leaving the enzyme interacting with the inhibitor, KM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 30 minutes at 37° C. In the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 5 extra minutes at room temperature in the dark. A 1 uM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor. The maximum demethylase activity of LSD1 was obtained in the absence of inhibitor and corrected for background fluorescence in the absence of LSD1. The IC50 value of each inhibitor was calculated with GraphPad Prism Software.
- Inhibition of LSD1 The compounds of the invention can be tested for their ability to inhibit LSD1. The ability of the compounds of the invention to inhibit LSD1 can be tested as follows. Human recombinant LSD1 protein was purchased from BPS Bioscience Inc (catalog reference number 50100: human recombinant LSD1, GenBank accession no. NM_015013, amino acids 158-end with N-terminal GST tag, MW: 103 kDa). In order to monitor LSD1 enzymatic activity and/or its inhibition rate by our inhibitor(s) of interest, di-methylated H3-K4 peptide (Anaspec) was chosen as a substrate. The demethylase activity was estimated, under aerobic conditions, by measuring the release of H2O2 produced during the catalytic process, using the Amplex Red hydrogen peroxide/peroxidase assay kit (Invitrogen).Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of at least eight 3-fold serial dilutions of the respective test compound (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in duplicate. After leaving the enzyme interacting with the inhibitor, KM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 30 minutes at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 5 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor.The maximum demethylase activity of LSD1 was obtained in the absence of inhibitor and corrected for background fluorescence in the absence of LSD1. The IC50 value of each inhibitor was calculated with GraphPad Prism Software.
- Assessment of MPO and TPO Activity Assay (IC50) The experiments were performed in phosphate-buffered saline (PBS), pH7.4. A 10 mM luminol (A4695, Sigma Aldrich, St Louis, MO, USA) stock was prepared in distilled water and further diluted in PBS to a final concentration of 100 μM. H2O2 was prepared as 1 mM stock in PBS, yielding a final concentration of 50 μM after addition into the assay. The compounds were serially diluted in DMSO in a separate plate as a 100× stock solution, and MPO (purified from HL60 cells) and TPO (produced in insect cells, RSR Ltd, Cardiff, UK), were diluted to yield a final concentration of approximately 14 and 150 ng/mL, generating 5600 and 9300 light counts per seconds (LCPS) upon incubation with luminol. The experiment was run by pipetting 2 μL 100× stock solution of the compound and 200 μL diluted enzyme in PBS into wells in a 96-well Optiplate (6005290, Perkin Elmer/Thermo Fischer, Waltham, MS, USA), followed by addition of 10 μL H2O2 containing PBS. Chemiluminescence measurement (Perkin Elmer Wallac Microbeta Trilux 1450-029 (12-detector), Turkuu, Finland) was started directly and recorded after 2, 10 and 15 minutes. Chemiluminescence recorded after 15 minutes was used to calculate the IC50 values.
- LSD1 Assay Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of various concentrations of inhibitor (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in triplicate. After leaving the enzyme interacting with the inhibitor, 12.5 μM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 1 hour at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 30 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan).
- Fluorometric Assay The capability of compounds described herein to inhibit the enzymatic activity of vascular adhesion protein-1 (VAP-1) was determined by fluorometric assay. The assay procedure provided by R&D Systems was modified slightly for use as an inhibitor screening assay. The assay measured the H2O2 generated from the oxidative deamination of benzylamine by rhVAP-1 by converting Amplex Red to the fluorescent product, resorufin, via horseradish peroxidase (HRP) and H2O2. Reaction buffer was 10 mM NaHCO3, pH 7.4. A standard curve was prepared by serially diluting H2O2 in reaction buffer. A 10 μM solution of resorufin was prepared in reaction buffer and was dispensed to 2 wells. These wells served as positive control for maximum fluorescence. Reaction buffer was added to the individual wells so that the final volume in each well was 100 μL. Amplex Red was diluted to 1 mM in reaction buffer. A 10 U stock of HRP was prepared in reaction buffer. A reaction cocktail was prepared by mixing equal parts 1 mM Amplex Red with 10 U HRP with 3 parts reaction buffers. The reaction cocktail was added to the appropriate wells, so that that final concentration in the well was 0.05 mM Amplex Red and 0.5 U HRP. A 200 μM solution of benzylamine was prepared in reaction buffer. Benzylamine was added to the appropriate wells so that the final concentration was 50 μM. Inhibitors were diluted in DMSO to 20 and distributed to the appropriate wells. UP-1207 served a positive control. rhVAP-1 was purchased from R&D Systems. The concentration used for each lot was determined so that the activity was equal to the first lot. Two wells were left blank as controls. The plate was incubated for 30 minutes at 37 C., protected from light under foil. The plate was read at 530/35 emission and 590/35 excitation. Data processing was performed using Excel and Prism software.
- LSD1 Assays Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of at least eight 3-fold serial dilutions of the respective inhibitor (e.g., from 0 to 75 μM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in duplicate. After leaving the enzyme interacting with the inhibitor, KM of di-methylated H3-K4 peptide was added to each reaction and the experiment was left for 30 minutes at 37° C. in the dark. The enzymatic reactions were set up in a 50 mM sodium phosphate, pH 7.4 buffer. At the end of the incubation, Amplex Red reagent and horseradish peroxidase (HPR) solution were added to the reaction according to the recommendations provided by the supplier (Invitrogen), and left to incubate for 5 extra minutes at room temperature in the dark. A 1 μM H2O2 solution was used as a control of the kit efficiency. The conversion of the Amplex Red reagent to resorufin due to the presence of H2O2 in the assay, was monitored by fluorescence (excitation at 540 nm, emission at 590 nm) using a microplate reader (Infinite 200, Tecan). Arbitrary units were used to measure level of H2O2 produced in the absence and/or in the presence of inhibitor. The maximum demethylase activity of LSD1 was obtained in the absence of inhibitor and corrected for background fluorescence in the absence of LSD1. The IC50 value of each inhibitor was calculated with GraphPad Prism Software. The results presented in Table 1 below show the results of the LSD1 inhibition studies for a number of the Example compounds. In Table 2 the IC50 values for all examples tested in this assay are shown. Parnate (tranylcypromine; i.e., 2-trans phenylcyclopropylamine) was found to have a IC50 value of 35±10 micromolar. The studies show that the compounds of the invention have unexpectedly potent LSD1 inhibition.
- VAP-1 Assay The capability of compounds described herein to inhibit the enzymatic activity of vascular adhesion protein-1 (VAP-1) was determined by fluorometric assay. The assay procedure provided by R&D Systems was modified slightly for use as an inhibitor screening assay. The assay measured the H2O2 generated from the oxidative deamination of benzylamine by rhVAP-1 by converting Amplex Red to the fluorescent product, resorufin, via horseradish peroxidase (HRP) and H2O2. Reaction buffer was 10 mM NaHCO3, pH 7.4. A standard curve was prepared by serially diluting H2O2 in reaction buffer. A 10 μM solution of resorufin was prepared in reaction buffer and was dispensed to 2 wells. These wells served as positive control for maximum fluorescence. Reaction buffer was added to the individual wells so that the final volume in each well was 100 μL. Amplex Red was diluted to 1 mM in reaction buffer. A 10 U stock of HRP was prepared in reaction buffer. A reaction cocktail was prepared by mixing equal parts 1 mM Amplex Red with 10 U HRP with 3 parts reaction buffers. The reaction cocktail was added to the appropriate wells, so that that final concentration in the well was 0.05 mM Amplex Red and 0.5 U HRP. A 200 μM solution of benzylamine was prepared in reaction buffer. Benzylamine was added to the appropriate wells so that the final concentration was 50 μM. Inhibitors were diluted in DMSO to 20 and distributed to the appropriate wells. LJP-1207 served a positive control. rhVAP-1 was purchased from R&D Systems. The concentration used for each lot was determined so that the activity was equal to the first lot. Two wells were left blank as controls. The plate was incubated for 30 minutes at 37 C., protected from light under foil. The plate was read at 530/35 emission and 590/35 excitation. Data processing was performed using Excel and Prism software.
- MAO Enzyme Inhibition Assay The effects of the test compounds on hMAO isoform enzymatic activity were evaluated by measuring their effects on the production of hydrogen peroxide (and therefore, of resorufin) from p-tyramine, using the Amplex Red MAO assay kit (Molecular Probes, Eugene, Oregon, USA) and microsomal MAO isoforms prepared from insect cells infected with recombinant baculovirus containing cDNA inserts for human MAO-A or MAO-B. The production of H2O2 was quantified in a multidetection microplate fluorescence reader (FLX800, Bio-Tek Instruments, Inc., Winooski, VT) based on the fluorescence generated (excitation, 545 nm; emission, 590 nm) over a 15 min period, in which the fluorescence increased linearly.
- LOX Enzyme Activity Assay The following reagents were prepared:Reagents500 mM CHES, pH 9 (with NaOH), filtered (MW=207.29)20.7 g in 200 ml in dH2O10% Pluronic F-127 (store at 4° C.)1 g in 10 ml in dH2O10 % BSA (store at 4° C.)−2.5 g in 25 ml dH2O1 M MgCl2.6H2O (MW=203)5.1 g in 25 ml dH2O5 M Urea (MW=60.06)60 g in 200 ml dH2O5 M NaCl (MW=58.44)14.6 g in 50 ml dH2O8.5 M Cadaverine Dihydrochloride (MW=175.10): Sigma, Cat No: C85611.49 g in 1 ml dH2O10 mM Na3VO4, pH 10 (with HCl), boil to activate (MW=183.91): Sigma, Cat No: S65080.1839 g in 10 ml dH2O20 mM Amplex Red (MW=257.25): Invitrogen, Cat No: A12222.5 mg in 1 ml DMSO (aliquot into 40 μl and store at −20° C.)1000 U/ml HRP in dH2O (store at 4° C.): Sigma, Cat No: P2088H2O2 (store at 4° C.): Sigma, Cat No: H1009DMSOLOX Assay Buffer: Volume (μl) Reagent 1 × plate Final Concn 500 mM CHES, pH 9 5000 100 mM 10% Pluronic F-127 125 0.05% 10% BSA 1250 0.5% 1M MgCl2 25 1 mM 5M Urea 5000 1M 5M NaCl 500 100 mM dH2O 13100 — Total Volume 25 000 —Inhibitors (Test Compounds):10 mM stock diluted to 10, 3, 1, 0.3, 0.1, 0.03, 0.01, 0.003, 0.001, and 0.0003 mM in drug plate, resulting in a concentration of 100, 30, 10, 3, 1, 0.3, 0.1, 0.03, 0.01, and 0.003 uM in the assay.LOX enzyme:LOX enzyme was obtained from pig skin by the method of Shackleton et al 1990.Assay Plates:Black, flat bottom 96 well platesProcedure:1. Dilute LOX enzyme in Assay Buffer (˜4 ml for one plate, 8 ml for two plates) (dilution dependent on batch activity)2. Add 0.5 μl test compound serial dilutions, in duplicate3. Add 0.5 μl serial dilutions of positive control, BAPN, down column 11 (no duplication)4. Add following controls: 0.5 μl DMSO (100% activity control)5. Cover plate and incubate for 20 min at room temperature on a plate shaker6. Prepare Start Mix: Volume Reagent 1 × plate 2 × plate Final Concn Assay Buffer 2 ml 3 ml — 8.5M Cadaverine 23 μl 34.5 μl 97.8 mM 20 mM Amplex Red 10 μl 15 μl 100 μM 1000 U/ml HRP 10 μl 15 μl 5 U/ml7. Add 10 μl Start Mix to No HRP control wells8. Add HRP to the Start Mix. Add 10 ul to all wells EXCEPT No HRP control wells9. Incubate for 45 min at room temp on a plate shaker, protected from light10. Measure fluorescence using a plate reader: Excitation wavelength: 545 nm Emission wavelength: 585 nm HRP Counter Assay Protocol1. Dilute 5 μl H2O2 in 640 μl dH2O. Add 1 μl diluted H2O2 to 10 ml Assay Buffer. Vortex2. Add 40 μl H2O2+Assay Buffer into every well on the counter assay plate EXCEPT no H2O2 control wells (add 40 μl Assay Buffer only)3. Add 0.5 μl test compound serial dilutions, in duplicate4. Add 0.5 μl serial dilutions of positive control, Na3VO4, down column 11 (no duplication)5. Add following controls: 0.5 μl DMSO (100% activity control) 1 μl diluted H2O2 (blow out control)6. Incubate for 20 min at room temp on a plate shaker.
- MPO Peroxidation (Amplex Red) Assay MPO peroxidation activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Amplex Red (Invitrogen catalog #A12222) which can be oxidized to the highly fluorescent resorufin. Amplex Red is oxidized by the peroxidase action of MPO to resorufin. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 40 nM H2O2 (Sigma #349887) to 100 nL inhibitor in 100% DMSO in a 384 well Perkin Elmer Optiplate. Enzyme and compound were preincubated for ten minutes at rt.After the ten minute preincubation, 25 μL of an Amplex Red mixture containing 200 μM Amplex Red and 10 mM H2O2 was added to the plate. Kinetic determinations were carried out immediately on a Perkin Elmer Envision (15 minute kinetic read, Ex: 535 nm, Em: 590 nm).IC50 values were calculated by determining the slope of the linear portion of the kinetic trace (180-540 secs), and using that calculated slope to determine % inhibition occurring at each concentration of inhibitor using the following equation:Y = A + B - A 1 + ( C / x ) Dwhere A=minimal Y value (activity level of inhibited sample), B=maximal Y value (activity level of uninhibited sample), C=Log IC50, D=Hill Slope, x=concentration of inhibitor.
- MPO Peroxidation Assay (Amplex Red Assay) MPO peroxidation activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Amplex Red (Invitrogen Cat. #A12222) which can be oxidized to the highly fluorescent resorufin. Amplex Red is oxidized by the peroxidase action of MPO to resorufin. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 40 nM H2O2(Sigma #349887) to 100 nL inhibitor in 100% DMSO in a 384 well Perkin Elmer Optiplate. Enzyme and compound were preincubated for ten minutes at rt.After the ten minute preincubation, 25 μL of an Amplex Red mixture containing 200 μM Amplex Red and 10 mM H2O2 was added to the plate. Kinetic determinations were carried out immediately on a Perkin Elmer Envision (15 minute kinetic read, Ex: 535 nm, Em: 590 nm).IC50 values were calculated by determining the slope of the linear portion of the kinetic trace (180-540 secs), and using that calculated slope to determine % inhibition occurring at each concentration of inhibitor using the following equation:Y = A + B - A 1 + ( C / x ) Dwhere A=minimal Y value (activity level of inhibited sample), B=maximal Y value (activity level of uninhibited sample), C=Log IC50, D=Hill Slope, x=concentration of inhibitor.
- MPO Peroxidation Assay (Amplex Red Assay) MPO peroxidation activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Amplex Red (Invitrogen catalog # A12222) which can be oxidized to the highly fluorescent resorufin. Amplex Red is oxidized by the peroxidase action of MPO to resorufin. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 40 nM H2O2(Sigma #349887) to 100 nL inhibitor in 100% DMSO in a 384 well Perkin Elmer Optiplate. Enzyme and compound were preincubated for ten minutes at room temperature.After the ten minute preincubation, 25 μL of an Amplex Red mixture containing 200 μM Amplex Red and 10 mM H2O2 was added to the plate. Kinetic determinations were carried out immediately on a Perkin Elmer Envision (15 minute kinetic read, Ex: 535 nm, Em: 590 nm).IC50 values were calculated by determining the slope of the linear portion of the kinetic trace (180-540 secs), and using that calculated slope to determine % inhibition occurring at each concentration of inhibitor using the following equation:Y = A + B - A 1 + ( C / x ) D where A=minimal Y value (activity level of inhibited sample), B=maximal Y value (activity level of uninhibited sample), C=Log IC50, D=Hill Slope, x=concentration of inhibitor.
- In Vitro Measurements of porcine D-Amino Acid Oxidase (DAAO) Activities The pkDAAO (porcine kidney DAAO) activity was measured by using D-Proine as a substrate to produce hydrogen peroxide (H2O2). The produced H2O2 would be oxidized by peroxidase, and the produced free radicals would further react with 1,2-Phenylenediamine (OPD) reagent. The reaction product had an absorbance on 450 nm. The OD450 would be measured to represent the activity of pkDAAO. All compounds were dissolved in DMSO. Each compound was diluted with DMSO in 3 or 4-fold serial dilution to create a 9-point dose response curve. Each sample was added in triplicate, 10 μL/well, into 96-well assay microplate. Positive control wells were added with 10 μL of DMSO. The diluted compounds were incubated with pkDAAO in dark for 10 minutes and then reacted with D-Proline. The final reaction mixture was composed of 0.01 U/mL pkDAAO, 0.03% OPD, 25 U/mL HRP and 40 mM D-Proline in PBS. The reaction plates were then incubated in the dark at room temperature. The OD450 absorbance readout was detected at 0 and 20 minute by Molecular Device Spectra Max Plus reader. The percentage of inhibition values for each well were calculated with the following equation:The percentage of inhibition=(OD450sample, 20 min−OD450sample, 0 min)/(OD450DMSO, 20 min−OD450DMSO, 0 min)×100%The nonlinear curve fitting model in GraphPad Prism 5 was used to calculate IC50 value for each compound.
- Evaluation of LSD1 Enzyme Activity The purpose of this assay was to detect the inhibitory activity of the compounds against LSD1 in vitro. The enzyme used in this assay was human LSD1 and the standard substrate was histone H3K4me peptide (20 M); the activity of the compounds was determined by the enzyme fluorescence coupling method using a combination of horseradish peroxidase (HRP) and Amplex Red to detect the H2O2 generated after the reaction. The IC50 values of the compounds were measured at 10 concentrations after 3 times dilution from 10 μm. Before the compound was added to the substrate to start the reaction, enzyme and substrate were incubated for 30 minutes. Fluorescence detector: EnVision, excitation wavelength: Ex/Em=530/590 nM.
- In Vitro Measurements of Human D-Amino Acid Oxidase (hDAAO) Activity Assay The hDAAO inhibitory activities were measured by using D-Serine as a substrate to produce H2O2. The produced H2O2 would be oxidized by peroxidase, and the produced free radicals would further react with Amplex Red reagent to emit fluorescence. The intensity of fluorescence at 590 nm would be measured to represent the activity of hDAAO. All compounds were dissolved in DMSO. Each compound was diluted with DMSO in 3-fold serial dilution to create a dose response curve. Each sample was added in triplicate, 1 L/well, into 96-well black plates. Positive control wells were added with 1 μL of DMSO. Then 49 μL of assay buffer (100 mM Tris-HCl, pH 8.5) containing 1.2 ng/mL hDAAO, 900 nM FAD, 0.2 units/mL HRP, and 100 μM Amplex Red was added to each well of the plate using a multichannel pipette. Next, 50 μL of 100 mM D-Serine in assay buffer was added. The reaction plates were then incubated in the dark at room temperature. The fluorescence readout was detected at 0 and 20 mins by Molecular Device Gemini EM fluorescence reader using the following settings: excitation filter 530 nm, and emission filter 590 nm. The percentage of inhibition values for each well was calculated with the following equation:The percentage of inhibition=(fluorescence sample, 20 min−fluorescence sample, 0 min)/(fluorescence DMSO, 20 min−fluorescence DMSO, 0 min)×100%
- Enzyme Activity Assay The purpose of this test is to test the in vitro inhibitory activities of the compounds against LSD1. The enzyme used in this experiment was human LSD1, and the standard substrate was histone H3(1-21)K4me2 peptide (10 μM). HCI-2509 (SP2509) was used as reference compound, and the fluorescence coupling enzyme assay was employed. The production of FAD-dependent H2O2 as a result of demethylase activity of LSD1 was measured by coupling with HRP and Amplex Red. Compounds as well as control compound HCl-2509 were tested in 10-dose IC50 mode with a 3-fold serial dilution in duplicate starting at 10 μm. All compounds were pre-incubated 30 mins with enzyme before added substrate to start reaction. Fluorescence measurement: Ex/Em=535/590 by EnVision.
- Evaluation of Enzyme Activity Table 1: The purpose of the assay was to test the in vitro inhibitory activity of the compounds against LSD1. The enzyme used in the assay was human LSD1, and the standard substrate was histone H3K4me peptide (20 μM). The activity of the compounds was determined by the enzyme-coupling fluorescent method by the combined detection of H2O2 generated after the reaction of LSD1 by horseradish peroxidase (HRP) and the fluorescent reagent Amplex Red. Starting from 10 μM, the compounds were 3-fold diluted to detect the IC50 values of the compounds at 10 concentrations. The enzyme and substrate were incubated for 30 minutes before the compound was added to the substrate to start the reaction. Fluorescence detector: EnVision, excitation wavelength: Ex/Em=530/590 nM.
- ROS Inhibiting Drug A high-throughput screen was performed to find molecules that inhibit ROS production by neutrophils. Extracted human neutrophils were purified and kept in culture. The cells were then exposed to various drugs and ROS production was monitored over time. Compounds that also scavenged hydrogen peroxide (H2O2) and/or lowered neutrophil ATP levels (reflecting toxicity) were removed. The top hits from the screen were selected for further analysis.160 basal hits were tested for their ability to inhibit neutrophil ROS production. 64 molecules were able to inhibit ROS production in the presence of PMA activation. 67 molecules were able to inhibit ROS production in the presence of N-Formylmethionine-leucyl-phenylalanine (fMLP). Of those 47 molecules were able to inhibit ROS production by both stimulation methods.
- In Vitro Measurements of human D-Amino Acid Oxidase (DAAO) Activities The hDAAO (human DAAO) activity was measured by using D-serine as a substrate to produce H2O2. The produced H2O2 would be oxidized by peroxidase, and the produced free radicals would further react with Amplex Red reagent to emit fluorescence. The intensity of fluorescence at 590 nm would be measured to represent the activity of hDAAO. All compounds were dissolved in DMSO. Each compound was diluted with DMSO in 3-fold serial dilution to create a 9-point dose response curve. Each sample was added in triplicate, 1 μL/well, into 96-well black plates. Positive control wells were added with 1 μL of DMSO. Then 49 μL of assay buffer (100 mM Tris-HCl, pH 8.5) containing 1.2 ng/mL hDAAO, 900 nM FAD, 0.2 units/mL HRP, and 100 μM Amplex Red was added to each well of the plate using a multichannel pipette. Next, 50 μL of 100 mM D-Serine in assay buffer was added. The reaction plates were then incubated in the dark at room temperature. The fluorescence readout was detected at 0 and 20 minute by Molecular Device Gemini EM fluorescence reader using the following settings: excitation filter 530 nm, and emission filter 590 nm. The percentage of inhibition values for each well was calculated with the following equation:The percentage of inhibition=(fluorescencesample, 20 min−fluorescencesample, 0 min)/(fluorescenceDMSO, 20 min−fluorescenceDMSO, 0 min)×100%The nonlinear curve fitting model in GraphPad Prism 5 was used to calculate IC50 value for each compound.
- Enzyme Assay The functional activity of compounds inhibiting the DAAO enzyme was determined by utilizing the co-product of the catalysis of D-Serine, H2O2, which can be quantitatively measured using the Amplex (trade mark) Red (Invitrogen) detection. Amplex Red reagent is a colorless substrate that reacts with hydrogen peroxide (H2O2) with a 1:1 stoichiometry to produce highly fluorescent resorufin (excitation/emission maxima=570/585 nm). The changes in fluorescence were monitored by a fluorescence plate reader, Envision (Perkin Elmer) and increases in DAAO activity were readily detected upon addition of D-Serine and suppression of this response observed with the application of test compounds.Human DAAO enzyme was supplied by the Takeda Pharmaceutical Company (Osaka) and each batch was tested and used at concentrations giving comparable levels of activity. The Km of D-Serine was measured for each enzyme batch to maintain consistency; this Km was used in subsequent assays.On the day of the assay compounds were serially diluted in DMSO before being diluted 1:20 with assay buffer (20 mM Tris ph 7.4). A 5 μl portion of assay buffer was added to the wells of a 384 clear base black-walled plate (Corning), 5 μl of diluted compound was then added via automated plate-to-plate transfer using the Bravo liquid handler (Agilent technologies) followed by 5 μl of human DAAO enzyme, and then 5 μl D-Serine 50 mM was added to all but the negative control wells (final concentration of 10 mM). Finally 5 μl Amplex red reagent (Invitrogen) was added to all wells as per manufacturer's protocol. The plate was incubated for 60 minutes in the dark at 25° C. and the fluorescence in each well was measured in the Envision plate reader.
- In-vitro Monoamine Oxidase Inhibition Assay The assay was performed in a polystyrene 96-well plate having flat bottom containing 200 μL of the total reaction mixture. For each assay, mixture was composed of 136 μL of 50 mM phosphate buffer (pH 7.4), 2 μL of test compound(0.1 mM) and 45 μL of enzyme pre-incubated at 37 °C for 10 min. The enzymatic reaction was initiated by the addition of 5 μL of the substrate (p-tyramine 3 mM) and 12 μL of Amplex Red reagent and further incubated at 37 °C for 10 min. Consequently the production of H2O2 and resorufin was measured using microplate fluorescence reader (FLx 800, Bio-Tek Instruments, Inc., Winooski, USA) based on the fluorescence produced at excitation and emission wavelength of 544 nm and 590 nm, respectively. For all the test compounds, assay was performed in triplicate.
- Amplex Red Peroxide/Peroxidase-Coupled Assay The compounds of the invention can be tested for their ability to inhibit LSD1. The ability of the compounds of the invention to inhibit LSD1 can be tested as follows. Human recombinant LSD1 protein was purchased from BPS Bioscience Inc. In order to monitor LSD1 enzymatic activity and/or its inhibition rate by our inhibitor(s) of interest, di-methylated H3-K4 peptide (Millipore) was chosen as a substrate. The demethylase activity was estimated, under aerobic conditions, by measuring the release of H2O2 produced during the catalytic process, using the Amplex Red peroxide/peroxidase-coupled assay kit (Invitrogen).Briefly, a fixed amount of LSD1 was incubated on ice for 15 minutes, in the absence and/or in the presence of various concentrations of inhibitor (from 0 to 75 uM, depending on the inhibitor strength). Tranylcypromine (Biomol International) was used as a control for inhibition. Within the experiment, each concentration of inhibitor was tested in triplicate.
- DAAO in Vitro Activity Assay Inhibitory effect of compounds was determined in a cell free fluorescence assay. The H2O2 generated from the degradation of D-serine was linked to oxidation of Amplex Red in the presence of horseradish peroxidase (HRP). Inhibitor compounds are diluted in half log increments to create an 11-point dose response curve. Each dilution is spotted in duplicate into black 384-well plates. The assay buffer containing DAAO, flavin adenine dinucleotide, horseradish peroxidase, and Amplex Red were added to each well of the plate using a Titertek MultiDrop-384 reagent addition device. Next, assay buffer containing D-serine was added using the MultiDrop. The reaction was then incubated in the dark for10-30 min before reading the plates on a Perkin-Elmer Envision 2103 multilabel reader using the following settings: 10 flashes of the flash lamp, excitation filter 530 nm, emission filter 590 nm. The nonlinear curve fitting was used to calculate an IC50 value for each compound.
- Inhibition Assay KDM1A inhibition assay: a multistep enzymatic reaction in which the enzyme first produces H2O2 during the demethylation of lysine 4 in a 21 AA H3K4me2 N-terminal peptide. KDM1A chemoprobes were pre-incubated for 15 min with human recombinant KDM1A enzyme (BPS Bioscience, Ref. 50100) on ice in the assay buffer (50 mM sodium phosphate pH 7.4). The enzymatic reaction was initiated by the addition of KM dimethylH3K4 peptide substrate (Anaspec, Ref. 63677). After 30 min of incubation at 37° C. Amplex Red reagent and the horseradish peroxidase (HRP) solution were added according to the recommendations of the supplier (Invitrogen) and left to incubate for 5 min at room temperature in the dark. Conversion of the Amplex Red reagent to resorufin, was monitored by fluorescence (λex=540 nm, λem=590 nm) using a microplate reader (Infinite F200 Tecan). Signals were corrected for background and the IC50 value was calculated with GraphPad Prism Software.
- LSD1 Histone Demethylase Assay The primary assay for compound inhibitory activity was the LSD1 Inhibitor Screening Assay Kit (Cayman Chemical Company, Ann Arbor, Mich.; Cayman Chemical Item Number 700120). Briefly, test compounds were diluted to 20× the desired test concentration in 100% DMSO and 2.5 μL of the diluted drug sample was added to a black 384-well plate. The LSD1 enzyme stock was diluted 17-fold with assay buffer and 40 μM of the diluted LSD1 enzyme was added to the appropriate wells. The reaction mixture comprised horseradish peroxidase, dimethyl K4 peptide (corresponding to the first 21 amino acids of the N-terminal tail of histone H3), and 10-acetyl-3,7-dihydroxyphenoxazine was then added to wells. Generation of resorufin (generated by reacting with H2O2 produced in the reaction) was analyzed on an Envision microplate reader with an excitation wavelength of 530 nm and an emission wavelength of 595 nm.
- Inhibition of Histone Demethylase Activity Inhibition of LSD activity can be determined by a variety of both in vitro and in vivo methods known to one skilled in the art. For example, enzymatic activity can be determined in in vitro enzyme assay systems. In various embodiments, the enzymatic activity of LSD1 can be determined in a spectrophometric assay. Briefly, the assay is based on the multistep enzymatic reaction in which LSD1 first produces H2O2 during the demethylation of lysine 4 on a peptide corresponding to the first 21 amino acids of the N-terminal tail of histone H3. In the presence of horseradish peroxidase, the H2O2 produced reacts with ADHP to produce the highly fluorescent compound resorufin that can be analyzed with an excitation wavelength of 530-540 nm and an emission wavelength of 585-595 nm. The assay requires a source of LSD1 enzyme, either purified from natural sources (e.g. a tissue or cultured cells), isolated as a recombinantly expressed protein, or as a unpurified protein in whole cell extracts. In one embodiment, the disclosed compounds exhibit inhibition of LSD protein activity with an IC50 in an EMSA assay of less than about 300 mM, less than about 100 mM, less than about 50 mM, less than about 10 mM, less than about 1 mM, less than about 500 nM, or of less than about 100 nM. In another embodiment, the disclosed compounds exhibit inhibition of LSD1 protein activity with an IC50 in an EMSA assay of less than about 300 mM, less than about 100 mM, less than about 50 mM, less than about 10 mM, less than about 1 mM, less than about 500 nM, or of less than about 100 nM. In another embodiment, the disclosed compounds exhibit inhibition of LSD2 protein activity with an IC50 in an EMSA assay of less than about 300 mM, less than about 100 mM, less than about 50 mM, less than about 10 mM, less than about 1 mM, less than about 500 nM, or of less than about 100 nM.
- Cell Based Assay As a means of assessing the activation of PI3K γ in response to stimuli, the phosphorylation status of the protein, Akt, a downstream product of PI3K γ signalling, was determined following stimulation with MCP-1.U937 cells were differentiated to macrophage-type cells by incubation with PMA (100 ng/mL) for 48 to 72 hr. Cells were then pre-incubated with either the test compound or vehicle for 2 hr and were then stimulated briefly with MCP-1 (10 nM, 1 min) and the reaction stopped by replacing the media with 4% formaldehyde solution. Endogenous peroxide activity and formaldehyde were inactivated by incubating with quenching buffer (0.1% sodium azide, 1% H2O2 in PBS with 0.1% Triton X-100) for 20 min. The cells were washed with buffer (PBS containing 0.1% Triton X-100) and were incubated with blocking solution (1% BSA in PBS) for 1 hr and were then re-washed with buffer and incubated overnight with either anti-pAkt antibody or anti-pan-Akt antibody.
- In vitro MKP-1 Phosphatase Dose Response Active/Probe Assessment Assay - Effects of Catalase The MKP-1 dose response Active/Probe assessment-Catalase assay has been developed to evaluate the effects of adding 100 U/mL of Catalase on the MKP-1 inhibition of actives identified in the MH-76391 In vitro MKP-1 HTS assay AID #374, and subsequently confirmed in the HTS dose response confirmation assay AID #551. Protein tyrosine phosphatases have an active site cysteine that is very susceptible to inactivation by oxidation. In addition, a number of compounds such as quinone-like compounds are capable of generating reactive oxygen species via redox cycling in the presence of DTT. Adding Catalase to inactivate hydrogen peroxide (H2O2)does not affect the activity of MKP-1 in the assay but can reverse the inhibition of some inhibitors or significantly increase their IC50 values.The MKP-1 Phosphatase Dose Response Active/Probe Assessment Assay - Effects of Catalase has been Developed and Run at the University of Pittsburgh Molecular Screening Center (PMLSC) part of the Molecular Library S
- Inhibition Assay Procedure: 48 Ml 1xReaction Buffer was initially added to each compound test well in the 96-well black plate arranged, followed by addition of 2 Ml 100xcompound solution; the test for each concentration was performed in duplicate. To the positive control well, 2 Ml DMSO+48 Ml 1xReaction Buffer were added; while 100 Ml 20 Mm H2O2 working solution was directly added to the positive validation well. To the negative control well, 2 Ml DMSO+98 Ml 1xReaction Buffer were added, and each test was performed in duplicate. 50 Ml 4xAchE application solution was added to each of the compound test wells and the positive control wells. 100 Ml 2xworking solution was added to each of all the wells and mixed until homogenous. The enzymatic reaction was started with the volume of the overall reaction system reaching 200 Ml, which resulted in the final concentrations of the compound solution of 10 umol/L, 2 umol/L, 0.4 umol/L, 0.08 umol/L, 0.016 umol/L, 0.0032 umol/L and 0.064 umol/L.
- Inhibitory Activity The pharmacological activity of compounds disclosed herein was tested in the following screen (Test A) in which the compounds were tested in the presence of ascorbate, which reacts with MPO-derived hypochlorous acid (HOCl) to form dehydro-ascorbate. The loss of ascorbate is followed by measuring absorbance at 260 nm.Assay buffer: 100 μM diethyl triamine pentaacetic acid (DTPA) in buffer consisting of 10 mM Na2HPO4/NaH2PO4, 3 mM KCl in 140 mM NaCl, pH 7.4.Enzyme solution: MPO purified from the human cell line HL60, 1.38 nM (final concentration 0.7 nM) and L-ascorbate, 100 μM (final concentration 50 μM) in Assay bufferSubstrate solution: H2O2, 98 μM (final concentration 49 μM) Forty μL of the enzyme solution was added to 0.6 μL compound serially diluted in DMSO. Absorbance was measured at 260 nm to obtain a compound blank value. After an additional 10 min, 40 μL of the substrate solution was added and the absorbance at 260 nm was recorded between 4 and 40 min to obtain kinetic readings of enzyme activity.
- MPO Chlorination Assay (APF Assay) MPO chlorination activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Aminophenyl fluorescein (APF, Invitrogen Cat. #A36003). APF is cleaved by ( OCl) to yield the fluorescent compound fluorescein. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 120 mM NaCl to 100 nL inhibitor in 100% DMSO in a 384 well, non-binding surface clear bottom plate (Corning #3655). Enzyme, inhibitor, and chloride were preincubated for ten minutes at room temperature.After the ten minute preincubation, 25 μL of an APF mixture containing 10 mM APF, 120 mM NaCl and 10 μM H2O2 was added to the plate using the internal dispensing system of a Hammatsu FDSS 6000. Kinetic determinations were carried out immediately on the FDSS 6000 (3 minute kinetic read, 1 read every second, ex: 485 nm, em: 535 nm). IC50 values for inhibitors were calculated by taking the slope of the linear portion of the kinetic measurement (20 seconds to 80-120 secs).
- In Vitro DAAO Enzyme Assay The functional activity of compounds inhibiting the DAAO enzyme was determined by utilizing the co-product of the catalysis of D-Serine, H2O2 which can be quantitatively measured using the Amplex (trade mark) Red (Invitrogen) detection. Amplex Red reagent is a colorless substrate that reacts with hydrogen peroxide (H2O2) with a 1:1 stoichiometry in the presence of hydrogen peroxide to produce highly fluorescent resorufin (excitation/emission maxima=570/585 nm). The changes in fluorescence were monitored by a fluorescence plate reader, Envision (Perkin Elmer) and increases in DAAO activity were readily detected upon addition of D-Serine and suppression of this response observed with the application of test compounds.Human DAAO enzyme was supplied by the Takeda Pharmaceutical Company (Osaka) and each batch was tested and used at concentrations giving comparable levels of activity. The Km of D-Serine was measured for each enzyme batch to maintain consistency; this Km was used in subsequent assays.On the day of the assay compounds were serially diluted in DMSO before being diluted 1:20 with assay buffer (20 mM Tris ph 7.4). A 5 μl portion of assay buffer was added to the wells of a 384 clear base black-walled plate (Corning), 5 μl of diluted compound was then added via automated plate to plate transfer using the Bravo liquid handler (Agilent technologies) followed by 5 μl of human DAAO enzyme and then 5 μl D-Serine 50 mM was added to all but the negative control wells (final concentration of 10 mM). Finally 5 μl Amplex red reagent (Invitrogen) was added to all wells as per manufacturer's protocol. The plate was incubated for 60 minutes in the dark at 25° C. and the fluorescence in each well was measured in the Envision plate reader.The IC50 values for compounds were determined from ten point half log scale dose-response studies and represent the concentration of compound required to prevent 50% inhibition of DAAO activity in the presence of 10 mM D-Serine. Concentration response curves were generated using the average of duplicate wells for each data point and analyzed using non-linear regression and four parameter curve fit.
- In Vitro DAAO Enzyme Assay The functional activity of compounds inhibiting the DAAO enzyme was determined by utilizing the co-product of the catalysis of D-Serine, H2O2 which can be quantitatively measured using the Amplex Red (Invitrogen) detection. Amplex Red reagent is a colorless substrate that reacts with hydrogen peroxide (H2O2) with a 1:1 stoichiometry in the presence of hydrogen peroxide to produce highly fluorescent resorufin (excitationemission maxima=570/585 nm). The changes in fluorescence were monitored by a fluorescence plate reader, Envision (Perkin Elmer) and increases in DAAO activity were readily detected upon addition of D-Serine and suppression of this response observed with the application of test compounds.Human DAAO Enzyme was supplied by the Takeda Pharmaceutical Company (Osaka) and each batch was tested and used at concentrations giving comparable levels of activity. The Km of D-Serine was measured for each enzyme batch to maintain consistency; this Km was used in subsequent assays.On the day of the assay compounds were serially diluted in DMSO before being diluted 1:20 with assay buffer (20 mM Tris ph 7.4). A 5 μl portion of assay buffer was added to the wells of a 384 clear base black walled plate (Corning), 5 μl of diluted compound was then added via automated plate to plate transfer using the Bravo liquid handler (Agilent technologies) followed by 5 μl of human DAAO enzyme and then 5 μl D-Serine 50 mM was added to all but the negative control wells (final concentration of 10 mM). Finally 5 μl Amplex red reagent (Invitrogen) was added to all wells as per manufacturer's protocol. The plate was incubated for 60 minutes in the dark at 25° C. and the fluorescence in each well was measured in the Envision plate reader.The IC50 values for compounds were determined from ten point half log scale dose-response studies and represent the concentration of compound required to prevent 50% inhibition of DAAO activity in the presence of 10 mM D-Serine. Concentration response curves were generated using the average of duplicate wells for each data point and analyzed using nonlinear regression and four parameter curve fit.
- In vitro MKP-3 Phosphatase Dose Response Active/Probe Assessment Assay - Effects of Catalase The MKP-3 dose response Active/Probe assessment-Catalase assay has been developed to evaluate the effects of adding 100 U/mL of Catalase on the MKP-3 inhibition of actives identified in the MKP-3 HTS run at (Burham Institute) SDCCG center AID 425 and the MKP-1 HTS run at the PMLSC AID 374, and subsequently confirmed in the MKP-3 & MKP-1 HTS dose response confirmation assays AID's 553 & 551. Protein tyrosine phosphatases have an active site cysteine that is very susceptible to inactivation by oxidation. In addition, a number of compounds such as quinone-like compounds are capable of generating reactive oxygen species via redox cycling in the presence of DTT. Adding Catalase to inactivate hydrogen peroxide (H2O2)does not affect the activity of MKP-3 in the assay but can reverse the inhibition of some inhibitors or significantly increase their IC50 values. The MKP-3 Phosphatase Dose Response Active/Probe Assessment Assay - Effects of Catalase has been Developed and Run at the Univers
- Pharmacological Activity Assay MPO: The pharmacological activity of compounds disclosed herein was tested in the following screen (Test A) in which the compounds were tested in the presence of ascorbate, which reacts with MPO-derived hypochlorous acid (HOCl) to form dehydro-ascorbate. The loss of ascorbate is followed by measuring absorbance at 260 nm.Assay buffer: 100 μM diethyl triamine pentaacetic acid (DTPA) in buffer consisting of 10 mM Na2HPO4/NaH2PO4, 3 mM KCl in 140 mM NaCl, pH 7.4.Enzyme solution: MPO purified from the human cell line HL60, 1.38 nM (final concentration 0.7 nM) and L-ascorbate, 100 μM (final concentration 50 μM) in Assay bufferSubstrate solution: H2O2, 98 μM (final concentration 49 μM)Forty μL of the enzyme solution was added to 0.6 μL compound serially diluted in DMSO. Absorbance was measured at 260 nm to obtain a compound blank value. After an additional 10 min, 40 μL of the substrate solution was added and the absorbance at 260 nm was recorded between 4 and 40 min to obtain kinetic readings of enzyme activity. IC50 values of the compounds tested were obtained using recordings of absorbance at 260 nm 20 minutes after substrate addition and calculated using standard procedures.TPO: To detect thyroid peroxidase (TPO) inhibitory activity, the production of hypoiodous acid (HOI) was quantified. HOI was detected by reacting it with methionine, which is converted to dehydro-methionine, which in turn is detected by reacting it with excess iodide at acidic pH. The reaction converts I− to I3 − that has absorbance at 353 nm. In brief, 0.6 μL compound serially diluted in DMSO was added to 25 μL 50 nM baculovirus-expressed recombinant human TPO (obtained from RSR Ltd, Cardiff, UK) in assay buffer (100 mM Na2HPO4/NaH2PO4, pH 7.4), after which absorbance at 353 nm was read to obtain a blank value. The enzyme reaction was initiated by the addition of 25 μL of a mix consisting of 2 mM methionine, 20 μM NaI and 100 μM H2O2 in assay buffer, and stopped by the addition of 10 μL catalase, 0.25 mg/mL. After an additional 5 min, 25 μL 600 mM sulphuric acid followed by 25 μL 100 mM KI were added, and absorbance at 353 nm was read 5 min after this addition. IC50 values of the compounds tested were obtained using standard procedures.
- IL4I1 Enzymatic Assay Using this assay, the potency (EC50) of each compound was determined from a ten-point (1:3 serial dilution) titration curve using the following outlined procedure. To each well of a black flat-bottom Greiner (Cat #781076) 384 well-plate, 25 nL of compound (0.1% DMSO in final assay volume of 25 μL) was dispensed, followed by the addition of 12.5 μL of 1× assay buffer (50 mM Hepes 7.0 and 0.005% Tween20 (Sigma, Cat #P8341; low peroxide grade)) containing 2 nM of recombinant IL4I1 (R&D Systems, Cat #5684-AO-020). Plates were placed in an ambient temperature humidified chamber for a four-hour pre-incubation with compound. Subsequently, each reaction was initiated by the addition of 12.5 μL 1× assay buffer containing 2 mM of each aromatic amino acids (Phe/Tyr/Trp), 0.1 mM Amplex Red and 2 U/mL of HRP. The final reaction in each well of 25 μL consisted of 1 nM of IL4I1, 1 mM of each residues (Phe, Tyr and Trp), 0.05 mM Amplex Red and 1 U/mL of HRP. It should be noted that the concentrations of Amplex Red and HRP used here were in excess such that the conversion of H2O2 to resorufin product occurred
- DAAO Enzymatic Assay The DAAO enzymatic activity assay was modified according to the report of Oguri et al (Oguri, S., Screening of d-amino acid oxidase inhibitor by a new multi-assay method. Food chemistry 2007, 100 (2), 616). The DAAO activity was measured by using substrate D-alanine reaction produced hydrogen peroxide (H2O2) to further react with 3-(4-hydroxyphenyl) propionic acid (HPPA). The HPPA were oxidized by H2O2 and peroxidase to become the fluorogenic dimer which was measured to represent the activity of DAAO. The substrate of DAAO was prepared in 50 mM D-alanine (dissolved in 0.2 M Tris-HCl buffer, pH 8.3). A 100 ul of D-alanine solution was mixed with 4 ul (in 100%) dimethyl sulfoxide, DMSO) of different concentrations of drugs ranging from 31.36 nM, 94.08 nM, 0.28 uM, 0.85 uM, 2.54 uM, 7.62 uM, 22.86 uM, 68.59 uM, 0.21 mM, 0.62 mM, 1.85 mM, 5.56 mM, 16.67 mM, and 50.00 mM with a final DMSO concentrations of 0.167% in each reaction concentration. A 10 ul of D-alanine and drug mixture was incubated with 220 ul of Reaction Master Mix in black 96 well plate at 37° C. for 5 min. The Reaction Master Mix contained 110 ul of 5 U/mL porcine kidney DAAO (Sigma-Aldrich, USA) solution (dissolved with 0.2 M Tris-HCl buffer, pH 8.3), 1.1 mL of 15 U/mL peroxidase solution (dissolved with 0.2 M Tris-HCl buffer, pH 8.3), 1.1 mL of 20 mM HPPA solution (dissolved with 0.2 M Tris-HCl buffer, pH 8.3), and 2.2 ml of 2 M Tris-HCl buffer (pH 8.3) for 110 reaction assays.Fluorescence intensity (Fs) was measured at 405 nm by irradiation excitation at 320 nm. The higher is the DAAO enzymatic activity, the higher is the fluorescence intensity. The fluorometric inhibition indicator (Fi) was obtained from the following equation: Fi=(Fs−FDrug)/(FDMSO). Where the fluorescent drug blank (FDrug) were measured in the drug mixture solution (using 0.2 M Tris HCl buffer, pH 8.3, without D-alanine). A DMSO blank (FDMSO) was measured under a 100% DMSO solution. Although, in the assay for D-amino acid oxidase, FAD was generally included in the reaction mixture because this co-factor is easily dissociated from the holoenzyme, the present method was performed without FAD. The inhibitory effect of DAAO inhibitors was compared by using inhibitory concentrations which reduce 50% of DAAO activity (IC50). The IC50 value was calculated by GraphPad Prism, version 5 software (GraphPad Software, Inc., La Jolla, Calif.) (GraphPad Prism 5, GraphPad software Inc: California, USA) through nonlinear regression model.
- Pharmacological Activity Assay Methods for the determination of MPO inhibitory activity are disclosed in WO 02/090575. The pharmacological activity of compounds disclosed herein was tested in the following screen (Test A) in which the compounds were tested in the presence of ascorbate, which reacts with MPO-derived hypochlorous acid (HOCl) to form dehydro-ascorbate. The loss of ascorbate is followed by measuring absorbance at 260 nm.Assay buffer: 100 μM diethyl triamine pentaacetic acid (DTPA) in buffer consisting of 10 mM Na2HPO4/NaH2PO4, 3 mM KCl in 140 mM NaCl, pH 7.4.Enzyme solution: MPO purified from the human cell line HL60, 1.38 nM (final concentration 0.7 nM) and L-ascorbate, 100 μM (final concentration 50 μM) in Assay bufferSubstrate solution: H2O2, 98 μM (final concentration 49 μM)Forty μL of the enzyme solution was added to 0.6 μL compound serially diluted in DMSO. Absorbance was measured at 260 nm to obtain a compound blank value. After an additional 10 min, 40 μL of the substrate solution was added and the absorbance at 260 nm was recorded between 4 and 40 min to obtain kinetic readings of enzyme activity. IC50 values of the compounds tested were obtained using recordings of absorbance at 260 nm 20 minutes after substrate addition and calculated using standard procedures.To detect thyroid peroxidase (TPO) inhibitory activity, the production of hypoiodous acid (HOI) was quantified. HOI was detected by reacting it with methionine, which is converted to dehydro-methionine, which in turn is detected by reacting it with excess iodide at acidic pH. The reaction converts I− to I3 − that has absorbance at 353 nm. In brief, 0.6 μL compound serially diluted in DMSO was added to 25 μL 50 nM baculovirus-expressed recombinant human TPO (obtained from RSR Ltd, Cardiff, UK) in assay buffer (100 mM Na2HPO4/NaH2PO4, pH 7.4), after which absorbance at 353 nm was read to obtain a blank value. The enzyme reaction was initiated by the addition of 25 μL of a mix consisting of 2 mM methionine, 20 μM NaI and 100 μM H2O2 in assay buffer, and stopped by the addition of 10 μL catalase, 0.25 mg/mL. After an additional 5 min, 25 μL 600 mM sulphuric acid followed by 25 μL 100 mM KI were added, and absorbance at 353 nm was read 5 min after this addition. IC50 values of the compounds tested were obtained using standard procedures.
- In Vitro c-Met Kinase Enzyme Assay Briefly, histidine-tagged c-Met catalytic domain fusion protein was used for the assay. IC50 measurements were based on the degree of phosphorylation of poly Glu-Tyr that was coated (0.01 mg/per well) on 96-well microplates. The reaction was carried out in a 50 μL solution containing 50 mM HEPES (pH 7.5), 10 mM MnCl2, 10 mM MgCl2, 0.5 mM DTT, 100 μM Na3VO4, 5 μM ATP and serial dilutions of individual compounds. The reaction lasted for 25 minutes at 30° C. After the reaction was completed, the contents of the plates was discarded. Plates were then washed with TBS-T (250 μL/well, 5×) and then blocked with TBS-T containing 1% BSA for 2 hours. The contents of the plates was discarded, and 100 μL (per well) of peroxidase-labeled anti-phospho-tyrosine antibody diluted (1:60,000) in 1% BSA containing TBS-T were then added and incubated for 1 hour. Plates were washed with TBS-T (250 μL/well, 5×) and followed by the color reaction using 100 μL (1:1 mixture) of H2O2 and tetramethylbenzidine. The reaction was stopped in minutes with 100 μL of 2 N H2SO4. The optical density was measured immediately using a microplate reader at 450 nm with wavelength correction at 540 nm.
- Inhibition of Compounds on PARP1/7 Enzyme Activity (1) Pre-coating: Add 100 μL of a PBS buffer (10 mM NaH2PO4, 10 mM Na2HPO4, 150 mM NaCl, pH 7.4) containing 20 g/mL of histone to each well of a 96-well plate, and incubate at 4° C. overnight.(2) Add 30 μL of reaction buffer (50 mM Tris, 2 mM MgCl2, pH 8.0) containing 100 μM NAD+, 25 μM biotinylated NAD+, and 200 nM slDNA to each well.(3) Add 5 μL of the test substance or solvent to each well.(4) Add 20 μL of(PARP1 or PARP7 (50 ng/well), and incubate at 30° C. for 1 hour.(5) Add 50 μL of streptavidin-HRP to the reaction mixture, and incubate at 30° C. for 30 minutes.(6) Finally, add 100 μL of a citrate buffer containing H2O2 and luminol (0.1 M, pH 5.4), and measure the luminescent signal using a microplate reader (Molecular Devices SpectraMax M5).(7) Calculate the inhibition rate of PARP1 or PARP7 enzyme activity as [(control group−treatment group)/control group]×10000. Fit the dose-response data with standard dilutions using Prism GraphPad software and calculate the concentration required to achieve 5000 inhibition of PARP1 or PARP7 enzyme activity (IC50).
- 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
- In Vitro Enzyme Assay Briefly, histidine-tagged c-Met catalytic domain fusion protein (Invitrogen, # PV3143) was used for the assay. IC50 measurements were based on the degree of phosphorylation of poly Glu-Tyr (Sigma-Aldrich, # PO275) that was coated (0.01 mg/per well) on 96-well microplates (R&D systems, # DY990). The reaction was carried out in a 50 μL solution containing 50 mM HEPES (pH 7.5), 10 mM MnCl2, 10 mM MgCl2, 0.5 mM DTT, 100 μM Na3VO4, 5 μM ATP (Cell Signaling Technology, #9804) and serial dilutions of the test compound. The reaction lasted for 25 minutes at 30° C. After the reaction was completed, the contents of the plates were discarded. Plates were then washed with TBS-T (250 μL/well, 5×) and then blocked with TBS-T containing 1% BSA for 2 hours. The contents of the plates was discarded, and 100 μL (per well) of peroxidase-labeled anti-phospho-tyrosine antibody (Sigma, # A5964) diluted (1:60,000) in 1% BSA containing TBS-T were then added and incubated for 1 hour. Plates were washed with TBS-T (250 μL/well, 5×) and followed by the color reaction using 100 L (1:1 mixture) of H2O2 and tetramethylbenzidine (R&D Systems, # DY999). The reaction was stopped in minutes with 1004 of 2 N H2SO4. The optical density was measured immediately using a microplate reader at 450 nm with wavelength correction at 540 nm.
- Inhibitory Activity To detect thyroid peroxidase (TPO) inhibitory activity, the production of hypoiodous acid (HOI) was quantified. HOI was detected by reacting it with methionine, which is converted to dehydro-methionine, which in turn is detected by reacting it with excess iodide at acidic pH. The reaction converts I− to I3 − that has absorbance at 353 nm. In brief, 0.6 μL compound serially diluted in DMSO was added to 25 μL 50 nM baculovirus-expressed recombinant human TPO (obtained from RSR Ltd, Cardiff, UK) in assay buffer (100 mM Na2HPO4/NaH2PO4, pH 7.4), after which absorbance at 353 nm was read to obtain a blank value. The enzyme reaction was initiated by the addition of 25 μL of a mix consisting of 2 mM methionine, 20 μM NaI and 100 μM H2O2 in assay buffer, and stopped by the addition of 10 μL catalase, 0.25 mg/mL. After an additional 5 min, 25 μL 600 mM sulphuric acid followed by 25 μL 100 mM KI were added, and absorbance at 353 nm was read 5 min after this addition. IC50 values of the compounds tested were obtained using standard procedures.In general, the compounds disclosed herein, which were tested, had a surprisingly high selectivity for the MPO enzyme over the TPO enzyme within the range of 220-1600 for the ratio IC50 (TPO)/IC50 (MPO).
- Kinase Enzyme Assays The compounds of the invention were screened in vitro for their ability to inhibit c-Met kinase activity. Briefly, histidine-tagged c-Met catalytic domain fusion protein (Invitrogen, # PV3143) was used for the assay. IC50 measurements were based on the degree of phosphorylation of poly Glu-Tyr (Sigma-Aldrich, # P0275) that was coated (0.01 mg/per well) on 96-well microplates (R&D systems, # DY990). The reaction was carried out in a 50 μL solution containing 50 mM HEPES (pH 7.5), 10 mM MnCl2, 10 mM MgCl2, 0.5 mM DTT, 100 μM Na3VO4, 5 μM ATP (Cell Signaling Technology, #9804) and serial dilutions of the test compound. The reaction lasted for 25 minutes at 30° C. After the reaction was completed, the contents of the plates were discarded. Plates were then washed with TBS-T (250 μL/well, 5×) and then blocked with TBS-T containing 1% BSA for 2 hours. The contents of the plates was discarded, and 100 μL (per well) of peroxidase-labeled anti-phospho-tyrosine antibody (Sigma, # A5964) diluted (1:60,000) in 1% BSA containing TBS-T were then added and incubated for 1 hour, Plates were washed with TBS-T (250 μL/well, 5×) and followed by the color reaction using 100 ML (1:1 mixture) of H2O2 and tetramethylbenzidine (R&D Systems, # DY999). The reaction was stopped in minutes with 100 ML of 2 N H2SO4. The optical density was measured immediately using a microplate reader at 450 nm with wavelength correction at 540 nm.
- MPO Chlorination (APF) Assay MPO chlorination activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Aminophenyl fluorescein (APF, Invitrogen catalog #A36003). APF is cleaved by ( OCl) to yield the fluorescent compound fluorescein. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 120 mM NaCl to 100 nL inhibitor in 100% DMSO in a 384 well, non-binding surface clear bottom plate (CORNING #3655). Enzyme, inhibitor, and chloride were preincubated for ten minutes at rt.After the ten minute preincubation, 25 μL of an APF mixture containing 10 mM APF, 120 mM NaCl and 10 μM H2O2 was added to the plate using the internal dispensing system of a Hammatsu FDSS 6000. Kinetic determinations were carried out immediately on the FDSS 6000 (3 minute kinetic read, 1 read every second, ex: 485 nm, em: 535 nm). IC50 values for inhibitors were calculated by taking the slope of the linear portion of the kinetic measurement (20 seconds to 80-120 secs).IC50 values were calculated by determining the slope of the linear portion of the kinetic trace (180-540 secs), and using that calculated slope to determine % inhibition occurring at each concentration of inhibitor using the following equation:Y = A + B - A 1 + ( C / x ) Dwhere A=minimal Y value (activity level of inhibited sample), B=maximal Y value (activity level of uninhibited sample), C=Log IC50, D=Hill Slope, x=concentration of inhibitor.
- MPO Chlorination Assay (APF Assay) MPO chlorination activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Aminophenyl fluorescein (APF, Invitrogen catalog #A36003). APF is cleaved by ( OCl) to yield the fluorescent compound fluorescein. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 120 mM NaCl to 100 nL inhibitor in 100% DMSO in a 384 well, non-binding surface clear bottom plate (CORNING #3655). Enzyme, inhibitor, and chloride were preincubated for ten minutes at room temperature.After the ten minute preincubation, 25 μL of an APF mixture containing 10 mM APF, 120 mM NaCl and 10 μM H2O2 was added to the plate using the internal dispensing system of a Hammatsu FDSS 6000. Kinetic determinations were carried out immediately on the FDSS 6000 (3 minute kinetic read, 1 read every second, ex: 485 nm, em: 535 nm). IC50 values for inhibitors were calculated by taking the slope of the linear portion of the kinetic measurement (20 seconds to 80-120 secs).IC50 values were calculated by determining the slope of the linear portion of the kinetic trace (180-540 secs), and using that calculated slope to determine % inhibition occurring at each concentration of inhibitor using the following equation:Y = A + B - A 1 + ( C / x ) D where A=minimal Y value (activity level of inhibited sample), B=maximal Y value (activity level of uninhibited sample), C=Log IC50, D=Hill Slope, x=concentration of inhibitor.
- Cell-based ELISA Assay The ELISA portion of the assay was performed in a black Maxisorp 96-well plate that was coated overnight at 4° C. with 100 uL/well of the cell lysate (1:10 dilution of the lysate with PBS containing protease inhibitors, phosphatase inhibitors, and PMSF). The following day the wells were washed 3 times with 300 uL/well of Wash buffer (Tris-buffered saline with 0.1% Tween 20). The wells were blocked with 100 ul/well Blocking buffer (Tris buffered saline w/0.05% Tween 20 and 2.5% Bovine serum albumin). Each well was then washed two times with 300 uL/well of wash buffer. The anti O-GlcNAc antibody RL-2 (Abeam, Cambridge, Mass.), diluted 1:1000 in blocking buffer, was added at 100 uL/well. The plate was sealed and incubated at 37° C. for 2 h with gentle shaking. The wells were then washed 3-times with 300 uL/well wash buffer. To detect the amount of RL-2 bound horse-radish peroxidase (HRP) conjugated goat anti-mouse secondary antibody (diluted 1:3000 in blocking buffer) was added at100 uL/well. The plate was incubated for 60 min at 37° C. with gentle shaking. Each well was then washed 3-times with 300 uL/well wash buffer. The detection reagent was added, 100 uL/well of Amplex Ultra RED reagent (prepared by adding 30 uL of 10 mM Amplex Ultra Red stock solution to 10 mL PBS with 18 uL 3% hydrogen peroxide, H2O2). The detection reaction was incubated for 15 minutes at room temperature and then read with excitation at 530 nm and emission at 590 nm.
- Cell-based ELISA The ELISA portion of the assay is performed in a black Maxisorp 96-well plate that is coated overnight at 4° C. with 100 uL/well of the cell lysate (1:10 dilution of the lysate with PBS containing protease inhibitors, phosphatase inhibitors, and PMSF). The following day the wells are washed 3 times with 300 uL/well of Wash buffer (Tris-buffered saline with 0.1% Tween 20). The wells are blocked with 100 uL/well Blocking buffer (Tris buffered saline w/0.05% Tween 20 and 2.5% Bovine serum albumin). Each well is then washed two times with 300 uL/well of wash buffer. The anti O-GlcNAc antibody RL-2 (Abcam, Cambridge, Mass.), diluted 1:1000 in blocking buffer, is added at 100 uL/well. The plate is sealed and incubated at 37° C. for 2 h with gentle shaking. The wells are then washed 3-times with 300 uL/well wash buffer. To detect the amount of RL-2 bound horse-radish peroxidase (HRP) conjugated goat anti-mouse secondary antibody (diluted 1:3000 in blocking buffer) is added at 100 uL/well. The plate is incubated for 60 min at 37° C. with gentle shaking. Each well is then washed 3-times with 300 uL/well wash buffer. The detection reagent is added, 100 uL/well of Amplex Ultra RED reagent (prepared by adding 30 ul of 10 mM Amplex Ultra Red stock solution to 10 mL PBS with 18 uL 3% hydrogen peroxide, H2O2). The detection reaction is incubated for 15 minutes at room temperature and then read with excitation at 530 nm and emission at 590 nm.
- In Vitro c-Met and VEGFR-2 Enzyme Assay Briefly, 20 μg/mL poly (Glu,Tyr) 4:1 (Sigma) was pre-coated in 96-well plates as a substrate. A 50 μL aliquot of 10 μmol/L ATP solution diluted in kinase reaction buffer (50 mmol/L HEPES [pH 7.4], 50 mmol/L MgCl2, 0.5 mmol/L MnCl2, 0.2 mmol/L Na3VO4, and 1 mmol/L DTT) was added to each well; 1 μL of various concentrations of indicated compounds diluted in 1% DMSO (v/v) (Sigma) was then added to each reaction well. DMSO (1%, v/v) was used as the negative control. The kinase reaction was initiated by the addition of purified tyrosine kinase proteins diluted in 49 μL of kinase reaction buffer. After incubation for 60 min at 37 °C, the plate was washed three times with phosphate-buffered saline (PBS) containing 0.1% Tween 20 (T-PBS). Anti-phosphotyrosine (PY99) antibody was then added. After a 30-min incubation at 37 °C, the plate was washed three times, and horseradishperoxidase-conjugated goat anti-mouse IgG was added. The plate was then incubated at 37 °C for 30 min and washed 3 times. A 100 μL aliquot of a solution containing 0.03% H2O2 and 2 mg/ml ophenylenediamine in 0.1 mol/L citrate buffer (pH 5.5) was added. The reaction was terminated by the addition of 50 μL of 2 mol/L H2SO4 as the color changed, and the plate was analyzed using a multi-well spectrophotometer (SpectraMAX 190, Molecular Devices) at 490 nm.
- In Vitro Inhibition of DAGL Briefly, membrane proteome (1 mg/ml, 20 μL) was prepared from HEK293T cells (transiently transfected with hDAGLα-FLAG or hDAGLα-S472A-FLAG, hDAGLβ-FLAG or hDAGLβ-S443A-FLAG) as described in Example 16. The proteome was incubated at room temperature with vehicle (DMSO) or compound in 0.5 μL DMSO for 30 min. The membrane proteome sample was subsequently treated for 30 min with HT-01 probe (1 μM) or FP-Rh probe (1 μM). The reactions were quenched with 10 μL 3× Laemmli sample buffer (final concentrations: 60 mM Tris-Cl pH 6.8, 2% (w/v) SDS, 10% (v/v) glycerol, 5% (v/v) (3-mercaptoethanol, 0.01% (v/v) bromophenol blue). The samples were directly loaded and resolved on SDS page gel (10% acrylamide). The gels were scanned using a ChemiDoc MP system (Cy3 settings, 605/50 filter).The resolved proteins were transferred from the gels to a polyvinyldifluoride membrane for Western Blotting using a Trans-Blot Turbo (BioRad). FLAG-tagged enzymes were stained using rabbit anti-FLAG as primary antibody, and goat-anti-rabbit HRP as secondary antibody. The blot was developed in the dark using a 10 mL luminal solution, 100 μL ECL enhancer and 3 μL H2O2. Chemiluminescence was visualized using a ChemiDoc XRS (BioRad).The percentage of DAGL activity remaining in the assayed samples was determined by measuring the integrated optical intensity of the fluorescent protein bands of the Western Blot using image lab 4.1. The relative intensity was compared to the vehicle (DMSO) treated proteins, which were set to 100%. IC50 values were determined by plotting a log(inhibitor) vs. normalized response (Variable slope) dose-response curve generated using Prism software (GraphPad).
- MPO Chlorination Assay (APF Assay) MPO chlorination activity was measured in 100 mM KPi (pH 7.4) by utilizing the non-fluorescent reagent Aminophenyl fluorescein (APF, Invitrogen Cat. #A36003). APF is cleaved by ( OCl) to yield the fluorescent compound fluorescein. Reactions were carried out in 50 μL total volume by adding a 25 μL mixture of 200 pM myeloperoxidase and 120 mM NaCl to 100 nL inhibitor in 100% DMSO in a 384 well, non-binding surface clear bottom plate (Corning #3655). Enzyme, inhibitor, and chloride were preincubated for ten minutes at rt.After the ten minute preincubation, 25 μL of an APF mixture containing 10 mM APF, 120 mM NaCl and 10 μM H2O2 was added to the plate using the internal dispensing system of a Hammatsu FDSS 6000. Kinetic determinations were carried out immediately on the FDSS 6000 (3 minute kinetic read, 1 read every second, ex: 485 nm, em: 535 nm). IC50 values for inhibitors were calculated by taking the slope of the linear portion of the kinetic measurement (20 seconds to 80-120 secs).IC50 values were calculated by determining the slope of the linear portion of the kinetic trace (180-540 secs), and using that calculated slope to determine % inhibition occurring at each concentration of inhibitor using the following equation:Y = A + B - A 1 + ( C / x ) Dwhere A=minimal Y value (activity level of inhibited sample), B=maximal Y value (activity level of uninhibited sample), C=Log IC50, D=Hill Slope, x=concentration of inhibitor.The exemplified Examples disclosed below were tested in the MPO peroxidation assay described above and found to have MPO inhibitory activity. A range of IC50 values of ≤10 μM (10000 nM) was observed.
- Binding of the M6P Analogs of the Invention with CI-M6PR 96-Well plates (Maxisorp Nunc) are incubated overnight at 4° C. with 200 μl of PMP (pentamannose 6-phosphate) at the concentration of 200 μg ml−1, in carbonate buffer (NaHCO3/Na2CO3 at 0.1M, pH 9.6). The following day, the solution containing the residual PMP is discarded and the wells are saturated, for 1 h at ambient temperature, with 360 μl of 1% gelatin (Type A from Porcine Skin) diluted in PBS (1.9 mM NaH2PO4, 8.1 mM Na2PO4 and 154 mM NaCl, pH 7.4). The wells are then rinsed five times with PBS to which 0.2% gelatin has been added. All the washes and also the dilutions are carried out in the solution of PBS to which 0.2% gelatin has been added. The M6P analogs to be tested at the various concentrations (from 10−2 to 10−7 M) are pre-incubated in the presence of pre-biotinylated CI-M6PR (M6PRb) (2.5 μg mol−1) for 20 min, then 200 μl of the mixture are incubated in the wells for 2 h, at ambient temperature. After three washes, the wells are incubated for 1 h with a streptavidin-peroxidase solution (250 μl per well; 3.10−8 M). After three more washes, 200 μl of a solution of OPD (o-phenylenediamine, 1 mg ml−1 in citrate buffer, pH 5.0, and 1 μl 30% H2O2.ml−1; Sigma Aldrich) are added. After incubation for 20 min in the dark at ambient temperature, the optical densities are measured at the wavelength of 450 nm.The affinities of the phosphonate disaccharide 18 and carboxylate disaccharide 24 of formula (I) of the invention were measured and compared with those of their respective monosaccharide homologs.The affinity denotes the binding capacity (in the case in point by means of a covalent bond) of the M6P analogs for CI-M6PR.
- Effect of Compound I on CSF1R Kinase Activity 1. ELISA Assay: The enzyme reaction substrate poly(Glu, Tyr)4:1 was diluted to 20 μg/mL with potassium-free PBS (10 mM sodium phosphate buffer, 150 mM NaCl, pH7.2-7.4). Plates were coated with the dilution, allowed to incubate at 37° C. for 12-16 h, washed with T-PBS (0.1% Tween-20 in potassium-free PBS), and dried for later use. An ATP solution (final concentration of 5 μM) diluted with a reaction buffer (50 mM HEPES pH 7.4, 50 mM MgCl2, 0.5 mM MnCl2, 0.2 mM Na3VO4, 1 mM DTT), a test compound or solvent control, and a recombinant CSF1R kinase were added sequentially to individual wells to initiate the reaction. After reaction at 37° C. for 1 hour, the plates were washed with T-PBS, and the antibody PY99 dilution was added. The plates were incubated on a shaker at 37° C. for 0.5 h, and then washed with T-PBS. A horseradish peroxidase-labeled goat anti-mouse secondary antibody dilution was added, and the plates were incubated at 37° C. for 0.5 h. After the plates were washed, an OPD developing solution (diluted with 0.1 M citric acid-sodium citrate buffer (pH=5.4) containing 0.03% H2O2) was added at 2 mg/mL and the plates were allowed to react in the dark at 25° C. for 1 to 10 minutes. Finally, 2 M H2SO4 was added to stop the reaction. The plates were read with an adjustable wavelength microplate reader at a wavelength of 490 nm. The inhibition rate was calculated as follows.InhibitionRate%=(1‐CompoundODvalue‐Enzyme‐freecontrolODvalue)SolventODvalue‐Enzyme‐freecontrolODvalue×100%The IC50 values were calculated by a four-parameter regression program in the software embedded in the microplate reader.
- Diamine oxidase (DAO) selectivity assay Promega ROS-Glo H2O2 Assay Kit, 50 ml. Cat No. G8821Inhibitors (Test compounds):10 mM stock diluted to 10, 3, 1, 0.3, 0.1, 0.03, 0.01, 0.003, 0.001, and 0.0003 mM in drug plate, resulting in a concentration of 100, 30, 10, 3, 1, 0.3, 0.1, 0.03, 0.01, and 0.003 uM in the assay.Positive Control (Aminoguanidine):1 mM stock diluted to 1 to 0.0001 and 0.00003 mM in drug plate, resulting in a concentration of 3 to 0.001 and 0.0003 uM in the assay.DAO:DAO batch is obtained from Sigma Enzyme is reconstituted in sodium phosphate buffer at 10 mg/mLAssay Plates: 96 well white polystyrene, flat bottom plates: Fisher, Cat No. DPS-134-050AProcedure:1. Dilute 400 ul DAO enzyme in 4 mL Assay Buffer (enough for one plate). Add 40 ul DAO enzyme to all wells (excluding G+H 12, assay buffer only)3. Add 0.5 μl test compound serial dilutions, in duplicate4. Add 0.5 μl serial dilutions of Aminoguanidine down column 11 and to E+F 125. Add 0.5 μl DMSO (100% activity control) to C+D 126. Cover plate and incubate for 20 minutes at room temp on a plate shaker7. Prepare Start Mix:Volume Reagent 1 x plate 2 x plate Final ConenAssay Buffer 2 ml 3 ml 8.5M Cadaverine 23 μl 34.5 μl 97.8 mMH2O2 Substrate (1:80) 25 μl 37.5 μl 125 μM8. Add 10 μl Start Mix to all wells9. Incubate for 60 min at room temp on a plate shaker10. Prepare Detection Reagent:VolumeReagent 1 x plate 2 x plateLuciferin 5 ml 10 mlD-cysteine (1:100) 50 μl 100 μlSignal Enhancer (1:100) 50 μl 100 μl11. Add 50 μl Detection Regent to each well EXCEPT No Luciferin controls (A+B 12, add 50PI assay buffer)12. Incubate for 20 min at room temp on a plate shaker, protected from light13. Measure luminescence using a plate reader (integration 500 ms)Values for the blank (no DAO controls) are subtracted from all samples.
- Enzyme Kinase Activity Assay The enzyme reaction substrate Poly(Glu,Tyr) 4:1 was diluted with PBS without potassium ion (10 mM sodium phosphate buffer, 150 mM NaCl, pH7.2-7.4) to 20 μg/mL, 125 μL/well to coat the enzyme plate, and reacted at 37° C. for 12-16 hours. After the liquid was removed from the wells, the plate was washed three times with 200 μL/well of T-PBS (PBS containing 0.1% Tween-20) for 5 minutes each. The enzyme plate was dried in a 37° C. oven for 1-2 hours.50 μL of the ATP solution diluted with the reaction buffer (50 mM HEPES pH 7.4, 50 mM MgCl2, 0.5 mM MnCl2, 0.2 mM Na3VO4, 1 mM DTT) was added into each well at a 5 μM final concentration. The compounds were diluted to the appropriate concentration in DMSO, 1 μL/well or containing the corresponding concentrations of DMSO (negative control wells). The reaction was initiated by addition of each kinase domain recombinant protein diluted with 49 μL of reaction buffer. Two control wells without ATP were set in each experiment. The reaction mixtures were placed on a shaker (100 rpm) to react at 37° C. for 1 hour. The plates were washed with T-PBS for three times. 100 μL/well of the primary antibody PY99 dilution was added, and reacted on a shaker (100 rpm) at 37° C. for 0.5 hour. The plates were washed with T-PBS for three times. 100 μL/well of the secondary anti-horseradish peroxidase-labeled goat anti-mouse IgG dilution was added, and reacted on a shaker at 37° C. for 0.5 hour. The plates were washed with T-PBS for three times. 100 μL/well of 2 mg/mL OPD developing solution (diluted with 0.1M citric acid-sodium citrate buffer containing 0.03% H2O2 (pH=5.4)), and reacted in dark for 1-10 minutes at 25° C. (Ultrasound is needed in OPD dissolution, and the developing solution should be prepared on the site). The reaction was quenched with 50 μL/well of 2M H2SO4, and read out at 490 nm using a tunable microplate microplate reader SPECTRA MAX 190.
- Immumoenzymatic Assay Solutions of the tested compounds in DMEM medium {DMEM) 1x; Source: Cellgro; Catalogue: 10-013-CV} were prepared immediately before use. Eleven serial three fold dilutions with variation of concentrations from 20 nM to 0.2 pM were prepared. In 4 hours after seeding, serial dilutions of the compounds were added to the cells (100 ul to each well). Final concentration of tested compounds was varied from 10 nM to 0.1 pM, and DMSO4 0.5%. If it was necessary, higher concentrations of the disclosed azoles were investigated. Each dilution of the compound was tested on two identical wells. Then the cells were incubated for three days at 37° C./5% CO2 and fixed by addition of acetone/methanol (1:1) mixture in amount of 250 ul/well. In 1 min the cells were washed 3 times with PBS (Phosphate Buffered Saline) solution. Then the cells were blocked by addition of 10% fetal calf serum in PBS solution in amount of 150 ul/well for 1 h at room temperature. Then, the cells were incubated with mouse monoclonal antibodies to cor-antigen HCV, don C7-50 (Source: Affinity BioReagents; Catalogue: MA1-080) (100 ul/well, working dilution 1:500 in 10% fetal calf serum in PBS solution) for 2 h at 37° C. The cells were washed 6 times with PBS/0.05% Tween 20 solution, then, they were incubated for 1 h with goat anti-mouse immunoglobulin antibodies (conjugated with horseradish peroxidase, 100 ul/well, working dilution 1:2500 in 10% fetal calf serum in PBS solution). The cells were washed 6 times with PBS/0.05% Tween 20 solution, once with PBS solution, after that substrate (1 tablet of o-phenylenediamine (oPD)+12 ml citrate/phosphate buffer+5 ul 30% H2O2) in amount of 100 ul/well was added. The plates were kept for 30 min in the dark at room temperature. The reaction was arrested by the addition of 2N H2SO4 in amount of 100 ul/well, and optical density (wavelength 490 nm) was measured by means of multiscan plate reader Victor3 V 1420 (Perkin Elmer). IC50 values (azole concentration, lowering the level of virus RNA-replicon on 50%) for every tested azole were calculated with the help of XLfit 4 program.
- In Vitro c-Met Kinase Enzyme Assay Compounds were screened in vitro for their ability to inhibit c-Met kinase activity. The IC50 values of compounds for the inhibition of c-Met kinase were determined as described in the literature with some modifications (Wang, X. et al, Mol. Cancer Ther. 2003, 2(11):1085-1092; Calic, M. et al., Croatica Chemical ACTA. 2005, 78(3):367-374). Briefly, histidine-tagged c-Met catalytic domain fusion protein (Invitrogen, #PV3143) was used for the assay. IC50 measurements were based on the degree of phosphorylation of poly Glu-Tyr (Sigma-Aldrich, #P0275) that was coated (0.01 mg/per well) on 96-well microplates (R&D systems, #DY990). The reaction was carried out in a 50 μL solution containing 50 mM HEPES (pH 7.5), 10 mM MnCl2, 10 mM MgCl2, 0.5 mM DTT, 100 μM Na3VO4, 5 μM ATP (Cell Signaling Technology, #9804) and serial dilutions of individual compounds. The reaction lasted for 25 minutes at 30° C. After the reaction was completed, the contents of the plates was discarded. Plates were then washed with TBS-T (250 μL/well, 5×) and then blocked with TBS-T containing 1% BSA for 2 hours. The contents of the plates was discarded, and 100 μL (per well) of peroxidase-labeled anti-phospho-tyrosine antibody (Sigma, #A5964) diluted (1:60,000) in 1% BSA containing TBS-T were then added and incubated for 1 hour. Plates were washed with TBS-T (250 mL/well, 5×) and followed by the color reaction using 100 μL (1:1 mixture) of H2O2 and tetramethylbenzidine (R&D Systems, #DY999). The reaction was stopped in minutes with 100 μL of 2 N H2SO4. The optical density was measured immediately using a microplate reader at 450 nm with wavelength correction at 540 nm. IC50 values were calculated with the GraphPad Prism software. The linear range (i.e., the time period over which the rate remained equivalent to the initial rate) was determined for the kinase and IC50 determinations were performed within this range.
- In Vitro c-Met Kinase Enzyme Assays The compounds of the invention were screened in vitro for their ability to inhibit c-Met kinase activity. The IC50 values for the inhibition of c-Met kinase were determined as described in the literature with some modifications (Wang, X. et al, Mol. Cancer Ther. 2003, 2(11):1085-1092; Calic, M. et al., Croatica Chemical ACTA. 2005, 78(3):367-374). Briefly, histidine-tagged c-Met catalytic domain fusion protein (Invitrogen, #PV3143) was used for the assay. IC50 measurements were based on the degree of phosphorylation of poly Glu-Tyr (Sigma-Aldrich, #P0275) that was coated (0.01 mg/per well) on 96-well microplates (R&D systems, #DY990). The reaction was carried out in a 50 μL solution containing 50 mM HEPES (pH 7.5), 10 mM MnCl2, 10 mM MgCl2, 0.5 mM DTT, 100 μM Na3VO4, 5 μM ATP (Cell Signaling Technology, #9804) and serial dilutions of the test compound. The reaction lasted for 25 minutes at 30° C. After the reaction was completed, the contents of the plates were discarded. Plates were then washed with TBS-T (250 μL/well, 5×) and then blocked with TBS-T containing 1% BSA for 2 hours. The contents of the plates was discarded, and 100 μL (per well) of peroxidase-labeled anti-phospho-tyrosine antibody (Sigma, #A5964) diluted (1:60,000) in 1% BSA containing TBS-T were then added and incubated for 1 hour. Plates were washed with TBS-T (250 μL/well, 5×) and followed by the color reaction using 100 μL (1:1 mixture) of H2O2 and tetramethylbenzidine (R&D Systems, #DY999). The reaction was stopped in minutes with 100 μL of 2 N H2SO4. The optical density was measured immediately using a microplate reader at 450 nm with wavelength correction at 540 nm. IC50 values were calculated with the GraphPad Prism software. The linear range (i.e., the time period over which the rate remained equivalent to the initial rate) was determined for the kinase and IC50 determinations were performed within this range.
- HTS Assay The conditions of the assay are as follows:Microplate type: 1536 Well Black Round Bottom Polystyrene Not Treated (Corning cat no. 3936)Total reaction volume: 5 μLMRE11 concentration in the reaction: 18 nMDNA substrate concentration in the reaction: 40 nMNumber of compounds to test: 257Inhibitor concentration range tested: 7 nM-50 μMMultiplicates: 3Concentration points: 13Dilution step: 2.1Each plate contains a series of high and low signal control wells, where no compound is added:High signal: MRE11+DNA substrateLow signal: DNA substrate onlyThese are used during data evaluation.Two Extra Assay Controls:1) To check whether unwinding of DNA by the compounds alone occurs.The DNA substrate [CY5+BBQ(650)] is mixed with the compounds with no protein present.This is done as a single measurement at 25 μM inhibitor concentration.2) To check whether the compounds are able to quench the CY5.The CY5 single stranded oligo is mixed with the compounds with no protein present. This is done as a single measurement at 25 μM inhibitor concentration.The layout of the plates is created by the in-house software (CZ-Openscreen Prague) and this information is transferred to the robotic HTS station.Assay Steps1) Prepare 50 mL of master mix:16.7 mL 5× reaction buffer (150 mM Bis Tris pH 7; 5 mM DTT)1042 μL 400 mM MnCl232.3 mL H2O2) Fill the plates with 3 μL of master mix per well using MultiDrop (Thermo Scientific)3) Transfer of compounds to the plates at the robotic station with the contactless Echo dispenser (Labcyte)4) Measurement of autofluorescence with the EnVision reader (PerkinElmer)5) Prepare 20 mL of 90 nM MRE11 in T+50 buffer (25 mM Tris-HCl pH7.5, 50 mM KCl 8.7% glycerol, 0.5 mM EDTA)6) Add 1 μL of 90 nM MRE11 to the corresponding wells using MultiDrop7) Preincubation at RT for 30 min8) Prepare 20 mL of a 200 nM solution of 5′ overhang DNA substrate: 480 μL 6 μM DNA+19.52 mL H2O9) Prepare 4 mL of a 200 nM solution of the single stranded DNA (oligo 1): 8 μL 100 μM DNA+4 mL H2O10) Add 1 μL of each 200 nM DNA solution to the corresponding wells with the MultiDrop11) Fluorescence measurement with the EnVision reader every 45 minutesFluorescence readout: CY5λex/em=620/665 nmAnalysis
- In Vitro c-Met Kinase Enzyme Assays Compounds were screened in vitro for their ability to inhibit c-Met kinase activity. The IC50 values of compounds for the inhibition of c-Met kinase were determined as described in the literature with some modifications (Wang, X. et al, Mol. Cancer Ther. 2003, 2(11): 1085-1092; Calic, M. et al., Croatica Chemical ACTA. 2005, 78(3):367-374). Briefly, histidine-tagged c-Met catalytic domain fusion protein (Invitrogen, #PV3143) was used for the assay. IC50 measurements were based on the degree of phosphorylation of poly Glu-Tyr (Sigma-Aldrich, #P0275) that was coated (0.01 mg/per well) on 96-well microplates (R&D systems, #DY990). The reaction was carried out in a 50 μL solution containing 50 mM HEPES (pH 7.5), 10 mM MnCl2, 10 mM MgCl2, 0.5 mM DTT, 100 μM Na3VO4, 5 μM ATP (Cell Signaling Technology, #9804) and serial dilutions of individual compounds. The reaction lasted for 25 minutes at 30° C. After the reaction was completed, the contents of the plates was discarded. Plates were then washed with TBS-T (250 μL/well, 5×) and then blocked with TBS-T containing 1% BSA for 2 hours. The contents of the plates was discarded, and 100 μL (per well) of peroxidase-labeled anti-phospho-tyrosine antibody (Sigma, #A5964) diluted (1:60,000) in 1% BSA containing TBS-T were then added and incubated for 1 hour. Plates were washed with TBS-T (250 μL/well, 5×) and followed by the color reaction using 100 μL (1:1 mixture) of H2O2 and tetramethylbenzidine (R&D Systems, #DY999). The reaction was stopped in minutes with 100 μL of 2 N H2SO4. The optical density was measured immediately using a microplate reader at 450 nm with wavelength correction at 540 nm. IC50 values were calculated with the GraphPad Prism software. The linear range (i.e., the time period over which the rate remained equivalent to the initial rate) was determined for the kinase and IC50 determinations were performed within this range. Wang, X., et al. Potent and selective inhibitors of the Met [hepatocyte growth factor/scatter factor (HGF/SF) receptor] tyrosine kinase block HGF/SF-induced tumor cell growth and invasion. Mol. Cancer Ther. 2003, 2(11): 1085-1092. Calic, M., et al. Flavonoids as inhibitors of Lck and Fyn kinases. Croatica Chemica ACTA. 2005, 78(3):367-374.
- Tyrosine Kinase FGFR1 Activity Assay 1. Enzyme reaction substrate μPoly(Glu,Tyr)4:1 was diluted with PBS without potassium ion (10 mM sodium phosphate buffer, 150 mM NaCl, pH7.2-7.4) to 201 μg/mL, an enzyme plate was coated at 125 μL/well, and incubated at 37° C. for 12-16 hours. The liquid from the well was discarded. The plate was washed for three times with T-PBS (0.1% Tween-20 in potassium-free PBS, 200 μL/well), 5 minutes for each time. The elisa plate was dried in 37° C. dryer for 1-2 hours.2. 49 μL of ATP solution diluted in reaction buffer (50 mM HEPES pH 7.4, 50 mM MgCl2, 0.5 mM MnCl2, 0.2 mM Na3VO4, 1 mM DTT) was added into each well, and 1 μL of the test compound was added to each well, and then 50 μL of FGFR1 kinase domain recombinant protein diluted in reaction buffer was added to initiate the reaction, and two control wells without ATP were required for each experiment. The reaction was performed on a Shaker (100 rpm) at 37° C. for 1 hour. The liquid from the well was discarded, and the plate was washed with T-PBS for three times.3. The antibody PY99 dilution (antibody diluted 1:500 in T-PBS with BSA 5 mg/mL) was added at 100 μL/well, and shaken for 0.5 hours on a 37° C. shaker. The liquid from the well was discarded, and the plate was washed with T-PBS for three times.4. The horseradish peroxidase-labeled goat anti-mouse second antibody dilution (antibody diluted 1:2000 in T-PBS with BSA 5 mg/mL) was added at 100 μL/well, and shaken for 0.5 hours on a 37° C. shaker. The liquid from the well was discarded, and the plate was washed with T-PBS for three times.5. 2 mg/mL OPD coloration solution (diluted with 0.1 M citric acid-sodium citrate buffer containing 0.03% H2O2 (pH=5.4)) was added at 100 μL/well, and reacted for 1-10 minutes at 25° C. in darkness.6. The reaction was quenched with 50 μL/well of 2M H2SO4, and the plate was read using a tunable microplate microplate reader VERSAmax at 490 nm.
- Enzyme Assay The enzyme reaction substrate Poly(Glu, Tyr)4:1 was diluted with potassium-free PBS (10 mM sodium phosphate buffer, 150 mM NaCl, pH 7.2-7.4) to 20 μg/ml and microwell plate was coated with 125 ml/well mixture. The reaction was carried out at 37° C. for 12-16 h. Then the liquid was discarded and the microwell plate was washed with 200 ml/well T-PBS (PBS containing 0.1% Tween-20) three times, 5 minutes each. The microwell plate was dried for 1-2 hours at 37° C. oven. Each well was added with reaction buffer (50 mM HEPES, pH 7.4, 50 mM MgCl2, 5 mM MnCl2, 0.2 mM Na3VO4, 1 mM DTT) diluted ATP solution (50 mL) whose final concentration is 5 μM. Drug was diluted with 1% DMSO to a suitable concentration. 10 μl/well of drug was added and then 40 μl reaction buffer diluted VEGFR-2 tyrosine kinase protein was added. The microwell plate was placed into a shaker (100 rpm) and the reaction was carried out at 37° C. for 1 h. The microwell plate was washed with T-PBS three times. Three enzyme-free control wells and corresponding concentration of DMSO control wells were required for each experiment. 100 ml of primary antibody PY99 (p-Tyr (PY99), Cell Signaling Technology, diluted with T-PBS containing 5 mg/ml BSA, 1:1000 dilution) was added to each well and the plate was placed into a shaker to react for 0.5 h at 37° C. The plate was washed with T-PBS three times. 100 ml of secondary antibody horseradish peroxidase-labeled goat anti-mouse IgG (diluted with T-PBS containing 5 mg/ml BSA, 1:2000 dilution) was added to each well and the plate was placed into a shaker to react for 0.5 h at 37° C. The plate was washed with T-PBS three times. 100 ml of 2 mg/ml of OPD developing solution (diluted with 0.1 M citric acid-sodium citrate buffer containing 0.03% of H2O2 (pH=5.4)) was added to each well and the reaction was carried out at 25° C. in the dark for 1-10 minutes. OPD was dissolved under ultrasound and developing solution was freshly prepared. 50 ml of 2 M H2SO4 was added to each well to quench the reaction and OD value was measured by wavelength tunable microplate reader SPECTRA MAX 190. Wavelength was 490 nm.
- Diamine Oxidase (DAO) Selectivity Assay ReagentsPromega ROS-Glo H2O2 Assay Kit, 50 ml. Cat No. G8821Inhibitors (Test Compounds):10 mM stock diluted to 10, 3, 1, 0.3, 0.1, 0.03, 0.01, 0.003, 0.001, and 0.0003 mM in drug plate, resulting in a concentration of 100, 30, 10, 3, 1, 0.3, 0.1, 0.03, 0.01, and 0.003 uM in the assay.Positive Control (Aminoguanidine):1 mM stock diluted to 1 to 0.0001 and 0.00003 mM in drug plate, resulting in a concentration of 3 to 0.001 and 0.0003 uM in the assay.DAO:DAO batch is obtained from Sigma Enzyme is reconstituted in sodium phosphate buffer at 10 mg/mLAssay Plates: 96 well white polystyrene, flat bottom plates: Fisher, Cat No. DPS-134-050AProcedure:1. Dilute 400 ul DAO enzyme in 4 mL Assay Buffer (enough for one plate). Add 40 ul DAO enzyme to all wells (excluding G+H 12, assay buffer only)3. Add 0.5 μl test compound serial dilutions, in duplicate4. Add 0.5 μl serial dilutions of Aminoguanidine down column 11 and to E+F 125. Add 0.5 μl DMSO (100% activity control) to C+D 126. Cover plate and incubate for 20 minutes at room temp on a plate shaker7. Prepare Start Mix: Volume Reagent 1 × plate 2 × plate Final ConcnAssay Buffer 2 ml 3 ml —8.5M Cadaverine 23 μl 34.5 μl 97.8 mMH2O2 Substrate (1:80) 25 μl 37.5 μl 125 μM8. Add 10 μl Start Mix to all wells9. Incubate for 60 min at room temp on a plate shaker10. Prepare Detection Reagent: Volume Reagent 1 × plate 2 × plate Luciferin 5 ml 10 ml D-cysteine (1:100) 50 μl 100 μl Signal Enhancer (1:100) 50 μl 100 μl11. Add 50 μl Detection Regent to each well EXCEPT No Luciferin controls (A+B 12, add 50 μl assay buffer)12. Incubate for 20 min at room temp on a plate shaker, protected from light13. Measure luminescence using a plate reader (integration 500 ms)Values for the blank (no DAO controls) are subtracted from all samples. DMSO controls are set as 100% activity and samples are calculated as a % of the DMSO control. Data is plotted using Graphpad Prism software, and a non-linear regression line is calculated using a variable slope sigmoidal dose response equation.:Y=Bottom+(Top-Bottom)/(1+10{circumflex over ( )}((LogIC50−X)*HillSlope)).Where X is the logarithm of concentration and Y is the response. The IC50 is the concentration of the drug that produces a percentage control fluorescence value midway between the saturation and zero effect plateaus. Two independent assays are usually performed, and the mean IC50 is reported.
- Inhibition Assay A stock solution was prepared using a human MAO-B enzyme (purchased from Aldrich) and a Amplex Red monoamine oxidase assay kit according to a preparation manual. The kit includes a 5x reaction buffer, an Amplex red reagent (1 mg), HRP, DMSO, H2O2, p-tyramine (substrate of MAO-A, B), benzylamine (substrate of MAO-B), clorgiline (inhibitor of MAO-A), and pargyline (inhibitor of MAO-B). Among these reagents in the kit, benzylamine was used as a substrate for MAO-B, and pargyline was used as an MAO-B inhibitor. A solution as overall substrates was prepared as follows. 200 ul of a solution of 1 mg of Amplex red sufficiently dissolved in 200 ul of DMSO, 100 ul of a mixed solution of HRP and 1 ml of a 1x buffer, 200 ul of a solution of benzylamine dissolved in 1.2 ml of dH2O were added to 9.5 ml of a 1x buffer to reach a total volume of 10 mL, which is sufficient for 100 wells. 0.5 ul of a mixture of MAO-B inhibitor pargyline and 1 ml of dH2O was put into each well. First, the activity of MAO-B was determined using 10 uM of the synthesized compound. 96 wells were injected with positive and negative types, and the wile type. The positive type included only substrate and hydrogen peroxide, and the negative type included only substrate. For the wild type, corresponding wells were injected with the enzyme, substrate, and MAO-B inhibitor, but with no synthesized compound. Afterward, 2 ul of the synthesized compound (1 mM) was added into each well, and the human MAO-B enzyme was put only into the 1st row of wells. 0.5 ug of the human MAO-B was put into each well along with 100 ul of a 1x buffer. The human MAO-B enzyme was put into the 2nd row of the wells along with 0.5 ul of a pargyline, the MAO-B inhibitor. To reduce an experimental error for accuracy, the test was repeated three times for each compound. After 30 minutes, 100 ul of the substrate solution was added into each well in a darkroom. The test was performed in the darkroom due to light sensitivity of the Amplex reagent. Finally, a total volume of the reaction solution per well reached 200 ul. After about 2 to 3 hours, chromophoric degrees of the samples were measured. A variation in data values for the 1st and 2nd rows of the wells indicates the pure reaction activity of the MAO-B enzyme with the substrate. Using the samples with the synthesized compound the remaining activity of MAO-B after inhibited by the synthesized compound may be determined. This is because the activities of the other enzymes excluding the MAO-B enzyme may be excluded through this method. Compounds with high inhibitory activity at a concentration of 10 uM were screened from among the synthesized compounds at a compound concentration of 10 uM. Afterward, concentration-dependent IC50 values of these compounds may be obtained through an activity assay at different concentrations of 0.001 uM, 0.01 uM, 0.1 uM, 1 uM, and 10 uM.
- Fluorescence-based ELISA assay A variety of tissue culture cell lines, expressing endogenous levels of O-GlcNAcase, can be utilized; examples include rat PC-12, and human U-87, or SK-N-SH cells. In this assay, rat PC-12 cells were plated in 96-well plates with approximately 10,000 cells/well. Compounds to be tested were dissolved in DMSO, either 2 or 10 mM stock solution, and then diluted with DMSO and water in a two-step process using a Tecan workstation. Cells were treated with diluted compounds for 24 h (5.4 μL into 200 μL 1 well volume) to reach a final concentration of inhibitor desired to measure a compound concentration dependent response, typically, ten 3 fold dilution steps, starting at 10 μM were used to determine a concentration response curve. To prepare a cell lysate, the media from compound treated cells was removed, the cells were washed once with phosphate buffered saline (PBS) and then lysed for 5 minutes at room temperature in 50 μL of Phosphosafe reagent (Novagen Inc, Madison, Wis.) with protease inhibitors and PMSF. The cell lysate was collected and transferred to a new plate, which was then either coated to assay plates directly or frozen −80° C. until used in the ELISA procedure. If desired, the total protein concentration of samples was determined using 20 μL of the sample using the BCA method. The ELISA portion of the assay was performed in a black Maxisorp 96-well plate that was coated overnight at 4° C. with 100 μL/well of the cell lysate (1:10 dilution of the lysate with PBS containing protease inhibitors, phosphatase inhibitors, and PMSF). The following day the wells were washed 3 times with 300 μL/well of Wash buffer (Tris-buffered saline with 0.1% Tween 20). The wells were blocked with 100 μL/well Blocking buffer (Tris buffered saline w/0.05% Tween 20 and 2.5% Bovine serum albumin) Each well was then washed two times with 300 μL/well of wash buffer. The anti O-GlcNAc antibody RL-2 (Abcam, Cambridge, Mass.), diluted 1:1000 in blocking buffer, was added at 100 μL/well. The plate was sealed and incubated at 37° C. for 2 h with gentle shaking. The wells were then washed 3-times with 300 μL/well wash buffer. To detect the amount of RL-2 bound horse-radish peroxidase (HRP) conjugated goat anti-mouse secondary antibody (diluted 1:3000 in blocking buffer) was added at 100 μL/well. The plate was incubated for 60 min at 37° C. with gentle shaking. Each well was then washed 3-times with 300 μL/well wash buffer. The detection reagent was added, 100 μL/well of Amplex Ultra RED reagent (prepared by adding 30 μL of 10 mM Amplex Ultra Red stock solution to 10 mL PBS with 18 μL 3% hydrogen peroxide, H2O2). The detection reaction was incubated for 15 minutes at room temperature and then read with excitation at 530 nm and emission at 590 nm. The amount of O-GlcNAcylated protein, as detected by the ELISA assay, was plotted for each concentration of test compound using standard curve fitting algorithms for sigmoidal dose response curves.
- Intracellular Axl Phosphorylation Inhibitory Activity A phosphorylated Axl (hereinafter, referred to as pAxl) inhibition test was conducted using a human non-small cell lung cancer-derived cell line NCI-H1299.The NCI-H1299 cells were suspended in a medium (RPMI1640 medium containing 10% fetal bovine serum), then inoculated at 15000 cells/100 μl/well to each 96-well multiwall plate, and cultured at 37° C. for 1 day in the presence of 5% CO2. On the next day, the medium was discarded, and a medium was added at 100 μl/well to the plate, followed by culture at 37° C. for 1 day in the presence of 5% CO2. Each test compound was dissolved in DMSO and diluted with an FBS-free medium to prepare a sample solution (DMSO concentration: 2%). A medium or a medium supplemented with the sample was added at 25 μl/well (DMSO concentration: 0.4%) to the plate and incubated at 37° C. for 1 hour in the presence of 5% CO2.GAS6 (R&D Systems Inc., model: 885-GS) was diluted into 6 μg/ml with an FBS-free medium, then added at 25 μl/well to the plate, and incubated at 37° C. for 10 minutes in the presence of 5% CO2 after stirring.The supernatant was discarded, and a solution of a 37% formalin solution diluted to 4% with phosphate-buffered saline (PBS) (hereinafter, a 4% formalin solution) was added at 0.1 ml/well to the plate, which was then left standing at room temperature for 10 minutes. Next, the 4% formalin solution was discarded, and a solution of Triton X-100 diluted to 0.1% with PBS (hereinafter, referred to as a wash buffer) was added at 0.2 ml/well to the plate and discarded by decantation. An excess of water was removed on paper towel.Subsequently, 10% NaN3 and 110 μl of H2O2 were added to 10.7 mL of a wash buffer (hereinafter, referred to as a quenching buffer), and this quenching buffer was added at 0.1 ml/well to the plate, which was then left standing at room temperature for 15 minutes.The quenching buffer was discarded, and a wash buffer was added at 0.2 ml/well to the plate and discarded by decantation. An excess of water was removed on a paper towel. Skimmed milk (WAKO #198-10605) was added (final concentration 5%) to a wash buffer (hereinafter, referred to as a blocking buffer), and this blocking buffer was added at 0.25 ml/well to the plate, which was then left standing at room temperature for 1 hour.The blocking buffer was discarded, and Anti-phospho-Axl (Y702) (D12B2) rabbit monoclonal antibody (Cell Signaling Technology, Inc., catalog No. 5724) was reacted at a concentration of 1/1000 with the plate, which was then left standing overnight at 4° C. Each well was repetitively washed with a wash buffer five times, and Peroxidase AffiniPure Donkey Anti-Rabbit IgG (H+L) (Jackson ImmunoResearch Inc., catalog No. 711-035-152) was reacted at a concentration of 1/2000 with the plate at room temperature for 1 hour. A similar washing operation was carried out, and Super Signal ELISA pico chemiluminescent substrate (Thermo Fisher Scientific, Inc., catalog No. 37069) was added at 0.05 ml/well to the plate and gently stirred, followed by incubation for 20 minutes. Then, developed light was measured using ARVO sx (PerkinElmer Inc.) to measure the pAxl (Y702) level.