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25 protocols using t1426

1

Reversible BTK Inhibitor Characterization

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A mixture of 2 μM BTK (Invitrogen PV3587) and either 9 (0.6 μM) or PP-ir (0.6 μM) was incubated at room temperature for 60 minutes in an assay buffer of 20 mM Hepes pH 7.5, 10 mM MgCl2, 150 mM NaCl, 5% Glycerol, 0.05% Triton-X 100, and 1 mM 2-mercaptoethanol. In parallel 9 (0.6 μM) and PP-ir (0.6 μM) were also incubated with the BTK enzyme storage buffer alone (50 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM EDTA, 0.05% Triton X-100, 4 mM 2-mercaptoethanol, 50% Glycerol). A trypsin stock solution (Sigma T1426) was prepared to 1 mg/ml in assay buffer. 60 μL of both the enzyme/compound mixture and the storage buffer/compound mixture were added to 120 μL of 1 mg/ml trypsin. Liquid chromatography-mass spectrometry of the samples was performed by the analytical chemistry group of the Molecular Medicine Research Institute (www.mmrx.org). In order to calculate inhibitor reversibility, the average mass spectrometry peak area of the compound/BTK/trypsin samples was divided by the peak area for the samples containing compound/storage buffer/trypsin to get the % Reversibility.
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2

Fluorimetric Trypsin Activity Assay

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To measure trypsin activity, mouse pancreas was disrupted using the Multi-Beads Shocker system (Yasui Kikai), and in buffer containing 5 mM 2-Morpholinoethanesulfonic acid (pH 6.5), 1 mM MgSO4, and 250 mM sucrose. Trypsin activity in homogenates was measured fluorimetrically using Boc-Gln-Ala-Arg-MCA (Peptide Institute. Inc.) as a substrate, in the Infinite 200 PRO (Tecan), according to the method of Kawabata et al.31 (link). Trypsin activity in each sample was determined using a standard curve for purified trypsin (T1426, Sigma).
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3

Fibrinolysis and Proteolytic Degradation Kinetics

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Fibrinolysis and proteolytic degradation of fibrin mediated by plasmin and trypsin were studied in vitro. A total of 0.5 mL of ExThr or EnThr fibrin containing 20 or 30 mg/mL of fibrinogen without aprotinin were polymerized in identical tubes. Then, 1 mL of 0.1 U/mL plasmin (P1867, Sigma-Aldrich, Saint Louis, MO, USA) or 0.1% trypsin (T1426, Sigma-Aldrich, Saint Louis, MO, USA) in 0.9% sodium chloride solution with 0.02% sodium azide (S2002, Sigma-Aldrich, Saint Louis, MO, USA) was gently added to fibrin samples and incubated at 37 °C until complete dissolution. The plasmin and trypsin solutions were changed every 3 days. The size of the fibrin clots was measured every 8 h.
The clot prepared into a cylindrical tube was measured with a ruler and its initial height (h1) was recorded. Then, the height of the clot was measured at certain time points (h2). Degradation (D%) was calculated according to the Equation (1):
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4

Trypsin Inhibition Assay for Icariin Analogs

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Icariin and compounds 1–9 were assayed against bovine trypsin (Sigma-Aldrich, T1426) at 1x and 10x the IC50 concentration. Compounds 3 and 7 were also assayed at 50x and 250x the IC50 concentration. In assay buffer (50 mM Tris-HCl, 20 mM CaCl2, pH 8.19 with or without 0.5% igepal), 0.002 mg freshly made trypsin is incubated with drugs for 5 minutes at 25 °C. 1 mM of substrate (Nα-benzoyl-L-arginine 4-nitroanilide hydrochloride, Sigma-Aldrich, B3133) is added to start the reaction. Final reaction volume is 100 μl. Product formation is monitored by increasing absorbance at 410 nm at 25 °C for 30 minutes in kinetic mode using a SpectraMax M5 plate reader (Molecular Devices). All values were measured in duplicate.
To assay the effect of increasing PDE5 concentration on icariin and icariin analogs, the PDE5 inhibition assay described in the methods section was done with modifications. Compounds at approximately 1x the PDE5 IC50 concentration were incubated with 1 or 2 nM PDE5, and GMP production was measured as described. All values were measured in triplicate.
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5

Trypsin-Mediated Hydrolysis of Casein and Blue Whiting Proteins

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Casein and BW-WM protein were added Trizma buffer (50 mM, pH 8.0) and hydrolysed using trypsin from bovine pancreas (T1426 from Sigma) at 45 °C for 4 h as recommended by Shalaby et al. [37 (link)]. The two blue whiting protein hydrolysates (BW-HA, BW-HP) were not hydrolysed with trypsin prior to analyses. Protein in hydrolysates were quantified on the Cobas c111 system (Roche Diagnostics GmbH, Mannheim, Germany) using the TP2 kit from Roche. Renin inhibition was measured using the Renin Assay Kit (MAK157, from Sigma-Aldrich) as described in the user manual. ACE-inhibition was measured using the method by Shalaby et al. [37 (link)], as previously described [20 (link)].
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6

Renin Activity Assay Protocol

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Renin activity assay was performed as previously described.9 (link) Briefly, renin activity in urine and renal inner medulla was determined by the delta value of the Ang I generation using an ELISA kit from the sample incubating at 4 °C and 37 °C for 1 hour, respectively. Total renin content was measured with excessive angiotensinogen plus trypsinization and active renin content with excessive angiotensinogen. Urine and tissue samples were spiked with 1 µmol/L synthetic renin substrate tetradecapeptide (R8129; Sigma-Aldrich, St Louis, MO). After incubation at 37 °C for 18 hours, Ang I generation was assayed by using an Ang I enzyme immunoassay kit (S-1188; Peninsula Laboratories International, SanCarlos, CA), according to the manufacturer’s instructions. The values were expressed as nanograms per milliliter per hour of generated Ang I. For measurement of total renin content, trypsinization was performed to activate prorenin to renin.17 (link) The samples were incubated with trypsin derived from bovine pancreas (100 g/L, T1426, Sigma-Aldrich) in 37 °C for 18 hours. The reaction was then terminated with soybean trypsin inhibitor (100 g/L, T6522; Sigma-Aldrich) at 37 °C for 1 hour. Renin activity was determined in the native condition, active renin content with excessive angiotensinogen, and total renin content with excessive angiotensinogen plus trypsinization.
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7

Platelet Proteomics: Detailed Workflow

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Platelet proteomics analyses were performed, based on procedures reported earlier (13 (link), 15 (link), 23 (link)), with modifications. Well purified platelet samples (5 × 108 platelets) were prepared in SDS lysis buffer, and protein concentrations were determined using a bicinchoninic acid assay (Pierce, Thermo-Fisher Scientific, Bremen, Germany). Cysteines were reduced by 30 min incubation at 56 °C with 10 mm dithiothreitol; free sulfhydryl groups were alkylated with 30 mm iodoacetamide for 30 min at room temperature. Samples of 150 μg protein were then processed using filter-aided sample preparation (FASP) with a 30 kDa molecular weight cut-off spin filter (24 (link), 25 (link)).
Proteins were digested in 50 mm triethylammonium bicarbonate (TEAB), 200 mm guanidinium hydrochloride, and 2 mm CaCl2, pH 8.0 in the presence of trypsin (1:20 w/w, T-1426, Sigma, St. Louis, MO) at 37 °C. After incubation for 7 h, digested peptides were collected by centrifugation at 13,800 × g for 25 min. Filters were washed with 50 μl of 50 mm TEAB and 50 μl of LC-MS grade water to increase peptide yield. Trypsin digestion was monitored by monolithic RP HPLC as described (23 (link)). After lysis and digestion with trypsin, samples were used for either label-free proteome analysis, or iTRAQ-based (phospho)proteome analysis.
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8

Hydrolysis and Bioactivity Evaluation

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Casein and cod protein meals were added Trizma buffer (50 mM, pH 8.0) and hydrolyzed using trypsin from bovine pancreas (T1426, from Sigma-Aldrich) at 45 °C for 4 h as recommended by Shalaby et al. [42 (link)]. ACE-inhibition was measured using the method by Shalaby et al. [42 (link)], as previously described [43 (link)]. Renin inhibition was measured using the Renin Assay Kit (MAK157, from Sigma-Aldrich) as described in the user manual. Protein in hydrolysates were quantified on the Cobas c111 system (Roche Diagnostics GmbH, Mannheim, Germany) using the TP2 kit from Roche.
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9

HUVEC Fibrin Gel Bead Assay

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The HUVEC fibrin gel bead assay was performed as described (Nakatsu & Hughes, 2008 ). Briefly, EGM-2 complete medium was used to culture HUVECs 1 day before coating onto Cytodex 3 beads (Cat # C3275, Amersham Pharmacia Biotech, Erie, PA). About 400 HUVECs per bead were added to the FACS tube and were inverted to mix every 20 min for 4 h, followed by incubating overnight in T25 flasks. The next day, 500 cell-coated beads per well were mixed with fibrin gel composed of 2-μg·ml−1 fibrinogen (Sigma, F3879), 22-μ·ml−1 aprotinin (Sigma, A4529) and 0.625-U·ml−1 thrombin (Sigma, T6884). After clotting, 4000 HPFs in 1-ml EGM-2 complete medium containing the TAT-Sc or TAT-ANK were added to each fibrin gel. Medium containing SC-ANK or ANK was changed every day. The inverted microscope and ImageJ software were used to photograph and quantify sprouts. For isolating the mRNA of HUVECs in the fibrin gel, 3- and 4-mg·ml−1 trypsin (Sigma, T1426) were used to remove the pulmonary fibroblasts and fibrin gel, respectively. After complete digestion, the cell pellets from HUVECs from 12-well plate were resuspended in the TRIzol for RNA extraction.
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10

Antibody-based Target Identification Workflow

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The antibodies used in this study were as follows: anti-C1QTNF5, anti-Lamin B1, anti-Na+/K+-ATPase, anti-Myc, anti-β-Actin, anti-GAPDH, anti-GST and anti-His (A3021, A1910, A11683, AE070, AC026, AC002, AE001 and AE003, respectively; ABclonal, China); anti-α-Tubulin, anti-Flag and anti-HA (T6199, F1804 and H6908, respectively; Sigma); anti-NP (ab128193; Abcam); anti-H1N1 HA (11684-MM03; Sino Biological); goat anti-mouse or anti-rabbit IgG (115-035-174 and 111-005-144; Jackson Immuno Research Laboratories); goat anti-mouse antibodies conjugated with Alexa Fluor 488 (A-11001; Invitrogen). The main reagents used in this study were as follows: anti-Flag M2 beads, TPCK, sialidase and blasticidin (A2220, T1426, N7885 and 203350, respectively; Sigma); Lipofectamine 2000 (11668019; Thermo Fisher Scientific); Dual luciferase reporter assay kit (E1980; Promega); Neofect™ DNA transfection reagent (TF20121201; Neofect); Minute™ plasma membrane protein and cell component separation kit (SM-005; Invent Biotechnologies).
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