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15 protocols using boc qar amc

1

TMPRSS2 Enzyme Activity Assay

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The cell-based enzyme activity assay of TMPRSS2 was established in the previous study (Jin et al., 2020 (link)). 293T and 293T-TMPRSS2-expressing cells were seeded in a black, 96-well plate (20,000 cells/well). The next day, the growth medium was replaced with 80 μl of compounds or PBS alone to the wells in the indicated concentrations and incubated at room temperature for 1 hr. The 100 μM fluorogenic substrate Boc-QAR-AMC (R&D Biosystems) was added to each well and put in a 37℃ incubator for another 2 hr. Fluorescence (excitation 360 nm, emission 410 nm) was measured using Synergy H1 hybrid multi-mode microplate reader (BioTek Instruments, Inc).
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2

Fluorogenic Assay for Protease Activity

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Twenty-four hours after transfection, the media was replaced with 80 µL of phosphate-buffered saline (PBS). Inhibitors or PBS alone were added to the wells in the indicated concentrations and incubated at 25°C for 15 minutes. The fluorogenic substrate BOC-QAR-AMC (R&D Biosystems) was then added to each well to a final concentration of 100µM. Fluorescence (excitation 365 nm, emission 410 nm) was immediately measured every 15 minutes at 37°C using a GloMax plate reader (Promega).
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3

TMPRSS2 Proteolytic Activity Assay

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Vero E6 cells were transfected with mock (pcDNA3.1), TMPRSS2 (pcDNA3.1/TMPRSS2 Uniprot: O15393-1) or TMPRSS2(S441A) (pcDNA3.1/TMPRSS2-S441A) using Lipofectamine 3000 (Thermo Fisher Scientific) in 12-well plates. For the mouse TMPRSS2 assay, empty vector (pCMV6-Entry, Origene PS100001) and TMPRSS2-Myc-DDK (Origene MR207852) were used. After 24 h transfection, cells were washed with PBS and the medium replaced with HCell-100 medium (Wisent) containing 200 µM Boc-QAR-AMC (R&D Systems) and either vehicle (0.01% DMSO) or compounds at the indicated concentration for 24 h. To measure proteolytic activity, 90 µl of cell medium was transferred to a black 96-well plate, and fluorescence was measured at room temperature (excitation: 360 nm, emission: 460 nm) using an FLx800 TBE microplate reader (Bio-Tek Instruments). Background-subtracted (mock-transfected cells) proteolytic activities are presented as the percentage of activity relative to vehicle-treated cells (screen at 10 nM). IC50 values were determined after generating a nonlinear regression analysis from a log([Compound]) versus a proteolytic activity plot using GraphPad Prism software (v.9.0.1). GraphPad Prism was used to identify and eliminate outliers (Q = 1) and assess the goodness of the fits. IC50 values presented are the mean ± s.d. of at least three independent experiments.
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4

TMPRSS2-IP Enzymatic Activity Assay

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The TMPRSS2-IP lysate was combined with PBS supplemented with a fluorogenic peptide substrate, BOC-QAR-AMC (100 mM, R&D Systems®, Abingdon, UK), in a total volume of 50 µL within the wells of a 96-well plate. Fluorescence was continuously monitored for three hours at five-minute intervals using an excitation wavelength of 365 nm and an emission wavelength of 410 nm.
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5

Matriptase Inhibition Kinetics Assay

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First, 10 nM matriptase was added to purified KD1 soluble inhibitor (final concentrations ranging 0–750 nM) in a matriptase assay buffer. Immediately, 1 μM purified B4 was added to initiate the reaction. Yeast surface display matriptase inhibition was carried out using the same matriptase and substrate conditions as above, except induced yeast displaying inhibitor domains were first counted (10–108 yeast cells/sample) and incubated with matriptase prior to the addition of B4. Kinetic monitoring of fluorescent output from B4 was performed using methods and conditions described above. Conditions of B4 with matriptase alone or with buffer alone, with or without noninduced yeast, served as control samples. Separately, the same experiment was performed using commercial matriptase substrate, Boc-QAR-AMC (R&D), and fluorescent output (380 nm/460 nm) was measured over time.
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6

Quantifying Matriptase Activity in Cancer Cells

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A total of 1 × 105 cancer cells were seeded in 96-well plates in 2% fetal bovine serum-supplemented media. Plates were cultured for 24 h in a humidified tissue culture incubator at 37 °C in a 5% CO2 atmosphere. Following incubation, cells were washed twice with warm 1xPBS to remove residual serum, and serum free medium (DMEM alone) was added. Then, 1 μM purified B4 was immediately added to each condition and incubated at 37 °C in 5% CO2 for 1 h. B4 in serum free media alone served as a control condition. Plates were maintained at 37 °C in 5% CO2, and fluorescent output (535 nm/605 nm) was monitored every hour for at least 5 h. Rate of fluorescence change over time was quantified by fitting a linear curve using GraphPad software and averaging duplicate samples. Separately, the same experiment was performed using commercial matriptase substrate, Boc-QAR-AMC (R&D), and fluorescent output (380 nm/460 nm) was measured over time.
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7

Quantitative Trypsin-like Protease Assay

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Trypsin-like serine protease activity was measured using a synthetic tripeptide substrate Gln-Ala-Arg (QAR) with the fluorogenic leaving group AMC (Boc-QAR-AMC, R&D Systems). The conditioned media were collected by centrifugation at 24 h of co-culturing. In a 96-well plate, 10 μL of each medium sample were mixed with 90 µL of 0.1 M Tris at pH 8.5, containing 100 mM NaCl and 20 µM of the QAR substrate. The mixtures were read immediately using a SpectraMax i3x Multi-Mode Microplate Reader (Molecular Devices, San Jose, CA, USA) in the kinetic mode at 380 nm/480 nm excitation/emission for 2 h, with intervals of 2 min between readings.
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8

Inhibitor Kinetics Evaluation in TMPRSS2-Expressing Cells

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VeroE6-TMPRSS2 cells were seeded in a black, 96-well plate (5000 cells/well). Next day, the growth medium was replaced with 80 μl of inhibitors (TFQ or compound 7) or PBS alone to the wells in the indicated concentrations (0.4 μM, 2 μM, and 10 μM) and incubated at room temperature for 30 min. The fluorogenic substrate Boc-QAR-AMC (R&D Biosystems) was then added to each well to different concentrations (0, 1.5625 μM, 3.125 μM, 6.25 μM, 12.5 μM, 25 μM, 50 μM, and 100 μM). Fluorescence (excitation 365 nm, emission 410 nm) was kinetically measured every 15 min for a total time of 150 min at 37 °C using Synergy H1 hybrid multimode microplate reader (BioTek Instruments, Inc). The Ki value was calculated by use of the competitive inhibition model in Graphpad Prism software.
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9

Quantifying Proteolytic Activity via Fluorogenic Substrate

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Proteolytic activity was quantified using 20 µM of fluorogenic substrate Boc-Gln-Ala-Arg-AMC (Boc-QAR-AMC) (Boc: t-Butyloxycarbonyl; AMC: 7-Amino-4-methylcoumarin; R&D systems, Abingdon, UK) in a sample volume of 100 µL. This substrate detects the activity of a wide range of trypsin-like proteases. The experimental protocol was similar to that described in previous reports [14 , 34 (link)]. The fluorescence signal resulting from substrate hydrolysis at the cell surface was continuously recorded over a time period up to 90 min using a TECAN plate reader (360 nm excitation/465 nm emission wavelength).
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10

Quantification of Proteolytic Activity

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Proteolytic activity was quantified using the fluorogenic substrate Boc-Gln-Ala-Arg-AMC (Boc-QAR-AMC) (Boc: t-Butyloxycarbonyl; AMC: 7-Amino-4-methylcoumarin; R&D systems, Abingdon, UK) or Ac-Lys-His-Tyr-Arg-AMC (Ac: Acetyl; KareBay Biochem Inc., Monmouth Junction, NJ, USA). The experimental protocol was similar to that described by Reihill et al. 24 (link). Boc-QAR-AMC detects the activity of a wide range of trypsin-like proteases25 (link), whereas Ac-KHYR-AMC has been reported to be an optimal prostasin substrate 23 (link). Each individual oocyte was placed into a well of a 96-well plate containing 100 μl of standard ND9 solution supplemented with 10 μM fluorogenic substrate. The fluorescence signal resulting from substrate hydrolysis at the cell surface was continuously recorded over a time period up to 190 min using a TECAN plate reader (360 nm excitation/465 nm emission wavelength).
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