TITLE: Fluorescence assay for MERS-CoV Mpro activity measurement
AUTHORS: Charline Giroud, oleg.fedorov

[DESCRIPTION]
This protocol details the fluorescence assay for MERS-CoV Mpro protease activity measurement. This method is intended to measure the activity of viral proteases by using a specific labelled peptide that allows the detection of the cleaved product. The substrate contains the cleavage-sequence specific to the tested protease and is labeled in C-terminal by the fluorophore Edans (ex 336 nm; em: 455 nm) and in N-ternimal by the quencher Dabcyl (ex 472 nm). In the case of a non-cleaved substrate, the proximity of Dabcyl to Edans prevents the emission and the detection of the fluorescence at 455 nm. The cleavage of the peptide by the protease allows Edans’ fluorescence emission and detection.

[STEPS]
SECTION: MERS-MPro IC50 Measurement
3. Add 50 µLof 2x protein 1.2 micromolar (µM) solution to each well containing the compounds to be tested previously dispensed onto the plate.

SECTION: MERS-MPro IC50 Measurement
4. Incubate the mix for 60 min at Room temperature to initiate the enzymatic reaction by the addition of 50 µL of 2x (20 micromolar (µM)) substrate solution using the plate reader injector.

SECTION: MERS-MPro IC50 Measurement
5. Read the fluorescence intensity at 350/460 nm every 30 s for 30 s in kinetic mode, which includes a shaking step of the plate before each measurement.

SECTION: MERS-MPro IC50 Measurement
6. Calculate the IC50 by plotting the initial velocity against various concentrations of tested inhibitors by using a four-parameter dose−response curve in Prism (v8.0) software.
   

SECTION: MERS-CoV Mpro Assay
1. This method is intended to measure the activity of viral proteases by using a specific labelled-peptide that allows the detection of the cleaved product. The substrate contains the cleavage-sequence specific to the tested protease and is labeled in C-terminal by the fluorophore Edans (ex 336 nm; em: 455 nm) and in N-ternimal by the quencher Dabcyl (ex 472 nm). In the case of a non-cleaved substrate, the proximity of Dabcyl to Edans prevents the emission and the detection of the fluorescence at 455 nm. The cleavage of the peptide by the protease allows Edans’ fluorescence emission and detection.
  

SECTION: Reagents and equipment
2. Assay buffer: 50 millimolar (mM)Tris pH 7.0, 150 millimolar (mM) NaCl, 10 % (v/v) glycerol and 1 millimolar (mM) TCEP (optional).
Incubation: 60 min at room temperature.
MERS-MPro: protein stocks were stored at -80C and used as 2 xsolution (1.2 micromolar (µM), 0.6 micromolar (µM)final assay concentration) in assay buffer.
Positive control: Ebselen (Pubchem CID 3194), 50 micromolar (µM) top final assay concentration.
Substrate: Edans-GVLQSGLV-LysDabcyl-K (LifeTein, USA) prepared as a stock solution at 10 mM in DMSO and used at 2x solution (20 micromolar (µM), 10 micromolar (µM) final concentration assay concentration) in assay buffer.
Liquid handler: Echo‱ acoustic liquid handler (Beckman Coulter, USA).
Plate reader: Pherastar FS, BMG Labtech (Germany), 350-460 FI optic module, the plate is read every 30 s for 120 min and shacked 5 s before each reading.
7. Calculate the mean (μ) and the standard deviation (σ) of fluorescence intensity and then calculate the signal-to-background ratio and the Z' or Zfactor. (s: signal; c: control).