License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Grant ID: U19AI171399
Disclaimer
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Abstract
This protocol details the Time-Resolved FRET (TR-FRET) assay for SARS-CoV-2 nsp3 macrodomain (Mac1) binding of adenosine diphosphate (ADP)–ribosylated (ADPr) peptide. This method is intended to measure the activity of Mac1 by using a specific ADPr-modified peptide that allows the detection of binding. When bound, the biotinylated-peptide and the HIS-tagged Mac1 form a proximity complex that is detected by TR-FRET using Streptavidin-Eu Cryptate and anti-HIS-XL665 as a donor/acceptor pair. Excitation of the Eu Cryptate complex at 325 nm emits a resonant energy of 625 nm which in turn excites the XL665 to emit fluorescence at 665 nm. This energy transfer occurs only when ADPr modified peptide is in sufficient proximity to Mac1 and inhibitors which displace the peptide will prevent energy transfer. Binding activity is reported as the ratio of Acceptor/Donor (Em/Em) X 10,000.
100 % volumeHTRF PPI Europium Detection BufferCISBIO BIOASSAYS, company of PerkinElmerCatalog #61DB9RDF
*Note: There are several forms of the Assay Buffer in this experiment. The Assay Buffer is the final, active buffer used throughout the experiment and has all of the five above reagents included. HTRF PPI Europium Detection Buffer needs to be added fresh before each experiment. Thus, there was an intermediate Buffer called Mac1 Buffer that contained HEPES, NaCl, BSA, and Tween only. Mac1 Buffer was filtered and stored at 4˚C. HTRF PPI buffer was then added to Mac1 Buffer fresh (to a final concentration of 10%) prior to performing the experiment--creating the active Assay Buffer.
Detection Solution Reagents (Concentration listed are from Stock Solutions)
1 % volumeStreptavidin-XL665CISBIO BIOASSAYS, company of PerkinElmerCatalog #610SAXAC
Note: Streptavidin-XL665 was dissolved in triply distilled water and diluted with HTRF PPI buffer to its stock concentration and then was aliquoted into 1.5mL sterile conical tubes
100 Mass PercentMAb Anti-6HIS-Eu cryptate GoldCISBIO BIOASSAYS, company of PerkinElmerCatalog #61HI2KLA
Note: MAb Anti-6HIS-Eu cryptate Gold was dissolved in tripled distilled water and then aliquoted into 1.5mL sterile conical tubes
The Enzyme stock was originally 183000 nanomolar (nM) and was diluted to 50 nanomolar (nM) before every experiment in freshly madeAssay Buffer. The final assay concentration is 12.5 nanomolar (nM)
Substrate stock (ARTK(Bio)QTARK(Aoa-RADP)S) was dissolved in DMSO to the stock concentration. Before each experiment, the substrate stock was diluted to 1600 nanomolar (nM) in freshly made Assay Buffer.
Safety warnings
Please be sure to wear proper Personal Protective Equipment (PPE) while performing this experiment.
Before start
Note: Inhibitor compounds stock concentration is 20 millimolar (mM). Compounds are pre-dispensed into 384 plates and stored at -20˚C until use.
Prepare Reagents
Prepare Reagents
PREPARE all of the reagents/buffers required for this experiment.
Assay Buffer
A
B
C
D
E
Reagent
Stock
Loaded into Combi
Final in assay plate
Units
HEPES pH=7.0
250
25
25
mM
NaCl
200
20
20
mM
BSA
0.5
0.05
0.05
mg/ml
Tween 20
0.5
0.05
0.05
%
HTRF PPI Europium detection buffer
100
10
10
%
Reagents (dilute reagents in assay buffer for required volume)
A
B
C
D
E
Reagent
Stock
Loaded into Combi
Final in assay plate
Units
His-SARS-CoV-2 MAC1
183000
50
12.5
nM
Substrate (Biotin-ADPr)
10000000
1600
400
nM
Detection Solution (dilute reagents in assay buffer for required volume)
A
B
C
D
E
Reagent
Stock
Loaded into Combi
Final in assay plate
Units
Streptavidin-XL665 (SA-XL)
1
0.25
0.125
%
MAb Anti-6HIS-Eu cryptate Gold
100
0.25
0.125
%
Prepare 384-well Plate
Prepare 384-well Plate
16m
PRIME Multi-Drop Combi Tube Dispensing Cassette with Assay Buffer by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.
Note: Be sure to cycle dispensing several times on a a clean plate lid (This confirms there are no bubbles in the Dispensing Cassette).
DISPENSE4 µL Mac1 Buffer to Columns 1 and 23 of assay plate
Note: These will represent the inhibitor control columns
EMPTY Multi-Drop Combi Tube Dispensing Cassette (by selecting the EMPTY button on the Combi Dispenser until the tubes of the cassette are emptied). Discard the Assay Buffer discharged from the cassette.
PRIME Multi-Drop Combi Tube Dispensing Cassette with His-SARS COV2 MAC1 Enzyme by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.
Note: Be sure to cycle dispensing several times on a a clean plate lid (This confirms there are no bubbles in the Dispensing Cassette).
DISPENSE4 µL50 nanomolar (nM) His-SARS COV2 MAC1 Enzyme to Columns 2-22 and 24 of assay plate
Note:
50 nanomolar (nM) His-SARS COV2 MAC1 is four times the final concentration for the assay. It will be diluted to be a final concentration of 12.5 nanomolar (nM) His-SARS COV2 MAC1 Enzyme
Column 2 and Column 24 are neutral control columns (Contain: Enzyme, Substrate, DMSO; no experimental compounds)
EMPTY Multi-Drop Combi Tube Dispensing Cassette (by selecting the EMPTY button on the Combi Dispenser until the tubes of the cassette are emptied). Discard the 50 nanomolar (nM) His-SARS COV2 MAC1 Enzyme discharged from the cassette.
PRIME Multi-Drop Combi Tube Dispensing Cassette with Assay Buffer by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely. Then, EMPTY the Multi-Drop Combi Tube Dispensing Cassette (by selecting the EMPTY button on the Combi Dispenser until the tubes of the cassette are emptied). Discard the Assay Buffer discharged from the cassette.
PRIME Multi-Drop Combi Tube Dispensing Cassette with1600 nanomolar (nM) MAC1 Substrate (Biotin-ADPr) by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.
Note: Be sure to cycle dispensing several times on a a clean plate lid (This confirms there are no bubbles in the Dispensing Cassette).
1600 nanomolar (nM) MAC1 Substrate (Biotin-ADPr) is four times the final concentration for the assay. It will be diluted to be a final concentration of400 nanomolar (nM) MAC1 Substrate (Biotin-ADPr)
EMPTY Multi-Drop Combi Tube Dispensing Cassette (by selecting the EMPTY button on the Combi Dispenser until the tubes of the cassette are emptied). Discard the 1600 nanomolar (nM) MAC1 Substrate (Biotin-ADPr) discharged from the cassette.
CENTRIFUGE plate1500 rpm, Room temperature, 00:01:00 to remove bubbles
PRIME Multi-Drop Combi Tube Dispensing Cassette with Assay Buffer by selecting the PRIME button on the Combi Dispenser until the tubes are filled completely. Then, EMPTY the Multi-Drop Combi Tube Dispensing Cassette (by selecting the EMPTY button on the Combi Dispenser until the tubes of the cassette are emptied). Discard the Assay Buffer discharged from the cassette.
PRIME Multi-Drop Combi Tube Dispensing Cassette with 0.25 % volume Detection Solutionby selecting the PRIME button on the Combi Dispenser until the tubes are filled completely.
Note: Be sure to cycle dispensing several times on a a clean plate lid (This confirms there are no bubbles in the Dispensing Cassette).
DISPENSE8 µL0.25 % volume Detection Solution into full plate
Note:
0.25 % volume Detection Solution is two times the final concentration for the assay. It will be diluted to be a final concentration of 0.125 % volume Detection Solution
EMPTY Multi-Drop Combi Tube Dispensing Cassette (by selecting the EMPTY button on the Combi Dispenser until the tubes of the cassette are emptied). Discard the 1600 nanomolar (nM) MAC1 Substrate (Biotin-ADPr) discharged from the cassette.
CENTRIFUGE 1500 rpm, Room temperature, 00:01:00 plate to remove bubbles
INCUBATE plate for 01:00:00 at Room temperature
Recommended: Clean/Empty the Multi-Drop Combi Reagent Dispenser and Dispensing Cassette during this incubation step
1h
Read Plate Fluorescence
Read Plate Fluorescence
READ and RECORD the plate Relative fluorescence units (RFU) via the "Mac1 Protocol" on the PHERAstar FS Control Software.
Diagram of assay
Diagram of assay
Figure 1 graphical depiction of assay principal and its use in screening campaign