Aug 04, 2025
DENV NS2B-NS3 fluorescence single point screening assay
- Haim Barr1,2,
- Noa Lahav1,2,
- Jiyun Zhu3,2
- 1The Weizmann Institute of Science;
- 2ASAP Discovery Consortium;
- 3Stanford University
- Haim Barr: General acknowledgement: The Wohl Drug Discovery institute, The Nancy and Stephen Grand Israel National Center for Personalized Medicine.;
- ASAP Discovery
Protocol Citation: Haim Barr, Noa Lahav, Jiyun Zhu 2025. DENV NS2B-NS3 fluorescence single point screening assay. protocols.io https://dx.doi.org/10.17504/protocols.io.e6nvwb6e9vmk/v1
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
Protocol status: Working
We use this protocol and it's working
Created: November 01, 2024
Last Modified: August 04, 2025
Protocol Integer ID: 111386
Keywords: Fluorescence assay, Assay, Inhibitor, Fragment, DENV, Screening, NS2B-NS3 protease, single point, protease inhibitors against denv ns2b, fluorescent assays for zikv ns2b, ns3 fluorescence, ns3 cleavage of substrate bz, ns3 fluorescence single point, screening assay purpose, denv ns2b, ns3 cleavage, screening assay, fluorescent assay, protease inhibitor, peptide substrate, zikv ns2b, assay purpose, enzyme, containing serine, enzyme activity, candidates for medicinal optimization general description, ns3, fluorescence, fluorescence signal, medicinal optimization general description, excitation of amc, enzymatic reaction, lower enzyme activity, result of lower enzyme activity
Funders Acknowledgements:
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
Purpose: performing single point test of selected compounds from screening libraries containing serine-targeting fragments and serine protease inhibitors against DENV NS2B-NS3 to find warheads and candidates for medicinal optimization
General description: This protocol details the fluorescent assays for ZIKV NS2B-NS3 cleavage of substrate Bz-Nle-KRR-AMC peptide. This method measures the fluorescence from the released AMC product as a result of the enzymatic reaction. When hydrolyzed, AMC is liberated from the peptide substrate. Excitation of AMC at 350 nm emits a resonant energy of 450 nm. When the enzyme is inhibited, the fluorescence signal will decrease as a result of lower enzyme activity. The screening method is validated by calculating the Z prime number of each plate, and the percentage of inhibition is calculated and then evaluated for inhibitory efficacy.
Outcome: hits were selected from screening assays with more than 50% inhibition
Materials
Assay Buffer Reagents (Concentration listed are from Stock Solutions)
- HEPES(Fisher Scientific). Dissolving HEPES powder in MilliQ water and adjust pH to 8.5 for a final concentration of 0.5 M. Filter with 0.2 um filter
- Sodium chloride (sigma aldrich). Dissolving crystal into MilliQ water for a final concentration of 5 M. Filter with 0.2 um filter
- glycerol (Sigma Aldrich)
- Igepal (Sigma Aldrich) dissolving one part of Igepal in 200 part of MilliQ water for a final concentration of 0.5 %
- TCEP (GoldBio). Dissolving in MilliQ water into final concentration of 1 M. Store in -20 ºC
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Additional Reagents:
242140 nanomolar (nM) DENV NS2B/NS3 Enzyme
- The Enzyme stock was originally 242140 nanomolar (nM) and was diluted to 10000 nanomolar (nM) before every experiment in freshly made Assay Buffer. The final assay concentration is 12.5 nanomolar (nM)
20000000 nanomolar (nM) Substrate Bz-Nle-KRR-AMC
- Substrate stock was dissolved in DMSO to the stock concentration. Before each experiment, the substrate stock was diluted to 10000 nanomolar (nM) in freshly made Assay Buffer.The final assay concentration is 500 nanomolar (nM)
Troubleshooting
Safety warnings
Please be sure to wear proper Personal Protective Equipment (PPE) while performing this experiment.
Before start
Thaw TCEP solution on ice to make sure it is fresh
DENV NS2B-NS3 expression and purification
The protein used in this assay was expressed and purified and received from batch QQ01DVNS2B -c001 -p007 from Centre for Medicines Discovery
Prepare Reagents
PREPARE all of the reagents/buffers required for this experiment.
Assay Buffer
| A | B | C | D | E | |
| Reagent | Stock | Final | Units | Note | |
| HEPES pH 8.5 | 500 | 10 | mM | ||
| NaCl | 5000 | 50 | mM | ||
| glycerol | 100 | 5 | % v/v | ||
| Igepal | 0.5 | 0.05 | % | ||
| TCEP | 1000 | 0.5 | mM | add freshly |
Reagents (dilute reagents in assay buffer for required volume)
| A | B | C | D | E | |
| Reagent | Stock | Prep (2x) | Final in assay plate | Units | |
| DENV-NS2B/NS3 | 242140 | 10000 | 5000 | nM | |
| Substrate (Bz-Nle-KRR-AMC) | 20000000 | 10000 | 5000 | nM | |
Prepare 384-well Plate
16m
DILUTE Dilute protein and substrate using the assay buffer
- Protein dilution: 150 µL protein stock solution is added into 3480 µL Assay Buffer
- Substrate dilution: 1 µL x 20 mM substrate is added into 2 mL Assay buffer
MIX Add 10 µL enzyme stock solution into 384-well plates containing inhibitor stocks (column 2-22)
add 20 µL reaction buffer to A1-H1, I24-P24 (blank control)
add 10 µL reaction buffer to I1-P1, A24-H24 (substrate control)
MIX 180 µL diluted enzyme solution with 3.6 µL x 10 mM DCI (3,4-Dichloroisocoumarin) and aliquot 10 µL into I2-P2, A23-H23 (positive control inhibitor)
MIX 180 µL diluted enzyme solution with 3.6 µL DMSO and aliquot 10 µL into A2-H2, I23-P23 (no inhibitor control)
Incubate at room temperature for 1 hour
REACT Add 10 µL substrate solution into enzyme solution in the plate and mix well.
Read Plate Fluorescence
READ and RECORD the plate Relative fluorescence units (RFU) using Cytation 3 Multi-Mode Reader (BioTek, Winooski, VT)
Expected result
AMC product will give RFU signal at ex 350/em 450
Experimental Design
Plate Layout
DATA PROCESSING
Calculate the Z prime number of the screening plates to validate the screening:
Z’ = 1 – 3 *(Std.Dev of positive + Std.Dev of negative )/ |(Average of positive – Average of negative)|
Calculate the percentage of inhibition:
Inhibition % = ([RFU no inhibitor]-[RFU with compounds])/(RFU no inhibitor) * 100%
PLOT DATA
In Prism software, plot percentage of inhibition with corresponding number of compounds
Result
Exemplar results are shown
Acknowledgements
The buffer recipe is provided by Noa Lahav from Weizmann Institute of Science