External ID: HMS1625

Protocol: The fix-reporter plasmid was conjugated into this strain which the stably integrates into the chromosome using the mini-Tn7 system (PMID: 15908923). This plasmid consists of the fixK promoter, which is a target of the fixLJ pathway driving expression of GFP.
The day before screen an overnight culture of B. multivorans strain VC7102, with fix reporter, is set up in tryptic soy broth (TSB) at 37 degrees C with shaking. The day of the screen the overnight culture is diluted 1:100 in fresh tryptic soy broth.
The day of the screen, 30 microL of tryptic soy broth (TSB) is pipetted into columns 1-22 of a 384-well plate (Corning 3764) using the Combi multidrop dispenser. To column 24, 30 microL of TSB containing 78 microM of Benserazide TSB is added for a positive control. To column 23, 30 microL of TSB containing with DMSO (0.078% v/v in TSB) is added for a negative control. 300 nL of each compound are pin-transferred to each plate. For every compound plate 2 replicate assay plates are set up. 30 microL of the 1:100 diluted-B. multivorans strain VC7102 is added to each well using the Combi. Initial OD600 and GFP are measured using the PerkinElmer EnVision. Plates are stacked 5 high, covered with lids and incubated at 37 degrees C overnight (~18 h).
The following day, assay plates are read using a PerkinElmer EnVision (600 nm filter and GFP).
Positive control: Benserazide 39 microM in column 24 (No positive control was used for plates 2089 & 2090; Plates 2091-2093: columns 1 & 24)
Negative control: DMSO 300 nL/well in column 23 (For plates 2089 & 2090 negative controls were located in columns 2 & 24; plates 2091-2093: columns 2 & 23)

Comment: Analysis method:
For each compound well, the initial GFP value was subtracted from overnight GFP value to calculate the deltaGFP. The mean and standard deviation of the negative control wells deltaGFP (column 23) on both replicate plates was calculated. Wells with replicate average deltaGFP at least 3 standard deviations above the plate negative control deltaGFP average were scored as potential positives.

To determine activity scores, Z-scores were calculated for each replicate separately based on the replicate negative control deltaGFP plate average and standard deviation. The replicate average deltaGFP Z-scores were used for activity scores, with activity score of 100 set to Z-score = 4 and activity score = 0 (no activity) set to Z-score = 0. Z-scores > 4 were considered activity score = 100, and Z-scores < 0 were considered activity score = 0.

External ID: CHEMBL3868897

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2016
Volume: 79
Issue: 9
First Page: 2324
Last Page: 2331
DOI: 10.1021/acs.jnatprod.6b00469

External ID: DSHEA-v1-PXR-antagonist-CTF

Protocol: For PXR luciferase reporter gene assays, we used hPXR-LucHepG2cells provided by Dr. Taosheng Chen (Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital). Cells were cultured in EMEM supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100ug/mL streptomycin, and 500ug/mL of geneticin.

PROTOCOL TABLE (as described by Inglese J, Shamu CE and Guy RK. 2007) [1]
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION.
1; Cells; 5 uL; hPXR-LucHepG2; white solid-bottom Greiner plate.
2; Incubation; 5h; 37C, 95% humidity, 5% CO2
3; Compounds and control; 23 nL; Kalypsis pintool (Wako USA).
4; Reagent; 1uL; rifampicin (RIF) in the antagonist mode.
5; Incubation; 24 hr; 37C, 5% CO2.
6; Reagent; 1 uL; CellTiter-Fluor detection reagent.
7; Incubation; 1 hr; 37C, 5% CO2.
8; Read; Fluorescence; ViewLux plate reader.
9; Reagent; 4 uL; ONE-Glo Luciferase detection reagent.
10; Incubation; 30 min; room temperature.
11; Read; Luminescence; ViewLux plate reader.

NOTES (numbers refer to Sequence numbers above)
1. Briefly, 5uL of hPXR-LucHepG2 cells in phenol red-free DMEM containing 5% charcoal-stripped FBS, 1 mM sodium pyruvate (Invitrogen), 2 mM L-glutamine (Invitrogen), and 100 U/mL penicillin and 100ug/mL streptomycin were dispensed using a BioRAPTR FRD at 4 x 105cells/mL (2000cells/well) in tissue culture-treated 1536-well white assay plates (GreinerBio-One).
2. Plates were incubated for 5h at 37C, 95% humidity, and 5% CO2 to allow for cell attachment.
3. Compounds (final concentration for most substances ranged from 15.6 nM to 45.9uM), positive SPA70 (final concentration range of 2.8 nM to 92uM for the antagonist mode), and cytotoxicity control tetraoctyl ammonium bromide (final concentration of 92uM) were transferred (23 nL) via pintool (Wako Automation).
4-5. After compound transfer, plates were dispensed with 1uL of RIF (final concentration of 2uM) in the antagonist mode, using a BioRAPTR FRD and incubated for 24 h at 37C and 5% CO2.
6-8. Following incubation, 1uL of CellTiter-Fluor (Promega, Madison, Wisconsin) was added using a BioRAPTR FRD, after which all plates were incubated (37C/ 5% CO2) for1 h and then measured for fluorescence intensity (Ex/Em= 405/540 nm) on a ViewLux plate reader to determine cell viability.
9-11. Directly after this fluorescence reading, 4uL of ONE-Glo Luciferasere agent (Promega) was added to each well using the BioRAPTR FRD, followed by a 30 min incubation (RT) and read for luminescence intensity on a ViewLux detector.

REFERENCES:
[1] Inglese J, Shamu CE and Guy RK, Reporting data from high throughput screening of small molecule libraries, Nature Chemical Biology, 2007, 3(8): 438-441. doi.org/10.1038/nchembio0807-438.
[2] Lin W, Wu J, Dong H, Bouck D, Zeng FY, Chen T. Cyclin-dependent kinase 2 negatively regulates human pregnane X receptor-mediated CYP3A4 gene expression in HepG2 liver carcinoma cells. J Biol Chem. 2008 Nov 7;283(45):30650-7. doi: 10.1074/jbc.M806132200. Epub 2008 Sep 9. PMID: 18784074; PMCID: PMC2662154.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods.

Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent antagonists are ranked higher than compounds that showed no activity.
2. For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = -1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 || ratio.curve_class == -2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

External ID: DSHEA-v1-PXR-antagonist-ONEGlo

Protocol: For PXR luciferase reporter gene assays, we used hPXR-LucHepG2cells provided by Dr. Taosheng Chen (Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital). Cells were cultured in EMEM supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100ug/mL streptomycin, and 500ug/mL of geneticin.

PROTOCOL TABLE (as described by Inglese J, Shamu CE and Guy RK. 2007) [1]
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION.
1; Cells; 5 uL; hPXR-LucHepG2; white solid-bottom Greiner plate.
2; Incubation; 5h; 37C, 95% humidity, 5% CO2
3; Compounds and control; 23 nL; Kalypsis pintool (Wako USA).
4; Reagent; 1uL; rifampicin (RIF) in the antagonist mode.
5; Incubation; 24 hr; 37C, 5% CO2.
6; Reagent; 1 uL; CellTiter-Fluor detection reagent.
7; Incubation; 1 hr; 37C, 5% CO2.
8; Read; Fluorescence; ViewLux plate reader.
9; Reagent; 4 uL; ONE-Glo Luciferase detection reagent.
10; Incubation; 30 min; room temperature.
11; Read; Luminescence; ViewLux plate reader.

NOTES (numbers refer to Sequence numbers above)
1. Briefly, 5uL of hPXR-LucHepG2 cells in phenol red-free DMEM containing 5% charcoal-stripped FBS, 1 mM sodium pyruvate (Invitrogen), 2 mM L-glutamine (Invitrogen), and 100 U/mL penicillin and 100ug/mL streptomycin were dispensed using a BioRAPTR FRD at 4 x 105cells/mL (2000cells/well) in tissue culture-treated 1536-well white assay plates (GreinerBio-One).
2. Plates were incubated for 5h at 37C, 95% humidity, and 5% CO2 to allow for cell attachment.
3. Compounds (final concentration for most substances ranged from 15.6 nM to 45.9uM), positive SPA70 (final concentration range of 2.8 nM to 92uM for the antagonist mode), and cytotoxicity control tetraoctyl ammonium bromide (final concentration of 92uM) were transferred (23 nL) via pintool (Wako Automation).
4-5. After compound transfer, plates were dispensed with 1uL of RIF (final concentration of 2uM) in the antagonist mode, using a BioRAPTR FRD and incubated for 24 h at 37C and 5% CO2.
6-8. Following incubation, 1uL of CellTiter-Fluor (Promega, Madison, Wisconsin) was added using a BioRAPTR FRD, after which all plates were incubated (37C/ 5% CO2) for1 h and then measured for fluorescence intensity (Ex/Em= 405/540 nm) on a ViewLux plate reader to determine cell viability.
9-11. Directly after this fluorescence reading, 4uL of ONE-Glo Luciferasere agent (Promega) was added to each well using the BioRAPTR FRD, followed by a 30 min incubation (RT) and read for luminescence intensity on a ViewLux detector.

REFERENCES:
[1] Inglese J, Shamu CE and Guy RK, Reporting data from high throughput screening of small molecule libraries, Nature Chemical Biology, 2007, 3(8): 438-441. doi.org/10.1038/nchembio0807-438.
[2] Lin W, Wu J, Dong H, Bouck D, Zeng FY, Chen T. Cyclin-dependent kinase 2 negatively regulates human pregnane X receptor-mediated CYP3A4 gene expression in HepG2 liver carcinoma cells. J Biol Chem. 2008 Nov 7;283(45):30650-7. doi: 10.1074/jbc.M806132200. Epub 2008 Sep 9. PMID: 18784074; PMCID: PMC2662154.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods.

Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent antagonists are ranked higher than compounds that showed no activity.
2. For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = -1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 || ratio.curve_class == -2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

External ID: DSHEA-v1-PXR-agonist-ONEGlo

Protocol: For PXR luciferase reporter gene assays, we used hPXR-LucHepG2cells provided by Dr. Taosheng Chen (Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital). Cells were cultured in EMEM supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100ug/mL streptomycin, and 500ug/mL of geneticin.

PROTOCOL TABLE (as described by Inglese J, Shamu CE and Guy RK. 2007) [1]
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION.
1; Cells; 5 uL; hPXR-LucHepG2; white solid-bottom Greiner plate.
2; Incubation; 5h; 37C, 95% humidity, 5% CO2
3; Compounds and control; 23 nL; Kalypsis pintool (Wako USA).
4; Reagent; 1uL; rifampicin (RIF) in the antagonist mode.
5; Incubation; 24 hr; 37C, 5% CO2.
6; Reagent; 1 uL; CellTiter-Fluor detection reagent.
7; Incubation; 1 hr; 37C, 5% CO2.
8; Read; Fluorescence; ViewLux plate reader.
9; Reagent; 4 uL; ONE-Glo Luciferase detection reagent.
10; Incubation; 30 min; room temperature.
11; Read; Luminescence; ViewLux plate reader.

NOTES (numbers refer to Sequence numbers above)
1. Briefly, 5uL of hPXR-LucHepG2 cells in phenol red-free DMEM containing 5% charcoal-stripped FBS, 1 mM sodium pyruvate (Invitrogen), 2 mM L-glutamine (Invitrogen), and 100 U/mL penicillin and 100ug/mL streptomycin were dispensed using a BioRAPTR FRD at 4 x 105cells/mL (2000cells/well) in tissue culture-treated 1536-well white assay plates (GreinerBio-One).
2. Plates were incubated for 5h at 37C, 95% humidity, and 5% CO2 to allow for cell attachment.
3. Compounds (final concentration for most substances ranged from 15.6 nM to 45.9uM), positive control rifampicin (RIF; final concentration range of 2.8 nM to 92uM for the agonist mode), and cytotoxicity control tetraoctyl ammonium bromide (final concentration of 92uM) were transferred (23 nL) via pintool (Wako Automation).
4-5. After compound transfer, plates were dispensed with 1uL of the media in the agonist mode using a BioRAPTR FRD and incubated for 24 h at 37C and 5% CO2.
6-8. Following incubation, 1uL of CellTiter-Fluor (Promega, Madison, Wisconsin) was added using a BioRAPTR FRD, after which all plates were incubated (37C/ 5% CO2) for1 h and then measured for fluorescence intensity (Ex/Em= 405/540 nm) on a ViewLux plate reader to determine cell viability.
9-11. Directly after this fluorescence reading, 4uL of ONE-Glo Luciferasere agent (Promega) was added to each well using the BioRAPTR FRD, followed by a 30 min incubation (RT) and read for luminescence intensity on a ViewLux detector.

REFERENCES:
[1] Inglese J, Shamu CE and Guy RK, Reporting data from high throughput screening of small molecule libraries, Nature Chemical Biology, 2007, 3(8): 438-441. doi.org/10.1038/nchembio0807-438.
[2] Lin W, Wu J, Dong H, Bouck D, Zeng FY, Chen T. Cyclin-dependent kinase 2 negatively regulates human pregnane X receptor-mediated CYP3A4 gene expression in HepG2 liver carcinoma cells. J Biol Chem. 2008 Nov 7;283(45):30650-7. doi: 10.1074/jbc.M806132200. Epub 2008 Sep 9. PMID: 18784074; PMCID: PMC2662154.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods.

Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent agonists are ranked higher than compounds that showed apparent antagonists.
2. For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = 1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == 1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == 2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == 1.2 || ratio.curve_class == 2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds also have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

External ID: DSHEA-v1-PXR-agonist-CTF

Protocol: For PXR luciferase reporter gene assays, we used hPXR-LucHepG2cells provided by Dr. Taosheng Chen (Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital). Cells were cultured in EMEM supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100ug/mL streptomycin, and 500ug/mL of geneticin.

PROTOCOL TABLE (as described by Inglese J, Shamu CE and Guy RK. 2007) [1]
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION.
1; Cells; 5 uL; hPXR-LucHepG2; white solid-bottom Greiner plate.
2; Incubation; 5h; 37C, 95% humidity, 5% CO2
3; Compounds and control; 23 nL; Kalypsis pintool (Wako USA).
4; Reagent; 1uL; rifampicin (RIF) in the antagonist mode.
5; Incubation; 24 hr; 37C, 5% CO2.
6; Reagent; 1 uL; CellTiter-Fluor detection reagent.
7; Incubation; 1 hr; 37C, 5% CO2.
8; Read; Fluorescence; ViewLux plate reader.
9; Reagent; 4 uL; ONE-Glo Luciferase detection reagent.
10; Incubation; 30 min; room temperature.
11; Read; Luminescence; ViewLux plate reader.

NOTES (numbers refer to Sequence numbers above)
1. Briefly, 5uL of hPXR-LucHepG2 cells in phenol red-free DMEM containing 5% charcoal-stripped FBS, 1 mM sodium pyruvate (Invitrogen), 2 mM L-glutamine (Invitrogen), and 100 U/mL penicillin and 100ug/mL streptomycin were dispensed using a BioRAPTR FRD at 4 x 105cells/mL (2000cells/well) in tissue culture-treated 1536-well white assay plates (GreinerBio-One).
2. Plates were incubated for 5h at 37C, 95% humidity, and 5% CO2 to allow for cell attachment.
3. Compounds (final concentration for most substances ranged from 15.6 nM to 45.9muM), positive control rifampicin (RIF; final concentration range of 2.8 nM to 92muM for the agonist mode), and cytotoxicity control tetraoctyl ammonium bromide (final concentration of 92muM) were transferred (23 nL) via pintool (Wako Automation).
4-5. After compound transfer, plates were dispensed with 1muL of the media in the agonist mode using a BioRAPTR FRD and incubated for approximately 24 h at 37 degrees C and 5% CO2.
6-8. Following incubation, 1uL of CellTiter-Fluor (Promega, Madison, Wisconsin) was added using a BioRAPTR FRD, after which all plates were incubated (37C/ 5% CO2) for 1 h and then measured for fluorescence intensity (Ex/Em= 405/540 nm) on a ViewLux plate reader to determine cell viability.
9-11. Directly after this fluorescence reading, 4uL of ONE-Glo Luciferasere agent (Promega) was added to each well using the BioRAPTR FRD, followed by a 30 min incubation (RT) and read for luminescence intensity on a ViewLux detector.

REFERENCES:
[1] Inglese J, Shamu CE and Guy RK, Reporting data from high throughput screening of small molecule libraries, Nature Chemical Biology, 2007, 3(8): 438-441. doi.org/10.1038/nchembio0807-438.
[2] Lin W, Wu J, Dong H, Bouck D, Zeng FY, Chen T. Cyclin-dependent kinase 2 negatively regulates human pregnane X receptor-mediated CYP3A4 gene expression in HepG2 liver carcinoma cells. J Biol Chem. 2008 Nov 7;283(45):30650-7. doi: 10.1074/jbc.M806132200. Epub 2008 Sep 9. PMID: 18784074; PMCID: PMC2662154.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods.

Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent agonists are ranked higher than compounds that showed apparent antagonist.
2. For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = 1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == 1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == 2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == 1.2 || ratio.curve_class == 2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds also have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

External ID: CHEMBL814496

Protocol: N/A

Comment: Journal: Bioorg. Med. Chem. Lett.
Year: 1997
Volume: 7
Issue: 5
First Page: 567
Last Page: 572
DOI: 10.1016/S0960-894X(97)00046-2

External ID: HERG01

Protocol: NCGC Assay Protocol Summary:

HERG assay (FluxORTM thallium flux assay) was initially developed by Invitrogen/Molecular Probes, and then miniaturized into 1536-well plate in a homogeneous format by NCGC. This assay measures the activity of potassium channel using thallium dye (FluxOR) flux as surrogate measurement for potassium into the cells with a FDSS-7000 kinetic plate reader (Hamamatsu Corp., Hamamatsu City, Japan). The hERG ion channel is transduced into mammalian cells (U2OS) using a baculovirus (Bacmam) construct harboring the hERG K+ ion channel. So far we screened LOPAC1280 library (Sigma), the NTP collection of 1408 compounds, and the NCGC Pharmaceutical Collection (NPC), in which many well defined HERG blockers are present. The rank order potencies of many of these compounds are similar to that of other HERG assays (membrane potential, Rb+ flux, patch clamp, etc). This quick and homogeneous assay is also found to be sensitive, specific, and robust.

Using the FluxORTM thallium flux assay, the activity of potassium channel using thallium dye (FluxOR) flux as surrogate measurement for potassium into the cells was measured in the U2OS cell line transduced with hERG K+ ion channel using a baculovirus (Bacmam) using Opti-MEM medium (Invitrogen) containing 2% fetal calf serum (FCS, HyCone) following loading buffer addition, compound treatment for around 10 minutes and finally adding stimulation buffer. The assay was performed in black clear Kalypsys 1536-well plates. In the screen, Astemizole was used as positive controls. Library compounds were measured for their ability to cause hERG channel blockage in the cell line, as reflected by a decrease in fluorescence intensity, in a concentration-dependent manner. Data were normalized to the controls for basal activity (DMSO only) and 100% inhibition (5uM Astemizole). AC50 values were determined from concentration-response data modeled with the standard Hill equation.

qHTS protocol for hERG-U2OS cellular assay

[Step] [Parameter] [Value] [Description]

1. Day 1: Replace medium in 70-80% confluent T225 flask with 2.5 mL of hERG-BacMam virus plus 12.5 mL of phosphate buffered saline (PBS) (corresponding roughly to a multiplicity of infection ratio of 100 virus particles/cell)
2. Incubation: 4 hrs @ room Temperature in Dark
3. Reagent; Remove virus; wash once with 25 ml DPBS
4. Reagent; 35 ml culture medium
5. Incubation; 37oC overnight
6. Day2: Reagent; 3 uL; 2000 U2OS cells/well
7. Time; 4 hr; 37oC incubation
8. Loading buffer; 1 uL; 0.7X;
9. Incubation: 1hr @ RT in Dark.
10. Compounds; 23 nL; 0.59 nM to 92 uM
11. Controls; 23 nL; Astemizole 1.4 nM to 92 uM
12. Time; 10min; 37oC incubation
13. Read fluorescence Intensity on FDSS for 10 Sec with 1 sec interval
14. Reagent; 1 uL; stimulation buffer
15. Read fluorescence Intensity on FDSS for 2 min with 1 sec interval
16. Detection; Fluorescence Intensity; FDSS

Comment: Compound Ranking:

1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. See data field "Curve Description". For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39. Fit_LogAC50 was used for determining relative score and was scaled to each curve class' score range.

External ID: UIHTS20180925

Protocol: Assay overview:
The purpose of this assay is to identify test compounds that differentially kill either epithelial cells or mesenchymal cells, critical components of EMT. The PC-3E+ and TEM4-18 cell lines, characterized as epithelial cells and mesenchymal cells respectively, were established in Henry Lab (Ref 1). For potential discriminative modulators of EMT, the two cells lines were labeled with GFP and mCherry respectively, and co-cultured together to eliminate those hits that non-discriminatingly kill both epithelial cells and mesenchymal cells by cytotoxicity irrelevant to the EMT properties.
Protocol for the EMT project:
The primary screening data were generated as described in HTS assay protocol table (Ref 2).

Table 1: HTS assay protocol table
Step Parameter Value Description
1. Plate cells 200 uL By MultiFlo. PC3E GFP 2,000 cells/ well and TEM418 mCherry 2,000 cells/well (1:1). Overnight incubation
2. Remove media Flip the plate
3. Add fresh media 150 uL By MultiFlo
4. Controls 200 uL C01-H01, C12 -H12, Hygromycin dose response from H to C were positive control. Wells A01, B01, A12 and B12 were negative control
5. Library 50 uL MSSP library 1 uM final from middle plate in full media
6. Incubation 72 hrs 37 C and 5% CO2
7. Assay readout GFP and mCherry channel imaging Perkin Elmer Operetta high content imaging system, with Harmony image analysis software.
8. Image analysis Green cells and Read cells counting Normalized to the average cell number of well B1 and B12 (no inhibition of cell viability) controls on each plate to get relative cell viability for each well.
9. Hit selection 11 hits The hit criteria for preferential cell killing are compounds that Redcells_Normalized is lower or equal 0.41, GreenCells_Normalized is higher or equal
0.55, RedCells/GreenCells_Normalized ratio is lower or equal 0.65, and Non-fluorescent by itself for Red cell killing OR Greencells_Normalized is
lower or equal 0.41, RedCells_Normalized is higher or equal 0.46, RedCells/GreenCells_Normalized ratio is higher or equal 1.8 and Non-fluorescent
by itself for Green cell killing.

The primary screening data (imaging data) were translated into Green or Red cell numbers in each well in the data file.

Comment: Preferential killing compounds are considered as active hits (score of 100) when meeting one of two groups of criteria:

1. Compounds that Redcells_Normalized is lower or equal 0.41, GreenCells_Normalized is higher or equal 0.55, RedCells/GreenCells_Normalized ratio is lower or equal 0.65, and Non-fluorescent by itself for Red cell killing.

OR

2. Greencells_Normalized is lower or equal 0.41, RedCells_Normalized is higher or equal 0.46, RedCells/GreenCells_Normalized ratio is higher or equal 1.8 and Non-fluorescent by itself for Green cell killing.

External ID: CHEMBL4303805

Protocol: N/A

Comment: Target ChEMBL ID: CHEMBL4303835
ChEMBL Target Name: SARS-CoV-2
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: SARS-CoV-2 Screening Data

External ID: CHEMBL3868903

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2016
Volume: 79
Issue: 9
First Page: 2324
Last Page: 2331
DOI: 10.1021/acs.jnatprod.6b00469

External ID: CHEMBL984935

Protocol: N/A

Comment: Journal: J. Nat. Prod.
Year: 2003
Volume: 66
Issue: 12
First Page: 1574
Last Page: 1577
DOI: 10.1021/np0302450

Target ChEMBL ID: CHEMBL614628
ChEMBL Target Name: Raji
ChEMBL Target Type: CELL-LINE - Target is a specific cell-line
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

External ID: CHEMBL984944

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2003
Volume: 66
Issue: 12
First Page: 1582
Last Page: 1585
DOI: 10.1021/np0302293

External ID: CHEMBL984943

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2003
Volume: 66
Issue: 12
First Page: 1582
Last Page: 1585
DOI: 10.1021/np0302293

External ID: CHEMBL984945

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2003
Volume: 66
Issue: 12
First Page: 1582
Last Page: 1585
DOI: 10.1021/np0302293

External ID: CHEMBL984940

Protocol: N/A

Comment: Journal: J. Nat. Prod.
Year: 2003
Volume: 66
Issue: 12
First Page: 1582
Last Page: 1585
DOI: 10.1021/np0302293

Target ChEMBL ID: CHEMBL614628
ChEMBL Target Name: Raji
ChEMBL Target Type: CELL-LINE - Target is a specific cell-line
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

External ID: CHEMBL4495582

Protocol: N/A

Comment: Target ChEMBL ID: CHEMBL4523582
ChEMBL Target Name: Replicase polyprotein 1ab
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

Data Source: SARS-CoV-2 Screening Data

External ID: CHEMBL984942

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2003
Volume: 66
Issue: 12
First Page: 1582
Last Page: 1585
DOI: 10.1021/np0302293

External ID: CHEMBL984941

Protocol: N/A

Comment: Journal: J Nat Prod
Year: 2003
Volume: 66
Issue: 12
First Page: 1582
Last Page: 1585
DOI: 10.1021/np0302293

External ID: APP-Toga-CHIKV-nsP2-f2-f9

Protocol: PROTOCOL TABLE (as described by Inglese J, Shamu CE and Guy RK. 2007)
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION.
1; Control / Compound; 20 nL; Echo 655 acoustic dispenser, Greiner 1536-well solid bottom black plate.
2; Enzyme; 4 uL; BioRAPTR FRD liquid dispenser (Beckman Coulter).
3; Incubation; 15 min; room temperature.
4; Reagent; 4 uL; 2.5 uM Peptide 2 substrate.
5; Incubation; 1 hr; room temperature.
6; Detection; Fluorescence; WiewLux microplate reader (PerkinElmer), 525 nm excitation, 598/25 nm emission.

NOTES (numbers refer to sequence numbers above).
1.Briefly, 20 nL DMSO, positive control ZnAc (20nM final concentration), and test compounds were transferred into a 1,536-well solid bottom black plate (789176-F, Greiner One) via Echo 655 acoustic dispenser (Beckman Coulter). For primary screens, compounds were tested at 7 concentrations, 1:3 dilution points ranging from 25 uM to 34 nM. Follow-up confirmatory screens were carried out at 11 concentrations, 1:3 dilution points from 25 uM to 0.42 nM.
2.Four uL nsP2pro enzyme mix (150 nM final concentration) in 10 mM Tris-HCl pH 8.0 with 0.01% Tween 20 assay buffer was dispensed into the plate using a BioRAPTR FRD liquid dispenser (Beckman Coulter).
3.The plate was incubated at room temperature (protected from light) for 15 min
4.Four microliter of peptide 2 substrate (2.5 uM final concentration) in assay buffer was added to the plate.
5.After 1 hour, plates were immediately read on a ViewLux high-throughput CCD imager (Exposure = 10 sec, Gain = High, Speed = Slow, Binning = 2X). The above assay was also incorporated in the NCATS HTS facility41, which allowed for robotic liquid and compound dispensing, microplate handling, and fluorescence reading.

REFERENCE:
Inglese J, Shamu CE and Guy RK, Reporting data from high throughput screening of small molecule libraries, Nature Chemical Biology, 2007, 3(8): 438-441. doi.org/10.1038/nchembio0807-438.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods [1].

Compound Ranking:
1.Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2.For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = -1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 || ratio.curve_class == -2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

Reference:
1. Inglese J, Auld DS, Jadhav A, et al. Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological activities in large chemical libraries. Proc Natl Acad Sci U S A. 2006;103(31):11473-11478.

External ID: APP-Toga-CHIKV-nsP2-f3_f16

Protocol: PROTOCOL TABLE (as described by Inglese J, Shamu CE and Guy RK. 2007)
SEQUENCE No. (e.g., 1, 2, 3, etc.); PARAMETER (e.g., Cells, Incubation, Reagent, etc.); VALUE; DESCRIPTION.
1a; Reagent; 3 uL; Papain in assay buffer.
1b; Reagent; 3uL; Assay buffer
2; Compound; 17 nL; Echo 655 acoustic dispenser (Beckman Coulter).
3; Incubation; 15 min; room temperature in the dark.
4: Reagent; 1 uL; Z-FR-AMC in assay buffer.
5; Incubation; 15 sec, 271g; centrifugation.
6; Detection; Fluorescence; time 0, Viewlux microplate reader (PerkinElmer) 355 nm excitation, 460 nm emission
7; Incubation; 10 min; room temperature
8; Detection; Fluorescence; time 10; ViewLux microplate reader (PerkinElmer), 355 nm excitation, 460 nm emission.

NOTES (numbers refer to sequence numbers above).
1a. Medium-binding black solid-bottom Greiner plates (cat. 789176-F). Dispense 3 uL of 1.33X papain in assay buffer (100 mM sodium acetate, pH 5.5, 5 mM dl-cysteine, 0.01% Tween-20 v/v) to columns 1, 2, 5-48 via Wako/Kalypsys dispenser. Papain (cat. P4762, Sigma) was dispensed to produce 5 nM final concentration. Enzyme solution kept on ice during experiment. Prepare papain as 50% glycerol (v/v) at final concentration of 10 mg/mL (427 uM, 100 U/mL). Sources: microplates (Greiner 789176-F), papain (Sigma P4762), sodium acetate (Bioworld 40120009-2), cysteine (Sigma 861677), Tween-20 (Sigma P1379), water (GIBCO 10977-015; Gibco).
1b. Dispense 3 uL of assay buffer (100 mM sodium acetate, pH 5.5, 5 mM dl-cysteine, 0.01% Tween-20 v/v) to columns 3 and 4 via Wako/Kalypsys dispenser. Assay buffer solution kept on ice during experiment.
2. Compound addition by single pin transfer (17 nL) using Wako pintool. Compound solutions in source plate: 169 nM to 10 mM DMSO stock solutions. Final concentrations: 0.664 nM to 39.2 uM, respectively. Final DMSO concentration: 0.5% (v/v).
3. RT incubation. Kalypsys lids used as microplate coverings. Protected from light.
4. Dispense 1 uL of 4x substrate mixture in assay buffer (100 mM sodium acetate, pH 5.5, 5 mM dl-cysteine, 0.01% Tween-20 v/v) to columns 1-48 via Wako/Kalypsys dispenser. Z-FR-AMC substrate was dispensed to produce 2 uM final concentration. Substrate solution kept on ice during experiment. Prepare Z-FR-AMC as 32.1 mM stock solution in DMSO. Source: Z-FR-AMC (HCl salt) (Bachem I-1160).
5. Centrifugation step to remove bubbles.
6. ViewLux microplate reader (PerkinElmer, Waltham, MA). Optics: excitation filter 340 (30) nm, emission filter 450 (20) nm. Energy = 2000. Exposure time = 2 sec.
7. RT incubation. Incubation time 10 min.
8. ViewLux microplate reader. Optics: excitation filter 340 (30) nm, emission filter 450 (20) nm. Energy = 2000. Exposure time = 2 sec.

REFERENCE:
Inglese J, Shamu CE and Guy RK, Reporting data from high throughput screening of small molecule libraries, Nature Chemical Biology, 2007, 3(8): 438-441. doi.org/10.1038/nchembio0807-438.

Comment: Disclaimer:
Although all reasonable efforts have been made to ensure the accuracy and reliability of the data, caution should be exercised when interpreting the results as artifacts are possible from nonspecific effects such as assay signal interference. The curve fitting and activity calls presented here are based on the NCATS analysis methods [1].

Compound Ranking:
1. Compounds are first classified as having full titration curves, partial modulation, partial curve (weaker actives), single point activity (at highest concentration only), or inactive. For this assay, apparent inhibitors are ranked higher than compounds that showed apparent activation.
2. For all inactive compounds, with a ratio activity curve class of 4, PUBCHEM_ACTIVITY_SCORE is 0. For all active compounds, a score range was given for each curve class type given above. Active compounds have PUBCHEM_ACTIVITY_SCORE between 40 and 100. For a ratio activity curve class = -1.1, score = 80+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 && abs(ratio.max_response) > 6*10, score = 60+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -2.1 || ( ratio.curve_class==-2.2 && abs(ratio.max_response) > 6*10), score = 40+abs((log_ac50+4.5)*inf_activity/20). For ratio.curve_class == -1.2 || ratio.curve_class == -2.2, score = 20+abs((log_ac50+4.5)*inf_activity/20). Inconclusive compounds, with a donor curve class other than 4, have PUBCHEM_ACTIVITY_SCORE of 10. Inconclusive compounds have PUBCHEM_ACTIVITY_SCORE between 1 and 39.

Reference:
1. Inglese J, Auld DS, Jadhav A, et al. Quantitative high-throughput screening: a titration-based approach that efficiently identifies biological activities in large chemical libraries. Proc Natl Acad Sci U S A. 2006;103(31):11473-11478.