External ID: CHEMBL5375826

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL1163120
ChEMBL Target Name: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit gamma
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: OPRM1-OPRD1_AG_LUMI_1536_1X%ACT PRUN

Protocol: Assay Overview:

The purpose of this assay is to identify compounds that activate heterodimer formation between the mu (OPRM1) and delta (OPRD1) opioid receptors, resulting in membrane recruitment of beta-arrestin. The assay monitors GPCR-beta-arrestin proximity using low affinity fragment complementation of beta-galactosidase (beta-gal). This assay employs U2OS cells which express OPRD1, OPRM1 fused to a beta-gal peptide fragment (enzyme donor), and beta-arrestin fused to the complementary beta-gal fragment (enzyme acceptor). Cells are incubated with test compound, followed by measurement of well luminescence. As designed, compounds that induce formation of OPRD1 homodimers or OPRM1-OPRD1 (Mu-Delta) heterodimers will cause beta-arrestin recruitment, resulting in reconstitution of the beta-gal holoenzyme. The reconstituted holoenzyme can then catalyze the hydrolysis of a substrate which yields a chemiluminescent signal, resulting in increased well luminescence. Deltorphin B will be used as the high (100% RLU) control for agonists, and wells containing cells treated with DMSO will be used as the low (0% RLU) control. Compounds were tested in singlicate at a final nominal concentration of 9.3 uM.

Protocol Summary:

The U2OS-OPRM1-OPRD1 (Mu-Delta) cell line was routinely cultured in T-175 sq cm flasks at 37 C and 95% relative humidity (RH). The growth media consisted of a 1:1 mixture of Ham's F-12 Nutrient Media (F-12) and Dulbecco's Modified Eagle Media (DMEM) supplemented with 10% v/v heat-inactivated certified fetal bovine serum, 25 mM HEPES, 250 ug/mL Geneticin, 250 ug/mL Hygromycin B, 0.25 ug/mL Puromycin and 1X antibiotic mix (penicillin, streptomycin, and neomycin).

The day before the assay 1000 cells in 3 uL of cell plating media were seeded into each well of 1536 well microtiter plates and allowed to incubate at 37 C, 5% CO2, and 95 % RH for 23 hours. Next, 28 nL of test compound in DMSO, Deltorphin B (0.9 uM final concentration) in DMSO, or DMSO alone were dispensed to the appropriate wells. The plates were then incubated for 3 hours at 37 C, 5% CO2, and 95 % RH. The assay was started by adding 2 uL of PathHuntertrade mark reagent (prepared according to the manufacturer's protocol); followed by 1 hour incubation at room temperature. Then, Well Luminescence was read on the ViewLux plate reader

The percent activation for each compound was calculated as follows:

% Activation = ( ( Ratio_Test_Compound - Median_Ratio_Low_Control ) / ( Median_Ratio_High_Control - Median_Ratio_Low_Control ) ) * 100

Where:

High_Control is defined as wells containing cells, Deltorphin B and DMSO.
Test_Compound is defined as wells containing cells, test compounds and DMSO.
Low_Control is defined as wells containing cells and DMSO.

A mathematical algorithm was used to determine nominally activating compounds in the primary screen. Two values were calculated: (1) the average percent activation of all compounds tested, and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter, i.e. any compound that exhibited greater % activation than the cutoff parameter was declared active.

PubChem Activity Outcome and Score:

The reported PubChem Activity Score has been normalized to 100% observed primary activation. Negative % activation values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-2, and for inactive compounds 2-0.

List of Reagents:

PathHuntertrade mark B-arrestin recruitment assay, containing the U2OS OPRM1 OPRD1 Beta-arrestin cell line; PathHunter Detection Kit (DiscoveRx, part, 93-0558C3)
Ham's F-12 media (Invitrogen, part 11765-054)
DMEM media (Invitrogen, part 11995-073)
Detachin (Genlantis, part T100100)
Heat Inactivated Fetal Bovine Serum (Invitrogen, part 10082-147)
Puromycin (Invitrogen, part A11138-02)
Hygromycin B (Invitrogen, part 10687-010)
Geneticin (Invitrogen, part 10131-027)
100X Penicillin-Streptomycin-Neomycin mix (Invitrogen, part 15640-055)
T-175 tissue culture flasks (Nunc, part 159910)
Agonist: Deltorphin B (Anaspec, part 62683)
1536-well plates (Greiner, part 789173)

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR.

External ID: CHEMBL5375822

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL5554
ChEMBL Target Name: Phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing beta polypeptide
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHRM1_AG_FLUO8_1536_1X%ACT PRUN

Protocol: Assay Overview:

The purpose of this assay is to identify compounds that act as agonists of the human M1 muscarinic receptor (CHRM1; M1). In this assay, CHO-K1 cells stably expressing human M1 are loaded, intracellularly with the calcium indicator dye, Fluo-8, followed by treatment with agonist control or test compounds. As designed, compounds that act as CHRM1 agonists will increase intracellular calcium mobilization, resulting in increased relative fluorescence of the indicator dye and well fluorescence. Compounds are tested in singlicate at a final nominal concentration of 3 uM.

Protocol Summary:

The CHO-hM1 cell line was routinely cultured in T-175 sq cm flasks at 37 C and 95% relative humidity (RH). The growth media consisted of Ham's F-12 Nutrient Media (F-12) supplemented with 10% v/v heat-inactivated qualified fetal bovine serum, 20 mM HEPES, 50 ug/mL Geneticin, and 1X antibiotic mix (penicillin and streptomycin).

The day before the assay 3000 cells in 3 uL of growth media were seeded into each well of 1536 well microtiter plates and allowed to incubate at 37 C, 5% CO2, and 95 % RH for 17-24 hours. Next, 2 uL of the fluorogenic Fluo-8 intracellular calcium indicator mixture (prepared according to the manufacturer's protocol) was added to each well. Plates were then incubated for 1 hour at 37 C, 5% CO2, and 95 % RH, followed by 30 minute incubation at room temperature. Then, 15 nL of test compound in DMSO were dispensed to appropriate wells. The assay was started by performing a basal read of plate fluorescence (470-495 nm excitation and 515-575 nm emission) for 5 seconds on the FLIPR Tetra (Molecular Devices). Then a real time fluorescence measurement was immediately performed for the remaining 140 seconds of the assay. A ratio for each well was calculated to normalize assay data, according to the following mathematical expression:

Ratio = I_Max / I_Min

Where:

I_Max represents the maximum measured fluorescence emission intensity over the 140 second read.
I_Min represents the minimum (basal) measured fluorescence emission intensity before compound was added.

The percent activation was calculated from the median ratio as follows:

%_Activation = ( ( Ratio_Test_Compound - Median_Ratio_Low_Control ) / ( Median_Ratio_High_Control - Median_Ratio_Low_Control ) ) * 100

Where:

Test_Compound is defined as wells containing test compound.
Low_Control is defined as wells containing DMSO.
High_Control is defined as wells containing Acetylcholine (EC100) and DMSO.

PubChem Activity Outcome and Score:

A mathematical algorithm was used to determine nominally activating compounds in the primary screen. Two values were calculated for each assay plate: (1) the average percent activation of test compound wells and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter for the entire run, i.e. any compound that exhibited greater % activation than the entire screen's cutoff parameter was declared active.

The reported PubChem Activity Score has been normalized to 100% observed primary activation. Negative % activation values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-1, and for inactive compounds 1-0.

List of Reagents:

Cell line: Chinese Hamster Ovary (CHO) cells containing hM1 receptor; (Conn Lab)
Calcium sensitive dye: Fluo-8 No Wash Calcium Assay Kit; (AAT Bioquest, part 36316)
Growth media: Ham's F-12; 10% FBS, 20mM HEPES, 50 ug/mL G418
Assay media: Ham's F-12, 10% FBS, 20 mM HEPES
Assay plates: Aurora black/clear 1536well FLIPR plate; (Aurora, part 00019326)
Probenecid: 250 mM (pH 8.0); (Sigma P8761)
Agonist: Acetylcholine (50 mM stock in water); Sigma A9187

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR.

External ID: CHEMBL5375818

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL2527
ChEMBL Target Name: Serine/threonine-protein kinase Chk2
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL4296186

Protocol: N/A

Comment: Compounds with activity <= 10uM or explicitly reported as active by ChEMBL are flagged as active in this PubChem assay presentation.

Target ChEMBL ID: CHEMBL350
ChEMBL Target Name: Klebsiella pneumoniae
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL5375814

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4630
ChEMBL Target Name: Serine/threonine-protein kinase Chk1
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL5375810

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4070
ChEMBL Target Name: Casein kinase II alpha (prime)
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: 7124-01_Inhibitor_SinglePoint_HTS_Activity

Protocol:
Protocol:
1) Plate 10 uL BL2-NFkB-luc cells at 12.5K cells/well, using a Multidrop Combi reagent dispenser (1,250 cells/uL).
2) Add 25 nL compound or positive control, by pin transfer; IKK inhibitor VII will be used at 50 uM.
3) Incubate at 37 masculineC for 1 hour (allowing compounds to enter cells for action).
4) Add 5 uL 192 ng/mL tCD40L per well for a final concentration of 64 ng/ml using a Thermo Multidrop Combi.
5) Incubate at 37 masculineC for 4 hrs, then leave plate at RT for 30 minutes.
6) Add 15 uL SteadyGlo luciferase substrate (Promega) per well using a Thermo Multidrop Combi.
7) Incubate at RT for 5min, then read Luminescence using LJL Analyst HT plate reader.

Comment: PRESENCE OF CONTROLS: Neutral control wells (NC) and positive control wells (PC) were included on every plate.

EXPECTED OUTCOME: Active compounds result in decreasing readout signal.

NORMALIZATION:
The raw signals of the plate wells were normalized using the 'Neutral Controls Minus Inhibitors' method in Genedata Assay Analyzer (v10.0.2):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of -100.
Experimental wells values were scaled to this range.

PATTERN CORRECTION: No plate pattern correction algorithm from Genedata Condoseo (v.10.0.2) was applied.

PUBCHEM_ACTIVITY_SCORE:
This was set as equal to the mean of the normalized sample replicate activities, rounded to the nearest integer .
The minimum PUBCHEM_ACTIVITY_SCORE required for a compound to be called a hit (the activity threshold, or AT) was set at -50.

PERCENTAGE OF ACTIVE REPLICATES:
For each sample, the percentage of replicates (PCT_ACTIVE_REP) which had activity scores >= AT was determined.
The minimum percentage of replicates required for a compound to be called a hit (PAR_T) was set at 55.

PUBCHEM_ACTIVITY_OUTCOME:
Samples passing BOTH threshold criteria were assigned an outcome of 2 (active):
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP >= PAR_T

Samples passing NEITHER threshold criteria were assigned an outcome of 1 (inactive):
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP < PAR_T

Samples passing AT only were assigned an outcome of 1 (inactive) :
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP < PAR_T

Samples passing PAR_T only were assigned an outcome of 1 (inactive) :
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP >= PAR_T

External ID: CHRM1_PAM_FLUO8_1536_1X%ACT PRUN

Protocol: Assay Overview:

The purpose of this assay is to identify compounds that act as positive allosteric modulators (PAMs) and increase activity of the human M1 muscarinic receptor (CHRM1; M1) in cells pre-treated with a known agonist. In this assay, CHO-K1 cells stably expressing human M1 are loaded with the Fluo-8 calcium indicator dye, followed by addition of test compounds and subsequent treatment with the activator acetylcholine at a concentration that results in 20% activation (EC20). As designed, compounds that act as CHRM1 PAMs will increase calcium mobilization, resulting in increased intracellular calcium and relative fluorescence of the indicator dye beyond that of the EC20 of acetylcholine. Compounds are tested in singlicate at a final nominal concentration of 3 micromolar.

Protocol Summary:

The CHO-hM1 cell line was routinely cultured in T-175 sq cm flasks at 37 degrees C and 95% relative humidity (RH). The growth media consisted of Ham's F-12 Nutrient Media (F-12) supplemented with 10% v/v heat-inactivated qualified fetal bovine serum, 20 mM HEPES, 50 micrograms/mL Geneticin, and 1X antibiotic mix (penicillin and streptomycin).

The day before the assay 3000 cells in 3 microliters of growth media were seeded into each well of 1536 well microtiter plates and allowed to incubate at 37 degrees C, 5% CO2, and 95 % RH for 17-24 hours. Next, 2 microliters of the fluorogenic Fluo-8 intracellular calcium indicator mixture (prepared according to the manufacturer's protocol) was added to each well. Plates were then incubated for 1 hour at 37 degrees C, 5% CO2, and 95 % RH, followed by 30 minute incubation at room temperature. Then, 15 nL of test compound in DMSO were transferred to appropriate wells. The assay was started by performing a basal read of plate fluorescence (470-495 nm excitation and 515-575 nm emission) for 5 seconds on the FLIPR Tetra (Molecular Devices) prior to all wells being treated with an EC20 concentration of acetylcholine. Then a real time fluorescence measurement was immediately performed for the remaining 140 seconds of the assay. A ratio for each well was calculated to normalize assay data, according to the following mathematical expression:

Ratio = I_Max / I_Min

Where:

I_Max represents the maximum measured fluorescence emission intensity over the 140 second read and;
I_Min represents the minimum (basal) measured fluorescence emission intensity before compound was added.

The percent activation was calculated from the median ratio as follows:

% Activation = ( ( Ratio_Test_Compound - Median_Ratio_Low_Control ) / ( Median_Ratio_High_Control - Median_Ratio_Low_Control ) ) * 100

Where:

Test_Compound is defined as wells containing test compound.
Low_Control is defined as wells containing Acetylcholine at EC20 and DMSO.
High_Control is defined as wells containing Acetylcholine (EC100) and DMSO.

A mathematical algorithm was used to determine nominally activating compounds in the primary screen. Two values were calculated for each assay plate: (1) the average percent activation of test compound wells and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter on an individual plate basis, i.e. any compound that exhibited greater % activation than the plate based cutoff parameter was declared active.

PubChem Activity Outcome and Score:

The inactive compounds of this assay have an activity score range of 0 to 78 and the active compounds have an activity score range of 50 to 100.

The reported PubChem Activity Score has been normalized to 100% observed primary activation. Negative % activation values are reported as activity score zero.

List of Reagents:

Cell line: Chinese Hamster Ovary (CHO) cells containing hM1 receptor; (Conn Lab)
Calcium sensitive dye: Fluo-8 No Wash Calcium Assay Kit; (AAT Bioquest, part 36316)
Growth media: Ham's F-12; 10% FBS, 20mM HEPES, 50?g/mL G418
Assay media: Ham's F-12, 10% FBS, 20 mM HEPES
Assay plates: Aurora black/clear 1536well FLIPR plate; (Aurora, part 00019326)
Probenecid: 250mM (pH 8.0); (Sigma P8761)
Potentiator: Acetylcholine (50mM stock in water); Sigma A9187

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR.

External ID: CHEMBL5375798

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: SIAE_INH_FP_1536_1X%INH PRUN

Protocol: Assay Overview:

The purpose of this biochemical assay is to identify compounds that act as inhibitors of sialic acid acetylesterase (SIAE). In this assay, SIAE protein is incubated with test compounds and fluorophosphonate-rhodamine (FP-Rh) activity-based probe. The reaction is excited with linear polarized light and the intensity of the emitted light is measured as the polarization value (mP). As designed, test compounds that act as SIAE inhibitors will prevent SIAE-probe interactions, thereby increasing the proportion of free (unbound) fluorescent probe in the well, leading to low fluorescence polarization. Compounds are tested in singlicate at a nominal test concentration of 9.66 micromolar.

Protocol Summary:

Prior to the start of the assay, 3 microliters of assay buffer (1X DPBS and 0.01% Pluronic F-127) were dispensed into column 1 thru column 3 of 1536 microtiter plates. Next, 3 microliters of assay buffer containing 0.73uM of SIAE protein were dispensed into columns 4 thru 48. Then, 39 nL of test compound in DMSO or DMSO alone (0.97% final concentration) were added to the appropriate wells and incubated for 45 minutes at 25 degrees Celsius.

The assay was started by dispensing 1.0 microliter of 300 nM FP-Rh in assay buffer to all wells. Plates were centrifuged and after 120 minutes of incubation at 25 degrees Celsius, fluorescence polarization was read on a Viewlux microplate reader (PerkinElmer, Turku, Finland) using a BODIPY TMR FP filter set and a BODIPY dichroic mirror (excitation = 525nm, emission = 598nm) for 25 seconds for each polarization plane (parallel and perpendicular).

Prior to further calculations, the following formula was used to calculate fluorescence polarization (FP):

FP = ( Raw1 - Raw2 ) / ( Raw1 + Raw2 )

Where:

Raw1 is defined as the S channel.
Raw2 is defined as the P channel.

The percent inhibition for each compound was calculated as follows:

100 *( ( Test_Compound - Median_Low_Control ) / ( Median_High_Control - Median_Low_Control ) )

Where:

Test_Compound is defined as wells containing SIAE protein in the presence of test compound and FP-Rh.
High_Control is defined as wells containing DMSO, FP-Rh but, no SIAE protein.
Low_Control is defined as the median of the wells containing test compounds.

PubChem Activity Outcome and Score:

A mathematical algorithm was used to determine nominally inhibiting compounds in the primary screen. Four values were calculated: (1) the average percent inhibition of all high controls tested plus three times the standard deviation of the high controls, (2) the average percent inhibition of all low controls tested minus three times the standard deviation of the low controls, (3) the average percent inhibition of all compounds tested between (1) and (2), and (4) three times their standard deviation. The sum of two of these values, (3) and (4), was used as a cutoff parameter, i.e. any compound that exhibited greater % inhibition/activity than the cutoff parameter was declared active.

The reported PubChem Activity Score has been normalized to 100% observed primary inhibition. Negative % inhibition values are reported as activity score zero.

The activity score range for active compounds is 100-2, for inactive 2-0.

List of Reagents:

SIAE protein (supplied by Assay Provider)
FP-Rh probe (supplied by Assay Provider)
DPBS (Mediatech, part 20-031-CV)
Pluronic F-127 (Invitrogen, part P6866)
1536-well plates (Greiner, part 789176)

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR.

External ID: CHEMBL5375796

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL5375857

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: 2084-01_Activator_SinglePoint_HTS_Activity

Protocol: MITF Primary Screening Protocol
(TRPM-1 Promoter//Luciferase reporter assay)

Day 1, plate cells 2000 per well in 30 uL media (phenol red free DMEM/10% iFBS/Pen/Strep/L-Glutamine)

Day 2, pin 100 nL into 30 uL assay volume in white, opaque Corning 8867 barcoded 384 well plates. (will also require sentinel pinning with the positive control, parthenolide)
Incubate 24 hours at 37 degrees C in Liconic incubator

Day 3, add 20 uL 100% Promega Steady glo with Thermo Combi fluid transfer apparatus.
Shake 15 seconds on "big bear" plate shaker.
Incubate at RT for 5 minutes.
Read on Perkin-Elmer Envision with US LUM settings for 0.5 sec per well

Comment: PRESENCE OF CONTROLS: Neutral control wells (NC) and positive control wells (PC) were included on every plate.

EXPECTED OUTCOME: Active compounds result in increasing readout signal.
NORMALIZATION:
The raw signals of the plate wells were normalized using the 'Neutral Controls Minus Inhibitors' method in Genedata Assay Analyzer (v7.0.3):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of 100.
Experimental wells values were scaled to this range.
PATTERN CORRECTION: The plate pattern correction algorithm 'Runwise Pattern (Multiplicative)' in Genedata (v7.0.3) was applied to the normalized plate data.

PUBCHEM_ACTIVITY_SCORE:
This was set as equal to the mean of the normalized and corrected sample replicate activities, rounded to the nearest integer .
The minimum PUBCHEM_ACTIVITY_SCORE required for a compound to be called a hit (the activity threshold, or AT) was set at 80.

PERCENTAGE OF ACTIVE REPLICATES:
For each sample, the percentage of replicates (PCT_ACTIVE_REP) which had activity scores >= AT was determined.
The minimum percentage of replicates required for a compound to be called a hit (PAR_T) was set at 100.

PUBCHEM_ACTIVITY_OUTCOME:
Samples passing BOTH threshold criteria were assigned an outcome of 2 (active):
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP >= PAR_T

Samples passing NEITHER threshold criteria were assigned an outcome of 1 (inactive):
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP < PAR_T

Samples passing AT only were assigned an outcome of 3 (inconclusive) :
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP < PAR_T

Samples passing PAR_T only were assigned an outcome of 3 (inconclusive) :
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP >= PAR_T

External ID: GDH-TPI_INH_ABS_1536_1X%INH CSRUN

Protocol: Assay Overview:

The purpose of this biochemical counterscreen is to determine whether compounds act as absorbance assay artifacts or are non-selective. This assay also serves as a counterscreen for a set of ongoing high throughput primary experiments entitled, "Absorbance-based biochemical primary high throughput screening assay to identify inhibitors of the aldolase of M. tuberculosis."

This counterscreen is similar in format to the aforementioned assay with the only two following differences: (i) the fructose-1,6-bisphosphate substrate is replaced with glyceraldehyde 3 phosphate, a product of its conversion by FBA and (ii) no (FBA) is used. The counterscreen hence recapitulates the two steps involved in the monitoring of FBA activity through the conversion of FB into the triose product glyceraldehyde 3 phosphate (G3P), which would be converted to dihydroxyacetone phosphate (DHAP) by the helper enzyme triose phosphate isomerase (TPI). A second helper enzyme, glycerophosphate dehydrogenase (GDH), converts the dihydroxyacetone phosphate to glycerol-3-phosphate with the concomitant oxidation of NADH to NAD, which is monitored by measuring the absorbance at 340 nm. In this new assay format, the A340 is independent of FBA activity, hence compounds that reduce absorbance at 340 nm are either absorbance artifacts or helper enzyme inhibitors that will not be pursued. Compounds are tested in singlicate at a final nominal concentration of 4.78 uM.

Protocol Summary:

Prior to the start of the assay, 5 uL /well of Buffer A (50 mM HEPES, 0.01% Triton X-100, 10% Glycerol, pH8.0) supplemented with 400 nM ZnCl2,240 uM NADH and the helper enzymes GDH-TPI (4 U/mL) was dispensed into all wells of a 1536-well plate except the "No enzyme" wells that contained the same supplemented buffer but no GDH-TPI enzymes. Next, 48 nL of test compounds were then delivered in each well using a PinTool. The assay was then initiated by dispensing 5 uL of Buffer A supplemented with 240 uM of the substrate glyceraldehyde-3-phosphate (G3P). Plates were incubated at room temperature for 20 minutes before A340 was measured using the EnVision plate reader (Perkin Elmer).

The percent inhibition for each compound was calculated as follows:

%Inhibition = 100 * ( ( Test_Compound - Median_Low_Control ) / ( Median_High_Control - Median_Low_Control ) )

Where:

Test_Compound is defined as wells treated with test compounds.
Low_Control is defined as wells treated with DMSO.
High_Control is defined as wells with no GDH-TPI enzyme.

A mathematical algorithm was used to determine nominally inhibiting compounds in the primary screen. Two values were calculated for each assay plate: (1) the average percent inhibition of test compound wells and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter for each plate, i.e. any compound that exhibited greater % inhibition than the cutoff parameter was declared active.

PubChem Activity Outcome and Score:

The reported PubChem Activity Score has been normalized to 100% observed inhibition. Negative % inhibition values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-13, and for inactive compounds 13-0.

List of Reagents:

ZnCl2 (Fisher Scientific, part Z33-500)
NADH (EMD Biosciences, part 481913)
GDH-TPI (Sigma, part G1881)
HEPES (EMD Biosciences, part EM-5310)
Triton X-100 (Sigma, part T8787)
Glycerol (Fisher, part AC327255000)
Glyceraldehyde-3-phosphate (Sigma, part D7137)
1536-well plates (Aurora, part 1091-11020-S)

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. In this case the results of each separate campaign were assigned "Active/Inactive" status based upon that campaign's specific compound activity cutoff value. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that quench or emit absorbance within the well. All test compound concentrations reported are nominal; the specific concentration for a particular test compound may vary based upon the actual sample provided by the MLSMR

External ID: CHEMBL5375853

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

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: SMAD3201

Protocol: Suspensions of trypsinized HEPG2 CAGA-GFP cells were dispensed into white, tissue culture-treated, solid 1536-well plates at 5uL/well (1000 cells/well final concentration) in DMEM medium supplemented with 1% FBS. Plates were incubated at 37 degrees C for 2 hours, after which 23 nL of compounds or DMSO were delivered to each well using a pin tool. One uL of recombinant TGF-beta in DMEM (1% FBS) was then dispensed (500 pg/mL final concentration), and plates were incubated at 37 degrees C for 18 hours. Two uL of CellTiter Glo (Promega), a luminescence-based viability reagent, was dispensed, followed by a 10 minute room temperature incubation. The plates were then measured on a PerkinElmer ViewLux plate reader for luminescence (clear filter) using a 5 second exposure. The %Activity was determined from the corrected luminescence values. Wells containing media only (no cells) were used to normalize %Activity of identified toxic compounds; media-only wells corresponded to 100%Activity (complete cell-killing), while DMSO-dosed cell controls were used to normalize 0%Activity (no toxicity).

Concentration-response curves were fitted to the signals arising from the resulting luminescence. The concentration-effect curves were then classified based on curve quality (r2), response magnitude and degree of measured activity, and compounds were subsequently categorized based on their curve class. Toxic compounds showed concentration-dependent decreases in luminescence, concordant with a decrease in intracellular ATP concentration (CellTiter Glo's marker of viability), and thus a decrease in the number of viable cells. Inactive (non-toxic) compounds showed no effect on luminescence signal. Active (toxic) compounds showed concentration dependent decrease in luminescence.

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".

2. For all inactive (non-toxic) compounds, PUBCHEM_ACTIVITY_SCORE is 0. For all active (toxic) compounds, a score range was given for each curve class type given above. Active (toxic) 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: CHEMBL4296192

Protocol: N/A

Comment: Target ChEMBL ID: CHEMBL352
ChEMBL Target Name: Staphylococcus aureus
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL5375843

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL4296783

Protocol: N/A

Comment: Target ChEMBL ID: CHEMBL354
ChEMBL Target Name: Escherichia coli
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL4296193

Protocol: N/A

Comment: Target ChEMBL ID: CHEMBL614425
ChEMBL Target Name: Acinetobacter baumannii
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL5375838

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL4296187

Protocol: N/A

Comment: Compounds with activity <= 10uM or explicitly reported as active by ChEMBL are flagged as active in this PubChem assay presentation.

Target ChEMBL ID: CHEMBL348
ChEMBL Target Name: Pseudomonas aeruginosa
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL4296190

Protocol: N/A

Comment: Compounds with activity <= 10uM or explicitly reported as active by ChEMBL are flagged as active in this PubChem assay presentation.

Target ChEMBL ID: CHEMBL365
ChEMBL Target Name: Cryptococcus neoformans
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL4296189

Protocol: N/A

Comment: Compounds with activity <= 10uM or explicitly reported as active by ChEMBL are flagged as active in this PubChem assay presentation.

Target ChEMBL ID: CHEMBL366
ChEMBL Target Name: Candida albicans
ChEMBL Target Type: ORGANISM - Target is a complete organism
Relationship Type: N - Non-molecular target assigned
Confidence: Target assigned is non-molecular

Data Source: CO-ADD Antimicrobial Screening

External ID: CHEMBL5375834

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: SBCCG-A764-CF-PAF-Primary-Assay

Protocol: Assay Materials:
KKLEB-NFkB-GFP cells (Assay Provider)
PAF(Assay Provider)
Fetal Bovine Serum (Hyclone SH30396.03)
Penicillin Streptomycin solution
L-glutamine (100X)
TrypLE (Invitrogen 12563)
DPBS without calcium and magnesium (1X)
Corning culture flasks
Black CellBind 1536-well plates (Corning 3833)
ATPlite (Perkin Elmer 6016739)

I. Cell Suspension
1- Dispense 3 uL/well of cells at 5X10;5 cells/mL to the whole plate (plate cells in 2% FBS assay media).
2- Spin down plates on Eppendorf centrifuge 5810 at 500 rpm for 1 minute.

II. Compound Addition:
3- Transfer test compounds to columns 5-48 and DMSO to columns 1-4 using the Labcyte ECHO 555.
4- Transfer volume of test compound and DMSO is 15nL, making 5uM compound concentration at 0.25% DMSO final.
5-Spin down plates on Vspin at 1000 rpm for 1 minute.
6-Put Kalypsys metal lids on plates, incubate plates at 37 degrees C with 5% CO2 for 2 hours.

III. Reagent Addition
7- Dispense 3 uL/well of serum free assay media to columns 1 and 2.
8- Dispense 3 uL/well of PAF (dilute in serum free assay media) to columns 3-48.
9- Spin down plates without lids on Vspin at 2000 rpm for 2 min
10- Put Kalypsys metal lids on plates, and incubate plates at 37 degrees C with 5% CO2 overnight.

IV. Reading plates:

11-Spin plates upside down with a container at 1000 rpm for 15 sec. Dab them with a tissue to dry them and Read immediately on envision for GFP fluorescence.
12-Dispense 6 uL/well of ATPlite (diluted in DPBS 1:1).
13-Spin down plates on Eppendorf centrifuge 5810 at 2000 rpm for 2 minutes without lids.
14-Incubate plates for 10 min at RT and run Luminescence read on Viewlux.

Comment: Compounds that demonstrated a corrected %Activity of >= 50% at 5 uM concentration are defined as actives in this assay.

The experimental values were normalized by the difference between values from neutral and stimulator control wells in each plate. Then normalized data was corrected to remove systematic plate patterns due to artifacts such as dispensing tip issues etc. Further information about data correction is available at http://www.genedata.com/products/screener.html.

To simplify the distinction between the inactives of the primary screen and of the confirmatory screening stage, the Tiered Activity Scoring System was developed and implemented. Its utilization for the assay is described below.

Activity Scoring
Activity scoring rules were devised to take into consideration compound efficacy, its potential interference with the assay and the screening stage that the data was obtained. Details of the Scoring System will be published elsewhere. Briefly, the outline of the scoring system utilized for the assay is as follows:
1) First tier (0-40 range) is reserved for primary and single-concentration confirmation screening data.
a. If outcome of the primary screen is inactive, then the assigned score is 0
b. If outcome of the primary screen is inconclusive, then the assigned score is 10
c. If outcome of the primary screen is active, then the assigned score is 20
d. If outcome of the single-concentration confirmation screen is inactive, then the assigned score is 21
e. If outcome of the single-concentration confirmation screen is inconclusive, then the assigned score is 25
f. If outcome of the single-concentration confirmation screen is active, then the assigned score is 30.
This scoring system helps track the stage of the testing of a particular SID. For the primary hits which are available for confirmation, their scores will be greater than 20. For those which are not further confirmed, their score will stay under 21.

2) Second tier (41-80 range) is reserved for dose-response confirmation data and is not applicable in this assay

3) Third tier (81-100 range) is reserved for resynthesized true positives and their analogues and is not applicable in this assay

External ID: CHRM1_ANT_FLUO8_1536_1X%INH PRUN

Protocol: Assay Overview:

The purpose of this assay is to identify compounds that act as antagonists and decrease activity of the human M1 muscarinic receptor (CHRM1; M1) that have been pre-treated with a known agonist, with the end result being a decrease in intracellular calcium. In this assay, CHO-K1 cells stably expressing human M1 are loaded with the Fluo-8 calcium indicator dye. Compounds are added followed by treatment with the activator acetylcholine at a concentration that results in 80% activation (Ec80). As designed, compounds that act as CHRM1 antagonists will decrease calcium mobilization, resulting in decreased relative fluorescence of the indicator dye below that of the Ec80 of acetylcholine. Compounds are tested in singlicate at a final nominal concentration of 3 uM.

Protocol Summary:

The CHO-hM1 cell line was routinely cultured in T-175 sq cm flasks at 37 C and 95% relative humidity (RH). The growth media consisted of Ham's F-12 Nutrient Media (F-12) supplemented with 10% v/v heat-inactivated qualified fetal bovine serum, 20 mM HEPES, 50 ug/mL Geneticin, and 1X antibiotic mix (penicillin and streptomycin).

The day before the assay 3000 cells in 3 uL of growth media were seeded into each well of 1536 well microtiter plates and allowed to incubate at 37 C, 5% CO2, and 95 % RH for 17-24 hours. Next, 2 uL of the fluorogenic Fluo-8 intracellular calcium indicator mixture (prepared according to the manufacturer's protocol) was added to each well. Plates were then incubated for 1 hour at 37 C, 5% CO2, and 95 % RH, followed by 30 minute incubation at room temperature. Then, 15 nL of test compound in DMSO were transferred to appropriate wells. The assay was started by performing a basal read of plate fluorescence (470 - 495 nm excitation and 515 - 575 nm emission) for 5 seconds on the FLIPR Tetra (Molecular Devices) prior to all wells being treated with an EC80 concentration of acetylcholine. Then a real time fluorescence measurement was immediately performed for the remaining 140 seconds of the assay.

Hits for this assay were determined according to the following mathematical expression:

Ratio = I_Max / I_Min

Where:

I_Max represents the maximum measured fluorescence emission intensity over the 140 second read and,
I_Min represents the minimum (basal) measured fluorescence emission intensity before compound was added.

The percent inhibition was calculated from the median ratio as follows:

%_Inhibition = ( 1 - ( Ratio Test_Compound - Median_Ratio_High_Control ) / ( Median_Ratio_Low_Control - Median_Ratio_High_Control ) ) ) * 100

Where:

Test_Compound is defined as wells containing test compound.
Low_Control is defined as wells containing Ec80 of acetylcholine and DMSO.
High_Control is defined as wells containing DMSO.

PubChem Activity Outcome and Score:

A mathematical algorithm was used to determine nominally inhibiting compounds in the primary screen. Two values were calculated for each assay plate: (1) the average percent inhibition of test compound wells and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter for each plate, i.e. any compound that exhibited greater % inhibition than that particular plate's cutoff parameter was declared active.

The reported PubChem Activity Score has been normalized to 100% observed inhibition. Negative % inhibition values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-7, and for inactive compounds 80-0.

In this assay not all plates were run in the same batch. This resulted in batch-to-batch variation among the different batches of plates, thereby necessitating the use of a plate-based activity cutoff. For this reason the inactive and active scores overlap.

List of Reagents:

Cell line: Chinese Hamster Ovary (CHO) cells containing hM1 receptor; (Conn Lab)
Calcium sensitive dye: Fluo-8 No Wash Calcium Assay Kit; (AAT Bioquest, part 36316)
Growth media: Ham's F-12; 10% FBS, 20mM HEPES, 50 ug/mL G418
Assay media: Ham's F-12, 10% FBS, 20 mM HEPES
Assay plates: Aurora black/clear 1536well FLIPR plate; (Aurora, part 00019326)
Probenecid: 250mM (pH 8.0); (Sigma P8761)
Potentiator: Acetylcholine (50 mM stock in water); Sigma A9187

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR.

External ID: CHEMBL5375830

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: SMAD3101

Protocol: Suspensions of trypsinized HEPG2 CAGA-GFP cells were dispensed into white, tissue culture-treated, solid 1536-well plates at 5uL/well (1000 cells/well final concentration) in DMEM medium supplemented with 1% FBS. Plates were incubated at 37 degrees C for 2 hours, after which 23 nL of compounds or DMSO were delivered to each well using a pin tool. One uL of recombinant TGF-beta in DMEM (1% FBS) was then dispensed (500 pg/mL final concentration), and plates were incubated at 37 degrees C for 18 hours. The plates were measured on an Acumen eX3 Explorer plate reader for GFP fluorescence (ex488/em500-530). GFP values were calculated by determining the mean GFP fluorescence of individual cells, and compiling these values for each well to determine a total well GFP signal. The %Activity was determined from the corrected fluorescence values. A titration of the known TGF-B inhibitor SB431542 was included to monitor plate performance, while unstimulated HEPG2 (-TGF-B) control wells were used to normalize %Activity of identified inhibitors; unstimulated wells corresponded to 100%Activity (full inhibition), while stimulated cell controls (+DMSO) were used to normalize 0%Activity (no inhibition).

Concentration-response curves were fitted to the signals arising from the resulting fluorescence. The concentration-effect curves were then classified based on curve quality (r2), response magnitude and degree of measured activity, and compounds were subsequently categorized based on their curve class. Active inhibitors showed concentration-dependent decreases in GFP fluorescence, concordant with a decrease in TGF-B/SMAD3-driven GFP expression. Inactive compounds showed no effect on fluorescence signal.

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: CHEMBL5375886

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4851
ChEMBL Target Name: Serine/threonine-protein kinase 38-like
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: SRC3_INH_LUMI_1536_1X%INH PRUN

Protocol: Assay Overview:

The purpose of this assay is to identify compounds that act as inhibitors of the steroid receptor coactivator 1 (SRC3), also known as nuclear receptor coactivator 3 (NCOA3). In this assay, HEK293 cells are transfected with a GAL4-responsive reporter plasmid (pGL4.31, Promega) and an expression vector encoding SRC-3 fused to the DNA-binding domain of GAL4(pBIND-SRC-3). The ability of compounds to reduce coactivator transcriptional activity is assessed by measuring luciferase expression from the reporter gene plasmid. As designed, compounds that inhibit SRC3 ability to induce transcription will lead to a decrease in expression of the luciferase gene, resulting in reduced well luminescence. Compounds are tested in singlicate at a final nominal concentration of 3.6 uM.

Protocol Summary:

Seven million HEK293 cells were seeded into T-175 flasks containing 23 mLs of DMEM media supplemented with 10% v/v fetal bovine serum and 1% v/v Anti-Anti. Flasks were then incubated for 48 hours at 37 C, 5% CO2 and 95% relative humidity (RH). The day prior to the assay, cells were harvested using TrypLE, resuspended in fresh media at a density of 1 million cells per mL and seeded into new T-175 flasks (23 mL per flask). After allowed to attach for one hour at 37 C, 5% CO2 and 95% RH, cells were transfected with 1 mL of preincubated mix of serum-free OptiMEM containing 23 ug of the pGL4.31 reporter plasmid, 2.3 ug of pBIND-SRC3 vector, and 80 uL of transfection reagents. Twenty four hours post transfection, cells were harvested using 5 mL of TrypLE and resuspended at a concentration of 750,000 cells per mL in phenol-red free DMEM media supplemented as described above.

The assay was started by dispensing 5 uL of cell suspension into each well of a white, solid-bottom 1536-well plate using a flying reagent dispenser (3,750 cells per well). The first two columns received cells transfected with reporter plasmid and an empty pBIND vector as a control for background luminescence. Cells were then treated with 18 nL/well of test compounds, DMSO as a negative control (final concentration 0.36%), or Gossypol as a positive control (36 uM final) using a PinTool transfer unit (GNF). Plates were then placed in the incubator at 37 C, 5% CO2 and 95% RH. Twenty four hours later, plates were removed from the incubator and equilibrated to room temperature for 10 minutes. Luciferase activity was detected by adding 5 uL per well of ONE-Glo luciferase detection reagent. After a 15 minute incubation time, light emission was measured using the ViewLux plate reader (PerkinElmer).

The percent inhibition of each test compound was calculated as follows:

%_Inhibition = ( 1 - ( median_positive_control - test_compound ) / ( median_positive_control - median_negative_control ) * 100

Where:

Test_Compound is defined as wells containing test compound treated cells.
Positive_Control is defined as wells containing Gossypol treated cells.
Negative_Control is defined as wells containing DMSO treated cells.

PubChem Activity Outcome and Score:

A mathematical algorithm was used to determine nominally active compounds. Two values were calculated: (1) the average percent inhibition of all compounds tested, and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter, i.e. any compound that exhibited greater %inhibition than the cutoff parameter was declared active.

The reported PubChem Activity Score has been normalized to 100% observed primary inhibition. Negative % inhibition values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-64, and for inactive compounds 64-0.

List of Reagents:

HEK-293 cells (ATCC, part CRL-1573)
DMEM media (Invitrogen, part 11965)
Fetal Bovine Serum (Hyclone, part SH30088.03)
Anti-Anti (Gibco, part 15240)
TrypLE (Invitrogen, part 12604)
T-175 flasks (Falcon, part 353112)
pGL4.31 (Promega, part C935A)
pBIND-SRC3 (Assay Provider)
TransIT 293 transfection reagent (Mirus Corporation, part MIR-2700)
ONE-Glo luciferase reagent (Promega, part E6130)
White, solid-bottom 1536-well plates (Greiner, part 789173)

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. In this case the results of each separate campaign were assigned "Active/Inactive" status based upon that campaign's specific compound activity cutoff value. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, cytotoxic compounds, compounds that perturb the UAS/GAL4 reporter system, and compounds that quench, inhibit, stabilize, or emit luminescence within the well. All test compound concentrations reported are nominal; the specific concentration for a particular test compound may vary based upon the actual sample provided by the MLSMR.

External ID: SRC1_INH_LUMI_1536_1X%INH PRUN

Protocol: Assay Overview:

The purpose of this assay is to identify compounds that act as inhibitors of the steroid receptor coactivator 1 (SRC1), also known as nuclear receptor coactivator 3 (NCOA1). In this assay, HEK293 cells are transfected with a GAL4-responsive reporter plasmid (pGL4.31, Promega) and an expression vector encoding SRC1 fused to the DNA-binding domain of GAL4 (pBIND-SRC-1). The ability of compounds to reduce coactivator transcriptional activity is assessed by measuring luciferase expression from the reporter gene plasmid. As designed, compounds that inhibit SRC1 ability to induce transcription will lead to a decrease in expression of the luciferase gene, resulting in reduced well luminescence. Compounds are tested in singlicate at a final nominal concentration of 3.6 uM.

Protocol Summary:

Seven million HEK293 cells were seeded in T-175 flasks 23 mL of DMEM media supplemented with 10% v/v fetal bovine serum and 1% v/v Anti-Anti. Flasks were then incubated for 48 hours at 37 C, 5% CO2 and 95% relative humidity (RH). The day prior to run the assay, cells were harvested using TrypLE, resuspended in fresh media at a density of 1 million cells per mL and seeded into new T-175 flasks (23 mL per flask). After being allowed to attach for one hour at 37 C, 5% CO2 and 95% RH, cells were transfected with 1 mL of preincubated mix of serum-free OptiMEM containing 23 ug of pGL4.31 reporter plasmid, 2.3 ug of pBIND-SRC1 vector and 80 uL of transfection reagents. Twenty four hours post transfection, cells were harvested using 5 mL of TrypLE and resuspended at a concentration of 750,000 cells per mL in phenol-red free DMEM media supplemented as described above.

The assay was started by dispensing 5 uL of cell suspension into each well of a white, solid-bottom 1536-well plate using a flying reagent dispenser (i.e. 3,750 cells per well). The first two columns received cells transfected with the reporter plasmid and an empty pBIND vector as a control for background luminescence. Cells were then treated with 18 nL/well of test compounds, DMSO as a negative control (final concentration 0.36%) or Gossypol as a positive control (36 uM final) using a PinTool transfer unit (GNF). Plates were then placed in the incubator at 37 C, 5% CO2 and 95% RH. Twenty four hours later, plates were removed from the incubator and equilibrated to room temperature for 10 minutes. Luciferase was detected by adding 5 uL per well of ONE-Glo luciferase detection reagent. After a 15 minutes incubation time, light emission was measured with the ViewLux reader (PerkinElmer).

The percent inhibition of each test compound was calculated as follow:

%_Inhibition = ( 1 - ( median_positive_control - test_compound ) / ( median_positive_control - median_negative_control ) * 100

Where:

Test_Compound is defined as wells containing test compound treated cells.
Positive_Control is defined as wells containing Gossypol treated cells.
Negative_Control is defined as wells containing DMSO treated cells.

PubChem Activity Outcome and Score:

A mathematical algorithm was used to determine nominally active compounds. Two values were calculated: (1) the average percent inhibition of all compounds tested, and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter, i.e. any compound that exhibited greater % inhibition than the cutoff parameter was declared active.

The reported PubChem Activity Score has been normalized to 100% observed primary inhibition. Negative % inhibition values are reported as activity score zero.

The PubChem Activity Score range for active compounds is 100-63, and for inactive compounds 63-0.

List of Reagents:

HEK-293 cells (ATCC, part CRL-1573)
DMEM media (Invitrogen, part 11965)
Fetal Bovine Serum (Hyclone, part SH30088.03)
Anti-Anti (Gibco, part 15240)
TrypLE (Invitrogen, part 12604)
T-175 flasks (Falcon, part 353112)
pGL4.31 (Promega, part C935A)
pBIND-SRC1 (Assay Provider)
TransIT 293 transfection reagent (Mirus Corporation, part MIR-2700)
ONE-Glo luciferase reagent (Promega, part E6130)
White, solid-bottom 1536-well plates (Greiner, part 789173)

Comment: Due to the increasing size of the MLPCN compound library, this assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. In this case the results of each separate campaign were assigned "Active/Inactive" status based upon that campaign's specific compound activity cutoff value. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, cytotoxic compounds, compounds that perturb the UAS/GAL4 reporter system, and compounds that quench, inhibit, stabilize, or emit luminescence within the well. All test compound concentrations reported are nominal; the specific concentration for a particular test compound may vary based upon the actual sample provided by the MLSMR.

External ID: CHEMBL5375880

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4851
ChEMBL Target Name: Serine/threonine-protein kinase 38-like
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: UNMCMD_DSG_PRIMARY_MLPCN

Protocol: Protocol:
1) Protein G beads (1.06 million beads per 384 well plate) are coupled with the DSG3 antigen by overnight incubation with a cell lysate containing an Fc-DSG3 construct.
2) Coupled beads are used at 3000 beads per well
3) scFv-GFP reagent is diluted in Assay buffer (PBS with 1mM CaCl2, 0.05% BSA, 0.01% Na Azide), added to 382 well assay plates, and incubated with a 20 microM solution of test compounds for 60 minutes at RT.
4) Vehicle control (2%DMSO) and Blocking control (1/40 dilution of soluble DSG3 antigen) are similarly incubated with scFv-anti-DSG3-GFP
5) Pre-coupled beads are added to each well and plates are incubated for 60 minutes with rotation
6) scFv-anti-DSG3-GFP binding to beads is detected using flow cytometry and reported as the Median Channel Fluorescence

Calculations:
Z and Z' values were calculated individually for all plates, most plates passed a Z'>0.3.
An average response value was computed for each plate. Compounds were considered active if the associated well fluorescence was greater than 3SD below the Average Median Fluorescence of the individual plate.

dif = PLATE_CUTOFF - RESPONSE

If diff < 0
Then PUBCHEM_ACTIVITY_SCORE = 0
Else If diff > 100
Then PUBCHEM_ACTIVITY_SCORE = 100
Else
PUBCHEM_ACTIVITY_SCORE = diff

If (PUBCHEM_ACTIVITY_SCORE > 0) AND (RESPONSE > 0)
THEN PUBCHEM_ACTIVITY_OUTCOME = 2 (or ACTIVE)
If (PUBCHEM_ACTIVITY_SCORE > 0) AND (RESPONSE = 0)
THEN PUBCHEM_ACTIVITY_OUTCOME = 3 (or INCONCLUSIVE)
Else
PUBCHEM_ACTIVITY_OUTCOME = 1 (or INACTIVE)

Comment: This reference is not indexed in PubChem
1. Stanley, J.R. 2008. Pemphigus. In Fitzpatrick's Dermatology in General Medicine. K.Wolff, Goldsmith,L.A., Katz,S.I., Gilchrest,B.A., Paller,A.S., and Leffell,D.J., editors. McGraw-Hill. New York. 459-468.

External ID: CHEMBL5375876

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL3267
ChEMBL Target Name: PI3-kinase p110-gamma subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL5375872

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL3130
ChEMBL Target Name: PI3-kinase p110-delta subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL2422684

Protocol: N/A

Comment: Journal: J. Nat. Prod.
Year: 2013
Volume: 76
Issue: 9
First Page: 1586
Last Page: 1591
DOI: 10.1021/np400242e

Target ChEMBL ID: CHEMBL614040
ChEMBL Target Name: J774.A1
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: CHEMBL5375868

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL3145
ChEMBL Target Name: PI3-kinase p110-beta subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL2422688

Protocol: N/A

Comment: Journal: J. Nat. Prod.
Year: 2013
Volume: 76
Issue: 9
First Page: 1586
Last Page: 1591
DOI: 10.1021/np400242e

Target ChEMBL ID: CHEMBL614040
ChEMBL Target Name: J774.A1
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: CHEMBL5375866

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL2421189

Protocol: N/A

Comment: Journal: J. Nat. Prod.
Year: 2013
Volume: 76
Issue: 9
First Page: 1586
Last Page: 1591
DOI: 10.1021/np400242e

Target ChEMBL ID: CHEMBL614040
ChEMBL Target Name: J774.A1
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: CHEMBL5375861

Protocol: N/A

Comment: Journal: ACS Med Chem Lett
Year: 2023
Volume: 14
Issue: 12
First Page: 1664
Last Page: 1672
DOI: 10.1021/acsmedchemlett.3c00274

Target ChEMBL ID: CHEMBL4005
ChEMBL Target Name: PI3-kinase p110-alpha subunit
ChEMBL Target Type: SINGLE PROTEIN - Target is a single protein chain
Relationship Type: D - Direct protein target assigned
Confidence: Direct single protein target assigned

External ID: CHEMBL2421187

Protocol: N/A

Comment: Journal: J. Nat. Prod.
Year: 2013
Volume: 76
Issue: 9
First Page: 1586
Last Page: 1591
DOI: 10.1021/np400242e

External ID: 20160513eIF4E

Protocol: The cells carrying the bicitronic reporter gene (E8-Luc) were plated in 96-well plates at a density of 1.2x10(5)/well (100 ul DMEM) overnight. 0.5 ul of tested compounds (0.5 mM) or DMSO were added into the plates, and treated the cells for 16 h. The plates were then washed with 100 ul of PBS twice using Aquamax Plate Washer (Molecular Devices), and lysated in 60 ul of lysis buffer (1% Triton X-100, 25 mM Gly-Gly, pH 7.8, 15 mM MgSO4, and 4 mM EGTA) at room temperature for 20 min. 10 ul of lysates were then subjected to luciferase activity assays using Spectramax L (Molecular Devices) and the Promega Luciferase Substrate. The relative luciferase activities were then converted into logarithm values (binary logarithm, i.e., log2).

The cutoff value set for positives is 0.5849, which indicates that a compound can decrease the luciferase activity to at least 66.7% of the DMSO group.

Comment:

External ID: 2137-01_Inhibitor_SinglePoint_HTS_Activity

Protocol:
Recombinant PDI produced in E.coli received from collaborator. Batches 1 and 2 (041311 and 042811) were mixed and aliquoted with a concentration of 1.85 mg/ml.


Assay Buffer:
100 mM Potassium Phosphate, pH 7.0 with 2 mM EDTA
Prepare 1M stock solutions of K2HPO4 (dibasic- 176 g/L)) and KH2PO4 (monobasic 136.09 g/L)
to prepare 1L of assay buffer add:
61.5 ml dibasic 1M solution
38.5 ml monobasic 1M solution
4 ml EDTA
896 ml sterile H2O


Prepare Bovine Insulin:
Bovine insulin was only available in 100 mg bottle sizes. Insulin is stored at - 20 C as lyophilized powder. Reconstitute 100 mg with 10 ml of 0.1 N HCL. Dilute 1:14 with assay buffer for a final concentration of 125 uM. Once reconstituted insulin may be stored at -20 C and thawed once.

PDI:
PDI mix of batches 1+2 is at 1.85 mg/ml stock solution. Dilute 1:231 in diluted insulin from step above (final concentration 8 ug/ml). This is referred to as insulin/PDI mix.

DTT:
1M Stock solution in sterile H20. Dilute 1:178 for a working solution of 5.6 mM (this will be diluted 1:16 in the assay well for final concenctration of 350 uM).

Rutin Hydrate for Positive Control:
Lot BCBD8327V has 5.9% loss on drying.
per 100 g Rutin hydrate 5.9 g H20 and 94.1 g Rutin
therefore: (5.9g) / (18.02 g/mole)= 0.327 moles H20
(94.1 g) / (610.52 g/mole) = 0.154 moles

Moles H20/Moles Rutin 0.327/0.154= 2.12
(610.52 g/mol) + (2.12 x 18.02 g/mol) -= 648.72 g/mole for this lot of Rutin hydrate
Prepare 20 mM stock of Rutin hydrate (12.974 mg/ml DMSO)
Dilute 20 mM stock in assay buffer to 1.6 mM by diluting 1:12.5
This will be diluted 1:16 in well for a final concentration of 100 uM.


Set up Reagents:
One bottle on bioraptr will hold rutin hydrate positive control.
Remaining bottles will contain Insulin/ PDI reaction mixture (125 uM insulin with 8 ug/ml PDI).
Combi NL will deliver DTT.

Run:
Dispense 7.0 ul of insulin/PDI mix to all wells using the BioraptR.
Dispense 0.5 uL 1.6 mM Rutin Hydrate to positive control wells using BioraptR.
Move plate to combiNL and deliver 0.5 ul DTT to all wells.
Incubate plate 90 minutes RT.
Take a T= 90 min read using absorbance (650 nm) protocol on the Envision.

Comment: PRESENCE OF CONTROLS: Neutral control wells (NC) and positive control wells (PC) were included on every plate.

EXPECTED OUTCOME: Active compounds result in decreasing readout signal.
NORMALIZATION:
The raw signals of the plate wells were normalized using the 'Neutral Controls Minus Inhibitors' method in Genedata Assay Analyzer (v7.0.3):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of -100.
Experimental wells values were scaled to this range.
All well activities were then multiplied by -1 to create a positive activity readout value range, to match Pubchem convention.

PATTERN CORRECTION: The plate pattern correction algorithm 'Runwise Pattern (Multiplicative)' in Genedata (v7.0.3) was applied to the normalized plate data.

PUBCHEM_ACTIVITY_SCORE:
This was set as equal to the mean of the normalized and corrected sample replicate activities, rounded to the nearest integer .
The minimum PUBCHEM_ACTIVITY_SCORE required for a compound to be called a hit (the activity threshold, or AT) was set at 30.

PERCENTAGE OF ACTIVE REPLICATES:
For each sample, the percentage of replicates (PCT_ACTIVE_REP) which had activity scores >= AT was determined.
The minimum percentage of replicates required for a compound to be called a hit (PAR_T) was set at 100.

PUBCHEM_ACTIVITY_OUTCOME:
Samples passing BOTH threshold criteria were assigned an outcome of 2 (active):
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP >= PAR_T

Samples passing NEITHER threshold criteria were assigned an outcome of 1 (inactive):
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP < PAR_T

Samples passing AT only were assigned an outcome of 2 (active) :
PUBCHEM_ACTIVITY_SCORE >= AT, and PCT_ACTIVE_REP < PAR_T

tSamples passing PAR_T only were assigned an outcome of 3 (inconclusive) :
PUBCHEM_ACTIVITY_SCORE < AT, and PCT_ACTIVE_REP >= PAR_T

External ID: PLK1100

Protocol: Four microliter of 25 nM FITC-p-9-mer + 60 nM Plk1 PBD in buffer solution (final concentrations 25 nM and 60 nM respectively) or 4 uL of 25 nM FITC-p-9-mer (final concentration 25 nM) in buffer will be dispensed into a 1,536 Greiner medium-binding black solid plate. Small molecules at final concentrations of 18 nM to 57 uM and positive control phospho-9-mer (sequence: Ac-PPLHSpTAI-NH2) at final concentrations 26 nM to 57 uM and phospho-13-mer (sequence: Ac-CETFDPPLHSpTAI-NH2) at final concentrations of 1 nM to 2.3 uM will be pin-transferred (23 nL) to the plate via a Kalypsys pin-tool robotics equipped with a 1,536-pin array. The reaction plate will be centrifuged for 1 min at 1000 rpm and incubated at room temperature for 10 min. The FITC fluorescence signals will be read using the PerkinElmer ViewLux plate reader at 480 / 20 nm excitation and 540 / 20 nm S and P polarization emission wavelengths. Reagent bottles will be kept submerged into 4 oC recirculating chiller bath and all liquid lines will be covered with aluminum foil to minimize degradation. Library plates will be screened starting from the lowest to the highest concentrations to minimize compound carryover. Vehicle only plates, with DMSO being pin-transferred instead of compound solutions, will be included regularly throughout the screen to record any systematic shifts in assay signal.

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: SBCCG-A686-Gli-Sufu-Antagonist-Primary-Assay

Protocol: Gli Antagonist Primary Screen Procedure

Cell Culture:

Media:

Sufu-KO-LIGHT cell line GROWTH MEDIUM
Final concentrations
DMEM Phenol Red containing (Hyclone #SH30243.02)
HI-FBS characterized (Hyclone SH30396.03 HI or equivalent) 10%
L-glutamine (Cellgro # 25-005-CI) 200 mM 100 mL 2 mM (1:100)
Penn/Strep (Cellgro #30-0020CI) 5000 IU/mL 100 mL 50 IU/mL (1:100)
Zeocin (Invitrogen R25005 or Sigma 46-0072) 5 g in 50 mL (100 mg/mL) 0.15 mg/mL (1:666.67)

Sufu-KO-LIGHT cell line ASSAY MEDIUM
Final concentrations
DMEM phenol red free (Hyclone SH30585.02)
HI-FBS characterized (HYCLONE SH30396.03 HI or equivalent) 10%
L-glutamine (Cellgro # 25-005-CI) 200 mM 100 mL 2 mM (1:100)
Na-pyruvate (Sigma S8636-100ML) 100 mM 1 mM (1:100)
Penn/Strep (Cellgro #30-0020CI) 5000 IU/mL 100mL 50 IU/mL(1:100)
HEPES (Omega Scientific # HB-20) 100 mL 1 M 25 mM (1:40)
Zeocin (Invitrogen R25005 or Sigma 46-0072) 5g in 50 mL (100 mg/mL) 0.15 mg/mL (1:666.67)

Other Reagents:

Sufu-KO-LIGHT cell line (Assay Provider)
PBS (Phosphate Buffered Saline)
TrypLE (c) Express cell dissociation reagent (Life Technologies)
T225 tissue culture flasks (Corning)
HYPERflasks (c) (Corning)
1536 well tissue culture plates Aurora (c) & Corning
1536 well Echo (c) compatible Cyclic Olefin Copolymer (COC) compound storage plates (Corning or Labcyte)
384 well low volume Echo (c) compatible COC compound storage plates (labcyte)
Bright-Glo (c) luciferase detection reagent (Promega)

Automation & Instrumentation:

HighRes Biosolutions (HRB) MicroStar robotics platform with Cellario (c) scheduling software integrating the following instruments:
Viewlux (c) microplate imager (PerkinElmer)
VSpin (c) microplate centrifuge (Velocity11/Agilent)
Multidrop Combi liquid handler/dispenser (Thermo)
Liconic tissue culture incubator (Liconic)
Echo (c) 550 acoustic liquid handler (Labcyte)

Other instrumentation:
Biotek Microflo Select (c) peristaltic liquid handler/dispenser
Thermo Centra CL2 Clinical Centrifuge
Nexcelom Bioscience Cellometer (c) Auto T4 cell counter
Eppendorf 5810 centrifuge

Assay Procedure:

Day 1
1) Cells harvested from 2 hyperflasks at 80-90% confluency per screening day.
2) Cells suspended in Sufu-KO-LIGHT assay medium to a density of 1.0e6 cells/mL
3) 5 uL/well cell suspension was dispensed to columns 3-48. 5 uL/well assay medium alone (without cells) was dispensed to columns 1-2 (positive control) in Corning white polystyrene tissue treated 1536 well assay plates (#3727) or Aurora (c) white polystyrene tissue treated 1536 well Low Base square well assay plates (#00029846) using Biotek Microflo Select (c) peristaltic liquid handler/dispenser.
4) Plates were centrifuged 1 min at 1000 rpm (200xG) on an Eppendorf 5810 centrifuge
5) Plates were covered with Kalypsys brand stainless steel assay plate lids and placed over night (16-18 hrs) in humidified Liconic brand automated tissue culture incubator. Plates were stacked vertically in towers which rotate intermittently within the incubator. 37 oC, 5% CO2

Day 2
1) Kalypsys stainless steel lids were removed and 2.5 nL MLSMR test agents at 10 mM in DMSO stored in Labcyte Echo (c) compatible Corning 1536 well Cyclic Olefin Copolymer (COC) plates were applied to assay wells (columns 5-48) using a Labcyte Echo (c) 550 acoustic liquid handling system. Final assay concentration of test agents in the assay was 5 uM. 2.5 nL DMSO controls were also added to control wells (columns 1-4). Final DMSO concentration in the assay was 0.05%.
2) Plates were centrifuged 1 min at 1000 rpm (200xG) on an Eppendorf 5810 centrifuge
3) Plates were covered with Kalypsys brand stainless steel assay plate lids and place over night (16-18 hrs) in humidity controlled Liconic Automated tissue culture incubator. Incubator stacks plates vertically in towers. 37 oC, 5% CO2

Day 3
1) Kalypsys stainless steel lids were removed and replaced with plastic assay plate lids from Corning 1536 well assay plates (#3727) and plates returned to incubator.
2) 3 uL /well Bright-Glo (c) luciferase detection reagent (Promega) was added to assay wells using Multidrop Combi liquid handler (Thermo) and immediately centrifuged for 30 seconds on a VSpin (c) integrated microplate centrifuge at 1500 rpm (Velocity11/Agilent Technologies) and incubated for 10 minutes uncovered at room temperature. NB: plastic assay lids were removed by the HRB robotic system before addition of Bright-Glo (c) and NOT replaced. Luminescence was read on a Viewlux (c) microplate imager (PerkinElmer). Read time: 300 sec, Binning: 4X.

Comment: Compounds that demonstrated %activity >= 55% are defined as actives in this assay.

To simplify the distinction between the inactives of the primary screen and of the confirmatory screening stage, the Tiered Activity Scoring System was developed and implemented.

Activity Scoring
Activity scoring rules were devised to take into consideration compound efficacy, its potential interference with the assay and the screening stage that the data was obtained. Details of the Scoring System will be published elsewhere. Briefly, the outline of the scoring system utilized for the assay is as follows:
1) First tier (0-40 range) is reserved for primary screening data. The score is correlated with % activity in the assay:
a. If outcome of the primary screen is inactive, then the assigned score is 0
b. If outcome of the primary screen is inconclusive, then the assigned score is 10
c. If outcome of the primary screen is active, then the assigned score is 20
Scoring for Single concentration confirmation screening is not applicable to this assay.
d. If outcome of the single-concentration confirmation screen is inactive, then the assigned score is 21
e. If outcome of the single-concentration confirmation screen is inconclusive, then the assigned score is 25
f. If outcome of the single-concentration confirmation screen is active, then the assigned score is 30
This scoring system helps track the stage of the testing of a particular SID. For the primary hits which are available for confirmation, their scores will be greater than 20. For those which are not further confirmed, their score will stay under 21.

2) Second tier (41-80 range) is reserved for dose-response confirmation data and is not applicable in this assay

3) Third tier (81-100 range) is reserved for resynthesized true positives and their analogues and is not applicable in this assay