External ID: HMS1262

Protocol: NEC is stored at -80 degrees at a concentration of 15mg/ml in single use aliquots.

On the day of the screen, 20ul of purified NEC is aliquoted using a Multidrop Combi reagent dispenser into 384 well plates (Corning 3824). 100nl of compound dissolved in DMSO was transferred to each well of the assay plated via pin transfer. The plates (NEC + compound) are incubated at room temperature for 3 hours. Acceptor and donor reagents (CisBio 620/665 pair) are combined then added to each well at 5 microL volumes at a concentration of 8 nM and 80nM respectively. The plates are spun at 1k rpm for 1 min and incubated overnight at 4 degrees, then for one hour the subsequent day at room temperature.

Flourescent measurements are read on the Envision 1 plate reader at ICCB-L. The raw data consists of two fluorescence readings - at 665 nm and 620 nm for the acceptor and donor respectively.

Comment: Data analysis:
The raw data consists of two fluorescence readings - at 665 and 620 nm for the acceptor and donor respectively. The data is processed as a ratio of the emission from the acceptor over the donor (homogeneous time resolved fluorescence ratio). Normalized percent inhibition (NPI) for all experimental wells is calculated based on plate averages for negative and positive control HTRF ratio. Positives are scored as any ratio with a 50% or greater inhibition as compared with the positive control (i.e. NEC + Untagged UL50). To be considered a hit, both replicates need to score as positive. Activity scores are derived from NPI, with 100 = 100% inhibition (> 100% set to 100) and 0 = no inhibition (< 0% set to 0). Note that some compounds with NPI <50% (activity scores < 50) are classified as potential hits based on additional criteria (typically by selecting wells with low ratios compared to other experimental wells on the plate).

External ID: HMS1482

Protocol: Prior to screening, cells were passaged in high glucose DMEM supplemented with 10% FBS, 1% P/S, 1 mM pyruvate, and HEPES. Media was changed every 1-2 days to prevent starvation and maintain cellular health.

On the day of screening, 384-well plates (Corning 3765) were filled with 30 uL of control cybrid cell suspension (33.3 cells/ul). Media for resuspension was DMEM supplemented with 10% FBS, 1% P/S, 1 mM pyruvate, and HEPES. Positive control columns were 23 and 24 for most plate setups. Initially, tunicamycin (15 nM) and galactose media (10 mM + 1 mM glucosamine) were used in columns 23 and 24, respectively. Over the course of the screen, galactose was substituted with Vidofludimus (11 uM). Next, 33 nL of each compound were pin-transferred to each plate in duplicate. Final assay well volume was 30 uL. Plates were stacked 2 high, covered with lids, and incubated at 37 degrees C for 2 days.

After 2 days of incubation, Hoescht (10 ul/well) was added to assay plates and fluorescence was read using the Acumen laser scanning cytometer. After, the bottom of plates were sealed with two layers of Brightmax Sealing Films. Then Promega NanoGlo Live cell reagent (20 ul/well) was added to each well and luminescence was read on a PerkinElmer EnVision plate reader after 5 minute of shaking.

Comment: Data analysis method and criteria for scoring active compounds:

Normalized luminescence values (luminescence / cell number) for each replicate were calculated (based on average of 2 luminescence reads per replicate). Z-scores were calculated using the plate average and standard deviation of experimental well normalized values. Each plate replicate was individually analyzed to measure reproducibility across plates. Z-scores were then averaged across replicates and a Z-score threshold of 1.96 was selected for positive hits, indicating increased mitochondrial supercomplex formation. Wells were excluded from further consideration based on low cell number (1 or both replicates with number of objects count < 1500). Activity scores were determined by scaling Z-scores from 0 (activity score = 0) to 4 (activity score = 100), with activity score > 50 being considered active. Z-scores < 0 were set to activity score = 0; Z-scores > 4 were set to activity score = 100 (100% activity).

External ID: GPR151_PHUNTER_AG_LUMI_1536_1X%ACT

Protocol: Assay Overview:
TThe goal of this NIH sponsored research project was to identify GPR151 agonists via high-throughput screening (HTS) efforts. In brief, the McDonald Lab transferred the GPR151 AG 384wpf assay to Scripps for implementation and miniaturization to 1,536-well format followed by screening against the Scripps Drug Discovery Library (SDDL). A counterscreen assay, employing GPR119 cells, was also implemented by Scripps to identify compounds that non-specifically affect the PathHunter detection method. This project was aided by cheminformatic efforts to help identify compounds that demonstrated authentic agonist pharmacology and non-promiscuous activity profiles across other primary screens run against the SDDL. At completion of the project, several compounds demonstrated activity in the GPR151 AG PathHunter assay. All compounds selected for titration were also subjected to LC-MS analysis to confirm mass and sample purity

Protocol Summary:
Prior to the start of the assay, cells were resuspended in growth media at 2000cells/well in 1536 well plates. This was followed by an incubation of 18 hours at 37C+5%CO2. Then 1uL of Opti-Mem added to all wells except high controls to which 3X EA reagentwas added to each of those wells (0.2X final in lysis buffer). Compounds were pinned at 11.20uM final concentration in 1.0% DMSO followed by a 90 minute incubation at 37C+5%CO2. At this stage 3uL of Promega Beta-Glo detection Buffer was added to all wells followed by a 1 hour incubation at room temperature. Finally the assay end point read was taken using the ViewLux imaging reader from PerkinElemer Lifesciences with a 5 second exposure. Raw assay data was imported into Scripps# corporate database and ascetrained for Z' greater than 0.5 in order to be processed futher.

The percent activation for each compound was calculated as follows:

Percent Response of compound= 100 * ((Test Well-Median Data Wells)/(Median High Control # Median Data Wells))
Where:
Test_Well is defined as wells containing GPR151 cells in the presence of test compound
High_Control represents wells containing GPR151 cells stimulated with 0.2X EA reagent
Low_Control is defined as wells containing GPR151 cells and DMSO
PubChem Activity Outcome and Score:
Standard Cutoff
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 100-1, for inactive 1-0.
List of Reagents:
GPR151 cells (supplied by Patricia McDonald)
Pen Strep (Invtirogen 15140)
FBS (Invtirogen 16140)
Hygromycin (Invtirogen 10687010)
Lysis buffer (CisBio 62CL2FDF)
EA Reagent (DiscoverX 30-411)
G418 (Gemini Bio 400-113)
Opti-MEM (Invtirogen 31985)
Trypsin (Invtirogen 15400054)
Beta Glo (Promega E4780)
1536-well plates (Greiner Bio-One, part 789173)

Comment: Due to the size of the Scripps Molecular Screening Center compound library, this assay have been run as multiple 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 Scripps Molecular Screening Center.

A mathematical algorithm was used to determine what we call the standard hit cut-off to identify active compounds. Two values were calculated: (1) the average percent activation of all compounds tested in the screen, 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 percent activation than the cutoff parameter was declared active. Using this "Standard Cutoff" (= 4.91%) the primary assay yielded 6,756 active compounds ("hits")."

External ID: MITF_INH_Alpha_1536_1X%INH PRUN

Protocol: Assay Overview:

The purpose of this biochemical assay is to identify MITF dimerization inhibitors that disrupt or prevent its homodimerization. This assay is a bead-based proximity assay, which employs acceptor beads and donor beads to generate a chemiluminescence signal. In this assay, Biotin-labelled MITF and His- tagged MITF homodimerization will bring donor and acceptor beads into close proximity. Laser excitation of the donor beads converts oxygen to an excited singlet state. Reaction of the singlet oxygen with the acceptor beads further activates a chemiluminescence reaction within the same bead resulting in emitted light at 520-620 nm. As designed, small molecule inhibitors that interfere with this interaction will increase the distance of the acceptor beads, thus leading to decreased signal. Compounds were tested in singlicate at a nominal test concentration of 2.6 micromolar.

Protocol Summary:
Prior to the start of the assay, 1.25#L of assay buffer (50mM HEPEs pH7.5, 250mM Sodium chloride, 0.1% Tween, 0.1% BSA) containing 10nM His-MITF_r259stop were dispensed into columns 1 thru column 2, and 1.25#L of assay buffer containing 10nM of His MBP MITF were dispensed into columns 3 thru column 48 of 1536 microtiter plates. Next, 10nL of test compounds in DMSO, 7,8-Dihydroxycoumarin (200#M final highest concentration) in DMSO, or DMSO alone (0.15% final concentration) were added to the appropriate wells before dispensing 1.25#L of 10#g/mL Acceptor beads into column 1 to 46 and 1.25#L of assay buffer into column 47 and 48. Plates were incubated in dark for 2hrs at room temperature. Then, dispenses of 1.25#L of 10nM Biotin-MITF into all columns, and 10#g/mL Donor beads into column 1 to 46 and 1.25#L of assay buffer into column 47 to 48 followed by 3hrs incubation in dark at RT, was done. Alphascreen signal was determined using an EnVision microplate reader (PerkinElmer, Waltham, MA) at 680nm excitation and 570nm emission.

The percent inhibition for each compound was calculated as follows:

100 *( ( Median_Low Control-Test Compound) / ( Median_Low Control - Median_High Control ) )

Where:

Test_Compound is defined as wells containing His-MITF + Biotin-MITF in the presence of test compound
High_Control is defined as wells containing His-MITF_r259stop + Biotin-MITF and DMSO.
Low_Control is defined as wells containing His-MITF + Biotin-MITF and DMSO

PubChem Activity Outcome and Score:

Standard Cutoff

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 100-1, for inactive 1-0.

List of Reagents:

His-tagged MITF protein (supplied by Min Guo)
His-tagged MITF_r259stop protein (supplied by Min Guo)
Biotinylated-MITF protein (supplied by Min Guo)
7,8-Dihydroxycoumarin (Sigma, part D5564)
HEPEs (Sigma, part H3375, H3784)
Sodium chloride (Fisher, part BP358-212)
Tween-20 (Fisher, part 50146671)
DMSO (Fisher, part D159)
BSA (Fisher, part BP1600-100)
AlphaScreen Beads Kit (Perkin Elmer, part 6760619L)
1536-well plates (Greiner Bio-One, part 789175)

Comment: Due to the size of the Scripps Molecular Screening Center compound library, this assay have been run as multiple 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 Scripps Molecular Screening Center.

External ID: HMS1485

Protocol: Prior to screening, HeLa cells were transduced with a lentivirus carrying the vector PHAGE-N CMVt N-RIG3 p53(R273C) encoding constitutively expressed SGFP2 fused to histone 2B and mRuby-p53(R273C). Following transduction, the cells were selected using neomycin and fluorescent activated cell sorting. The day before the compound treatment, cells were plated (750 cells/well) in a final volume of 30 L/well of Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% (v/v) fetal bovine serum using a Thermo Combi. Plates were spun for 45 s at 500 rpm and incubated overnight (~24 h) at 37 degrees C, 5% CO2.

On the day of the screening, 33 nL of each compound was transferred to assay wells via a custom pin-transfer workstation. Additionally, 33 nL of positive (Velcade 300 M) and negative (DMSO 100%) controls were transferred to each plate into the corresponding columns that did not contain experimental compounds. For every compound library plate, there were two daughter plates (A and B). Plates were stacked 5 high, covered with lids, and incubated at 37 degrees C for 24h and 48h.

Assay plates were read using an Acumen Laser Scanning Cytometer 24h and 48h after compound treatment, using the following settings: For SGFP2 (channel 2), the 488 nm laser was used, with 6 mW output, 600 voltage gain and sensitivity threshold at 1; and for mRuby (channel 3), the 561 nm laser was used, with 8 mW output, 600 voltage gain and sensitivity threshold at 1.

Comment: Total nuclei and %p53 positive was calculated for all wells at 24 and 48h using the Cellista software. Percentage of p53 positive cells values were normalized to the positive and negative controls to determine a normalized percent of p53 activation. This was done on a per plate basis. The proteasome inhibitor Velcade (Adipogen, AG-CR1-3602-M005) at 330 nM was used as positive control while only the vehicle (DMSO, Sigma, D8418, 0.1% final concentration) was used as negative control. From these values the following normalized values were calculated (for both 24h and 48h): Normalized total nuclei = (total nuclei in experimental well / plate average negative control total nuclei) * 100. Normalized %p53 positive = (%p53 positive in experimental well - plate average negative control %p53 positive cells) / (plate average positive control %p53 positive cells - plate average negative control %p53 positive cells) * 100.

Based on the normalized percent p53 positive values, a compound was considered active when replicate average normalized % p53 positive cells > 50% for either or both time points. Activity scores were based on the replicate average normalized %p53 positive cells at 24hr. Values less than 0 were set to 0, and values > 100 were set to 100 (100% activity). Compounds with an activity score > 50 were considered active; some compounds were scored active despite having an activity score < 50 since % p53 positive cells was > 50% only at 48hr.

The average normalized total nuclei values were categorized as:
Very Low: x < 25%
Low: 25% < X > 50%
Medium: 50% < X > 75%
High: x < 75%

The average normalized % of p53 positive cells values were categorized as:
Low: x < 25%
Medium: 25% < X > 50%
Strong: 50% < X > 75%
Very Strong: x < 75%

Compounds that scored as strong or very strong in this classification (at either time point) were selected for follow up.

External ID: VANDERBILT_HTS_GIRK2_MPD

Protocol: To screen for modulators of the G protein-gated inwardly-rectifying potassium channel subunit 2 (GIRK2) homomeric channels, HEK293 cells were engineered to overexpress GIRK2. These cells were screened using a high-throughput thallium-flux assay in a 384-well format. High-throughput thallium flux assays are based on three principles: (1) extracellular thallium can permeate through potassium channels into cells, (2) the fluorescent dye Thallos enters and stays in the cytoplasm of HEK293 cells, and (3) the fluorescence of Thallos increases dramatically when it interacts with thallium ions. Compounds that modulate the activity of an overexpressed channel, in this case GIRK2, are identified by the change in fluorescence that results from changes in thallium influx into cells through the overexpressed channel.

The screening protocol was conducted as follows. One hour prior to screening, cells were loaded with 1.5 micromolar (muM) Thallos in assay buffer (1x Hank's Balanced Salt Solution and 20 millimolar (mM) HEPES). The liquid handling and imaging was conducted using a kinetic-imaging plate reader, Panoptic (WaveFront Biosciences). Before screening, Thallos-containing buffer was removed from cells and replaced with 20 microliters (muL) per well of assay buffer. Compounds were dissolved in assay buffer at 20 muM. After 8 seconds of imaging, 20 muL of compound solution was added per well and allowed to incubate for 150 seconds. Next, 10 muL of a solution containing 2.0 mM thallium in Base Buffer (125 mM NaHCO3, 1 mM MgSO4, 1.8 mM CaSO4, 5mM Glucose, and 20 mM HEPES) was added to the wells. 30 seconds later, 12 muL of base buffer containing 2.0 mM thallium and 50 mM 2-methyl-2,4-pentanediol (MPD), a partially-activating concentration, was added to each well. MPD has is a previously-described GIRK2 channel activator. Data was collected for 60 seconds after this final addition. The positive control for this screen was 30 muM ivermectin, a natural product previously identified as a GIRK2 activator as part of a small-scale pilot screen. Microsoft Excel was utilized for data analysis. Data were normalized, F/Fo, on a well-to-well basis to account for differences in cell number. Compound activity was analyzed by comparing the sums of control-subtracted amplitudes of fluorescence intensity at 20 seconds after each thallium addition. The top 0.2% compounds corresponding to wells that demonstrated the largest increases in fluorescence were selected as "hits" for counter screening, as described below.

All 63,228 compounds screened using the method described above are listed in column OUTCOME_SCREEN_HITS. The 133 compounds selected as hits based on the above criteria are labelled with "100" in the ACTIVITY column. Fluorescent compounds were included in the inactive compounds and marked with "0" in the ACTIVITY column.

The 133 active compounds from column OUTCOME_SCREEN_HITS were tested for non-specific activity in untransfected HEK293 cells using assay conditions otherwise identical to the primary screen. Column OUTCOME_HEK_COUNTERSCREEN lists the 23 compounds that displayed an increase in fluorescence upon thallium addition with "100" in the ACTIVITY column.

The 110 compounds which were identified as hits in the primary screen but inactive when tested in untransfected HEK293 cells were tested for activity in GIRK2-overexpressing HEK293 cells that did not express NPY4 receptor. Column OUTCOME_GIRK2_COUNTERSCREEN lists the 44 compound that displayed an increase in fluorescence upon thallium addition with "100" in the ACTIVITY column.

The 44 active compounds from column OUTCOME_GIRK2_COUNTERSCREEN were tested at various concentrations to determine if compound activity was concentration dependent. Column OUTCOME_GIRK2_DOSE_RESPONSE provides the efficacy of these compounds; activity of all compounds at the provided concentrations was normalized to the activity of VU0537695 at 25 muM, which was the highest efficacy observed during this screening. For each compound concentration listed, the efficacy of that compound provided refers to the normalized, control-subtracted fluorescence intensity at 15 seconds after the addition of thallium. The 28 compounds that demonstrated >5% efficacy and concentration-dependent activity were labelled as "100" in the ACTIVITY column.

Finally, column PUBCHEM_ACTIVITY_OUTCOME combines all of the information from the above counterscreens together, indicating the 28 hits from this GIRK2 screen.

Comment: