External ID: CHEMBL828318

Protocol: N/A

Comment: Journal: J Med Chem
Year: 2005
Volume: 48
Issue: 15
First Page: 4947
Last Page: 4952
DOI: 10.1021/jm0408969

External ID: HMS1158_MLP

Protocol: A 5 mL overnight pre-culture of E. coli is started by inoculating a tube of lysogeny broth with a single colony from an agar plate. The tube is incubated at 37 degrees C overnight with shaking. The resulting saturated culture is removed from the shaker and diluted into fresh lysogeny broth at 1:100 proportion and incubated at 37 degrees C with shaking for two hours. The culture is removed from the shaker and absorbance is measured at 600 nm. The culture is diluted into fresh lysogeny broth to an estimated absorbance of 0.0002. For each library plate to be screened, two 384-well assay plates are filled with 30 microL per well of fresh lysogeny broth, except for the positive control columns, which are left empty. The multiple of two is necessary to expose the strain in duplicate to the same compounds from a given library plate.

300 nL of experimental compounds are transferred into the assay plates from library plates using a robotically manipulated stainless steel pin array, exposing the strain to the same compounds at the same concentration. The positive control columns are filled with 30 microL of the positive control compound in LB. Thirty microL of E. coli culture at absorbance of 0.0002 are then added to the assay plates, producing a total volume of 60 microL in each well. Plates are incubated at 37 degrees C without shaking and with humidification for 23 hours. The plates are removed from the incubator, and absorbance of the cultures is measured at 600 nm using a PerkinElmer EnVision plate reader. The absorbance is used as the readout.

Positive control: (R)-4-(4-(2-fluoro-4-methoxyphenyl)-2-oxopyridin-1(2H)-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide was present at 0.0754 microM in all wells of column 24.

Negative control: No treatment in remaining empty wells of the assay plate (minimally, wells in column 23).

Comment: A threshold constant was calculated by subtracting 3.6 X experimental well standard deviation for absorbance from the experimental well average absorbance, combining all plates in a screening run. Well absorbance was then subtracted from this threshold value. Wells were considered active if the resulting value after subtracting the threshold constant > 0 for at least one replicate. Activity scores were calculated by subtracting well absorbance from negative control plate average absorbance, dividing by the difference between plate negative and positive control plate average absorbance, and multiplying by 100. Resulting values > 100 were set to 100 and < 0 were set to 0, where 100 = 100% activity.

External ID: HMS791

Protocol: Prior to screening, FITC LANA1-23 was stored lyophilized at -80 degC and freshly purified chicken nucleosomes were stored at 4 degC in 20 mM Tris pH 7.5, 600 mM NaCl, 0.2 mM EDTA, 0.5 mM B-Mercaptoethanol.

On the day of screening, FITC LANA1-23 was resuspended at 50 uM in TEN-BT buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA (pH 8.0), 2.5 mM NaCl, 5 mM Beta-mercaptoethanol, 0.01% Triton-X-100) and diluted to a final concentration of 50 nM in TEN-BT buffer plus 240 nM of purified nucleosomes (480 nM LANA peptide binding sites). 30 uL per well were dispensed in column 1-22 in Corning #3575 black 384 well plates.

Wells in column 23 contained 30 uL of the same mixture (for pilot screen) or with the addition of 10 uM monensin (for HTS) as a negative control. In column 24, 1250 nM unlabeled WT LANA1-23 peptide (for pilot screen) or 10 uM mitoxantrone (for HTS) was added to the wells as a positive control. Compounds were transferred into wells via stainless steel pin array (100 nL) and the reaction was incubated at room temperature for 10 to 45 minutes (stable for up to 2 hours). Library plates were screened in duplicate, with both assay plates in a given set prepared on the same day.

Following a room temperature incubation of 10 to 45 minutes, the assay is read on a EnVision plate reader using a 480 nM excitation filter, 535 nM S and P emission filters and D505fp/D535 dichoric mirror. mP value for FP measurement = 1000*(S-G*P)/(S+G*P) where S= , P=, G= G-factor. The G Factor = 1.

Comment: LANA 1-23 peptide containing the first 23 amino acids of the LANA protein from Kaposi's sarcoma herpesvirus (KSHV) was synthesized with an N-terminal FITC via a beta alanine linker and HPLC purified (peptide sequence: [FITC]-Beta alanine-MAPPGMRLRSGRSTGAPLTRGSC-[NH2]).

Data analysis: Z-scores were calculated for each replicate well using the mean and standard deviation of plate experimental well FP values. Compounds were considered active if the Z-score for both replicates < -2. Wells with high total fluorescence intensity (high S and P channel values) were excluded from further consideration. Activity scores were calculated based on replicate average FP Z-scores. For wells with average Z-score >= 0, the activity score was set to 0. For wells with replicate average Z-score < 0, replicate Z-score was divided by 4 and multiplied by -100. The replicate average was then used to determine the well activity score. Values > 100 (replicate average Z-score < -4) were set to 100.

External ID: CHEMBL828320

Protocol: N/A

Comment: Journal: J Med Chem
Year: 2005
Volume: 48
Issue: 15
First Page: 4947
Last Page: 4952
DOI: 10.1021/jm0408969

External ID: CHEMBL828319

Protocol: N/A

Comment: Journal: J Med Chem
Year: 2005
Volume: 48
Issue: 15
First Page: 4947
Last Page: 4952
DOI: 10.1021/jm0408969

External ID: HMS1364-MLP_WT

Protocol: The day before screening, RN4220 was grown overnight (16-18 h) in sterile-filtered tryptic soy broth (TSB) at 30 degrees C with shaking.

On the day of screening, columns 1-24 of assay plates (Corning 3710, clear) were prefilled with 30 uL of TSB using the Combi. Next, 100 nL of each compound was pin-transferred to each plate. For every compound library plate, there were two daughter plates (A & B). Overnight cultures were diluted 625x into TSB. 50 uL of the diluted cultures were added to columns 1-24 of the corresponding assay plates. Wells in column 2 contained only medium (with culture) and served as the negative controls. Positive control (0.8 uL of erythromycin, 10 ug/mL) was added to column 1 using the Hewlett Packard D300. Final assay well volume was 80 uL. Plates were spun down and stacked 5 high, covered with lids (Corning 3009), and incubated at 30 degrees C overnight (~16 h).

The following day, assay plates were removed from the incubator and cell density quantitated using a PerkinElmer EnVision (600 nm filter).

Comment: Z-scores were calculated for every well based on plate average and standard deviation of experimental well absorbance (OD600). Wells were considered active for reduced WT survival if Z-score for both replicates <= -3 and absorbance for both replicates <= 0.18. Percent inhibition was calculated by subtracting well absorbance from negative control plate average absorbance, dividing by the difference between plate negative and positive control plate average absorbance, and multiplying by 100. The replicate values were then averaged to determine activity scores. Resulting values > 100 were set to 100 and < 0 were set to 0, where 100 = 100% activity.

External ID: HSPH_Screening_CFS_001

Protocol: Preparation of assay plates and seeding cells:
Polyacrylamide based gel substrates were miniaturized in glass bottom 96-well plates. In the first method, each 96-well plate was treated with NaOH (6N in water) for 1hr followed by silane solution ((3-aminopropyl)trimethoxysilane, 10% in water) for an additional 1hr. Then, glass surfaces were treated with glutaraldehyde (0.25% in PBS) for 30min and further washed and dried. Acrylamide gels (5.5% acrylamide, 0.076% bisacrylamide, Young's modulus = 1.8kPa, thickness = 200 microm) were cast in each well using a custom-made gel caster. The gel surfaces were functionalized using sulfo-SANPAH (sulfosuccinimidyl-6-[4 -azido-2 -nitrophenylamino]hexanoate, 0.2mg/mL), coated with green beads (0.2microm sulfate microspheres, Invitrogen, 0.002% in water), coated with bovine collagen I (40microg/mL in PBS) and were stored at 4C (Fig. 1A) for more than 1 day. After washing off collagen solution, primary human airway smooth muscle cells were seeded in each well (10,000 cells/well). 1 day after seeding, media was replaced with serum-deprivation media and cells were kept in serum free media for 2 days.

Measurements of contractile forces using Fourier-transform traction microscopy:
On the day of screening, 96-well plate was mounted upon a motorized stage within a temperature controlled chamber and imaged using an inverted microscope (DMI 6000B, Leica Inc.). In each well, images were obtained in quick succession: one phase contrast image of cells and a fluorescent images of beads. The image set was obtained before plating cells (reference), immediately prior to adding drugs (baseline), and 1 hr after drug addition (treatment). By comparing fluorescent images obtained during baseline or treatment with the corresponding image from reference, we computed the cell-exerted displacement field using particle image velocimetry. From the displacement field, we computed the contractile force (per unit area) using Fourier-transform traction microscopy modified to the case of cell monolayers. This modified approach takes into consideration effects of finite gel thickness as well as force imbalances associated with the microscope field of view as we described previously. From each force map, we computed the root mean squared value to represent the averaged contractile force. Drug effects were quantified as the 'force response ratio' (FRR), namely, the contractile force before versus after drug addition.

Small molecule library and pooling:
Prestwick 1 library was screened with pooling 4 compounds together.

Comment: Primary measurements of the screening are FRR (force response ratio). 1 means no change in average contractile force and less than 1 means the reduction of average contractile force after drug treatment.
Among the mixtures having FRR less than 1, 11 most effective mixtures were chosen as positives.

External ID: HMS1364-MLP_ugtP

Protocol: The day before screening, RN4220 ugtP was grown overnight (16-18 h) in sterile-filtered tryptic soy broth (TSB) at 30 degrees C with shaking.

On the day of screening, columns 1-24 of assay plates (Corning 3710, clear) were prefilled with 30 uL of TSB using the Combi. Next, 100 nL of each compound was pin-transferred to each plate. For every compound library plate, there were two daughter plates (A & B). Overnight cultures were diluted 625x into TSB. 50 uL of the diluted cultures were added to columns 1-24 of the corresponding assay plates. Wells in column 2 contained only medium (with culture) and served as the negative controls. Positive control (0.8 uL of erythromycin, 10 ug/mL) was added to column 1 using the D300. Final assay well volume was 80 uL. Plates were spun down and stacked 5 high, covered with lids (Corning 3009), and incubated at 30 degrees C overnight (~16 h).

The following day, assay plates were removed from the incubator and cell density quantitated using a PerkinElmer EnVision (600 nm filter). Library plates were screened in duplicate, with both assay plates in a given set prepared on the same day.

Comment: Z-scores were calculated for every well based on plate average and standard deviation of experimental well absorbance (OD600). Wells were considered active for reduced ugtP survival if Z-score for both replicates < -3 and absorbance for both replicates <= 0.15. Percent inhibition was calculated by subtracting well absorbance from negative control plate average absorbance, dividing by the difference between plate negative and positive control plate average absorbance, and multiplying by 100. The replicate values were then averaged to determine activity scores. Resulting values > 100 were set to 100 and < 0 were set to 0, where 100 = 100% activity.

External ID: HMS1149-MLP

Protocol: A 558 bp region upstream of hspX was PCR amplified and cloned upstream of the GFP-mut2 (Cormack et al., 1996). This construct was cloned into a modified version of the replicating plasmid pSE100 and transformed into CDC1551 to generate CDC1551(hspX'::GFP).

The M. tuberculosis CDC 1551 (hspX'::GFP) fluorescent biosensor was grown in pH 7.0 Middlebrook 7H9 medium to mid- to late-log phase. Black-walled, clear-bottom, tissue-culture treated 384-well microtiter plates (Corning #3712) were filled with 25 uL of buffered pH 7.0 7H9 medium using a Matrix Combi. 100 nL of compound was then transferred to each well via stainless steel pin array. Plates were manually sealed with DMSO-resistant aluminum seals and frozen at -80C until they were ready to be screened. The cultures were re-suspended in pH 7.0 7H9 and 25 uL was dispensed into each well of the 384-well assay plates already containing the perturbator utilizing a Cy-Bio Selma liquid handler robot to an OD595 of 0.05. The plates were then placed in a Ziploc bag with a moistened paper towel (to limit evaporation) and incubated for 6 days at 37C. Fluorescence and optical density (OD) readings were made on an EnSpire plate reader (Perkin Elmer, Inc.) at excitation and emission wavelengths of 488 and 509 nm as a top read, with the OD being taken at 595 nm as a bottom read.

The ~328,633 compound library was arrayed into black-walled, clear-bottom tissue-culture treated 384-well microtiter plates (Corning #3712) by pin transfer (100 nL), containing 25 uL of buffered pH 7.0 7H9 medium. In a previous screen utilizing the same compound library and screening method, four random compound plates were screened in duplicate to observe variation in hit robustness across plates and method. The result was that the duplicate plates did not vary in a statistically significant manner and due to the high volume of compounds to be screened (~328,633), replicates were not utilized.

Negative control: DMSO, 0.1% final concentration in buffered pH 7.0 7H9 in column 2 or column 23 of each plate

Positive control: 0.3 uM Rifampicin final concentration in buffered pH 7.0 7H9 in column 1 or column 24 of each plate

Comment: Analysis methods:
To calculate normalized fluorescence percent inhibition, plate average negative control fluorescence intensity (based on all plates within a screening run) was subtracted from well fluorescence intensity, divided by the difference between plate negative and positive control average fluorescence intensity (based on all plates within a screening run), and multiplied by 100. To calculate normalized growth inhibition, plate average negative control absorbance (based on all plates within a screening run) was subtracted from well absorbance, divided by the difference between plate negative and positive control average absorbance (based on all plates within a screening run), and multiplied by 100. Normalized fluorescence percent inhibition was divided by normalized growth inhibition to calculate a ratio. Wells were considered active if growth was not greatly decreased and showed either a 3-fold selectivity fluorescence to growth inhibition ratio (with 35-45% fluorescence inhibition) or a 1.5-fold selectivity fluorescence to growth inhibition ratio (with > 45% fluorescence inhibition). These compounds may be directly or indirectly inhibiting DosRS signaling. Wells were considered general inhibitors of M. tuberculosis growth if both fluorescence and growth inhibition > 50%. Activity scores were scaled from 100 to 0 and derived from normalized fluorescence percent inhibition, with 100 (or > 100) = 100% inhibition and 0 (or < 0) = no inhibition.

External ID: HMS750

Protocol: The stalled elongation complex used as a substrate in the screening assay was generated by pre-incubating 600 nM 3Dpol with 12 nM 5' fluorescein labeled 8-6 PETE RNA and 240 nM ATP for 30 minutes at room temperature in 50 mM HEPES, pH 7.0, 40 mM NaCl, 1.5 mM magnesium acetate, 60 microM ZnCl2, 4 mM DTT, and 0.1% Igepal detergent. This solution was dispensed into 384-well microplates (Corning 3710) at a volume of 25 microL/well. Experimental compounds were added by robotic pin transfer at 100 nL/well.

After an incubation time of ~60 min, the total fluorescence and fluorescence polarization signals from the labeled RNA were measured with Perkin Elmer EnVision microplate readers. This first reading provided data indicating whether compounds interfered with RNA binding to the stalled elongation complex. Polymerase elongation activity was then tested by adding 5 microL of a solution containing GTP, CTP, and UTP at 1.2 microM each, resulting in a final concentration of 200 nM for each of the four NTPs and 16.7 microg/ml for the compounds. This allowed for elongation to the end of the RNA template, and assay data were obtained with a second reading done after an incubation period of ~60 min, which is four times longer than the ~15 min needed for elongation under non-inhibited conditions.

Comment: Potential inhibitors were identified using a correlation plot combining standard Z-scores with an elongation efficiency measurement. A Z-score for each compound was calculated by the normal method of Z=(FPcompound-FPplate_mean)/StdDevplate_mean. An elongation efficiency value (FP %Elongation) was then calculated as E=(FPcompound-FPpositive)/(FPnegative-FPpositive), which reflects how the FP signal obtained in the presence of a compound compared to those of the unelongated positive controls (FPpositive) and fully elongated negative controls (FPnegative). Compounds that gave a FP signal greater than the starting material but less than the fully elongated controls thus had E values between 0% and 100%, while compounds that caused the RNA to dissociate from 3Dpol had negative E values due to the FP value associated with free RNA being lower than the unelongated FPpositive value. Finally, the elongation reaction also results in an increase in the total fluorescence intensity due to deprotonation of the fluorescein as it approaches the positively charged polymerase surface, providing an additional assessment of elongation. Compounds that resulted in total fluorescence %Elongation higher than that of the fully elongated control samples were rejected from the analysis. Positives were defined as having experimental FP Z-scores < -0.5 and FP %Elongation < 90%. Activity scores were calculated based on FP %Elongation. FP %Elongation <= 0 was scored as 100 for activity; FP %Elongation >= 100 was scored as 0 for activity. FP %Elongation values between 0 and 100 were subtracted from 100 to generate activity scores.