AID	Name	Type	Comment
2007	Summary of Broad Institute MLPCN Reversing Antifungal Drug Resistance Project.	summary	Summary
1979	Fluorescence Cell-Based Primary HTS of C.albicans growth in the presence of Fluconazole and compound	screening	Primary HTS

Broad Institute: Reversing Antifungal Drug Resistance

Project ID: 2037

Keywords: Candida albicans, drug resistance, Fluconazole, Hsp90, Calcineurin, stress response

Primary Collaborators: Susan Lindquist, Whitehead Institute for Biomedical Research, sll@wi.mit.edu

Assay Overview: The basic assay strategy will consist of highly Fuconazole-resistant C. albicans clinical isolate cultured in 384-well format in the presence of a sub-toxic concentration of Fluconazole. Test compounds that inhibit subsequent growth in the presence of Fluconazole will merit further evaluation for their synergy with Fluconazole. This whole cell phenotypic screening approach will only capture compounds that retain activity in biological media and are capable of entering and accumulating in fungi to bioactive concentrations. Grossly cytotoxic compounds will be removed through subsequent counterscreens. Compound activity will be measured by the metabolism of Alamar Blue, a cell stain that is metabolized to a fluorescent product by living cells but that remains non-fluorescent in wells with growth-inhibited organisms.

Probe attributes:
a. Compounds that inhibit yeast growth in the presence, but not in the absence of 8 ug/ ml Fluconazole.
b. Compounds that show a 10-fold specificity between the primary Candida test strain and mammalian cells.
c. Compounds that exhibit 10X greater inhibition against fungus than the hsp90 chaperon and /or calcineurin.
d. IC50 < 1uM

Expected Outcome: Active wells will show a reduced fluorescence intensity due to a reduction in the amount of Alamar Blue dye metabolized by fewer viable microorganisms.

Stock solutions
Geldanamycin (GA) 15mM stock solution in DMSO
Fluconazole (FLC, Sequoia Research Products Ltd) 2 mg/ml stock solution in PBS
Pen/Strep 100x in PBS

Synthetic Defined Growth Medium
RPMI 1640 medium, (powder without sodium bicarbonate; Invitrogen 31800-089)
Uridine 8 mg/ml in water (Sigma)
Glucose 40% (w/v) in water (Sigma)
MOPS Buffer (Sigma)

Fungal Inoculum
Test Strain: C. albicans CaCi-8 (Redding et al., 1994, Clin Infect Dis, 18: 240-242)
Inoculate 500 ul of strain from cryopreserved stock into 250 ml shaker flask containing 30 ml growth medium. Shake at 30C O/N.
Read OD 600 of fungal culture using standard plate reader. Dilute with Synthetic Defined Growth Medium to starting OD of the fungal inoculum of 0.00015 A600.

384-well plates (Corning).

Add Fluconazole stock solution (2 mg/mL in PBS) to Synthetic Defined Growth Medium to achieve 8 ug/ml. Add Pen/Strep at 0.1 ml per 10 ml media.
Using Thermo Combi, dispense 20 uL/well of Synthetic Defined Growth Medium into all wells.
Pin 100 nL from compound plates into assay plates using CyBiWell pinning instrument.
Add Fluconazole stock solution (2 mg/mL in PBS) to fungal inoculum to achieve 8 ug/ml. Add Pen/Strep at 0.1 ml per 10 ml media.
Using Thermo Combi, dispense 20 uL/well of Synthetic Defined Growth Medium plus culture into all wells.
Incubate plates in humidified (90 % humidity) incubator at 37C without agitation for 48 hrs.

Dilute Alamar Blue Reagent (Biosource International Cat# DAL1100) 1:40 in Ca/Mg-free PBS. Add 6.4 ul/well to plates with Combi (final dilution factor 1:200). Incubate 2 hrs at RT. Read Relative Fluorescence Intensity (RFU) of wells on standard plate reader as measure of relative fungal growth.

Plate reader set-up- Envision, Perkin Elmer: Ex 544nm, Em 590nm, Bandwidth 12nm, Top read.

Dose Data Analysis

Neutral control (NC) wells and positive control (PC) wells were included on every plate.
Active inhibitor compounds result in decreased fluorescent signal.

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 NC wells was set to a normalized activity value of 0.
The median raw signal of the intraplate PC wells was set to a normalized activity value of -100.
Experimental wells were scaled to this range, giving an activity score as percent change in signal relative to the intraplate controls.

No plate pattern correction algorithm was applied.

IC50 values were calculated using the curve fitting strategies in Genedata
Screener Condoseo (7.0.3). IC50 values were extrapolated up to 1 log
over the highest tested concentration.


PubChem Activity Score and Outcome

PUBCHEM_ACTIVITY_SCORE:

Inactive compounds = 0
Active compounds = -10*Log(IC50)

PUBCHEM_ACTIVITY_OUTCOME:

Activity_Outcome = 1 (inactive)
IC50 > 1 log over the highest tested concentration

Activity_Outcome = 2 (active)
IC50 <= 1 log over the highest tested concentration

Activity_Outcome = 3 (inconclusive)
Curve fitting strategy resulted in a constant fit with activity >30% but <70%
or
The fit was not valid due to poor fit quality.

Grant Number: MH086456-01