## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: MCF-7 ER Down Regulation Assay: The ability of compounds to down-regulate Estrogen Receptor (ER) numbers was assessed in a cell based immuno-fluorescence assay using the MCF-7 human ductal carcinoma breast cell line. MCF-7 cells were revived directly from a cryovial (approx 5×106 cells) in Assay Medium (phenol red free Dulbecco's Modified Eagle's medium (DMEM) (Sigma D5921) containing 2 mM L-Glutamine and 5% (v/v) Charcoal/Dextran treated foetal calf serum Cells were syringed once using a sterile 18 G×1.5 inch (1.2×40 mm) broad gauge needle and cell density was measured using a Coulter Counter (Beckman). Cells were further diluted in Assay Medium to a density of 3.75×104 cells per ml and 40 μl per well added to transparent bottomed, black, tissue culture treated 384 well plates (Costar, No. 3712) using a Thermo Scientific Matrix WellMate or Thermo Multidrop. Following cell seeding, plates were incubated overnight at 37° C., 5% CO2 (Liconic carousel incubator). Test data was generated using the LabCyte Echo® model 555 compound reformatter which is part of an automated workcell (Integrated Echo 2 workcell). 10 mM compound stock solutions of the test compounds were used to generate a 384 well compound dosing plate (Labcyte P-05525-CV1). 40 μl of each of the 10 mM compound stock solutions was dispensed into the first quadrant well and then 1:100 step-wise serial dilutions in DMSO were performed using a Hydra II (MATRIX UK) liquid handling unit to give 40 ul of diluted compound into quadrant wells 2 (0.1 mM), 3 (1 μM) and 4 (0.01 μM), respectively. 40 μl of DMSO added to wells in row P on the source plate allow for DMSO normalisation across the dose range. To dose the control wells 40 μl of DMSO was added to row O1 and 40 μl of 100 μM Faslodex® in DMSO was added to row O3 on the compound source plate. The Echo uses acoustic technology to perform direct microplate-to-microplate transfers of DMSO compound solutions to assay plates. The system can be programmed to transfer volumes as low as 2.5 nL in multiple increments between microplates and in so doing generates a serial dilution of compound in the assay plate which is then back-filled to normalise the DMSO concentration across the dilution range. Compounds were dispensed onto the cell plates with a compound source plate prepared as above producing a 12 pt duplicate 3 μM to 3 pM dose range with 3 fold dilutions and one final 10 fold dilution using the Integrated Echo 2 workcell. The maximum signal control wells were dosed with DMSO to give a final concentration of 0.3% and the minimum signal control wells were dosed with Faslodex® to give a final concentration of 100 nM accordingly. Plates were further incubated for 18-22 hours at 37° C., 5% CO2 and then fixed by the addition of 20 μl of 11.1% (v/v) formaldehyde solution (in phosphate buffered saline (PBS)) giving a final formaldehyde concentration of 3.7% (v/v). Cells were fixed at room temperature for 20 mins before being washed two times with 250 μl PBS/Proclin (PBS with a Biocide preservative) using a BioTek platewasher, 40 μl of PBS/Proclin was then added to all wells and the plates stored at 4° C. The fixing method described above was carried out on the Integrated Echo 2 workcell. Immunostaining was performed using an automated AutoElisa workcell. The PBS/Proclin was aspirated from all wells and the cells permeabilised with 40 μl PBS containing 0.5% Tween 20 (v/v) for 1 hour at room temperature. The plates were washed three times in 250 μl of PBS/0.05% (v/v) Tween 20 with Proclin (PBST with a Biocide preservative) and then 20 μl of ERα (SP1) Rabbit monoclonal antibody (Thermofisher) 1:1000 in PBS/Tween /3% (w/v) Bovine Serum Albumin was added. The plates were incubated overnight at 4° C. (Liconic carousel incubator) and then washed three times in 250 μl of PBS/0.05% (v/v) Tween 20 with Proclin (PBST).
- Assay organism: Homo sapiens
- Target name: Estrogen receptor
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: CC(C)(F)CN1C(c2c(F)cc(/C=C/C(=O)O)cc2F)c2[nH]c3ccccc3c2CC1(C)C
- Properties:
- ChEMBL ID: CHEMBL5923381
- Molecular weight: 456.51
- Heavy atoms: 33
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 2
- TPSA: 56.33
- LogP: 6.02
- Rotatable bonds: 5
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.35
- QED: 0.46

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 6.36
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 440; units nM; pChEMBL 6.36; comment 574825

## Query Molecule B
- Canonical SMILES: C[C@H](CF)CN1C(c2ccc(/C=C/C(=O)O)cc2)c2[nH]c3ccccc3c2CC1(C)C
- Properties:
- ChEMBL ID: CHEMBL6028262
- Molecular weight: 420.53
- Heavy atoms: 31
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 2
- TPSA: 56.33
- LogP: 5.6
- Rotatable bonds: 6
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.35
- QED: 0.51

## Molecule Similarity
- Weighted Tanimoto: 0.6

Answer: 5.77