Radioisotope-based assay ([γ-33P] ATP) consisting of measuring 33P incorporation on the substrate (poly [Glu, Tyr] 4:1) relative to DMSO. IC50 values were calculated from the corresponding 8-point half-log dose response curves.
Structure-activity relationship:
A library of 24 closely related analogs was developed by introducing small changes on key functional groups of eCF506 and their activity tested in MDA-MB-231 cells. IC50 values were subsequently determined against SRC and ABL for those compounds exhibiting high antiproliferative activity and for selected compounds with low activity.
Analysis of the properties of compounds 12a–e demonstrated that the presence of a tertiary amino group at the position 4 of the pyperidinyl ring is essential for the activity. Substitution of the methyl groups by larger aliphatic rings was tolerated, with compounds 12d and 12e being among the most potent SRC inhibitors of the series. Removal of the pyrimidine ring (compound 12f) resulted in >3000-fold decrease in antiproliferative activity. Screening of compounds 12g–x evidenced the limited structural variations permitted at the top of the molecule to achieve high bioactivity. Most modifications of the Boc and the methoxy groups of the phenyl moiety at the C3 position led to a significant reduction in bioactivity. Even minor chemical modifications such as the substitution of the carbamate group by urea (12i) or amide (12j), or the change of the methoxy by OH (12s), resulted in >200-fold decrease in both antiproliferative properties and SRC inhibitory activity. Remarkably, introduction of a benzylamino group instead of the Boc was tolerated well, as observed from the bioactivity exhibited by compound 12m. However, introduction of endocyclic nitrogen atoms in the ring (see 12n and 12o) dramatically reduced compounds’ activity, particularly in the ortho position. Interestingly, while the methoxy group is required for maintaining high levels of activity when the Boc group is present in the structure (see 12s–u), substitution of the Boc group by an ester tolerated the elimination of the methoxy group (see 12w and 12x).
Potency (off target):
IC50
Off target protein and potency:
SRC Family Members: 0.5-5.4 nM
Potency assay (off target):
Radioisotope-based assay ([γ-33P] ATP) consisting of measuring 33P incorporation on the substrate (poly [Glu, Tyr] 4:1) relative to DMSO. IC50 values were calculated from the corresponding 8-point half-log dose response curves.
Probe Selectivity in Vitro:
eCF506 exclusively inhibits SRC Family Kinases. It is important to highlight that eCF506 displays a vast difference in activity (>950-fold difference) between ABL and its primary target SRC. While small molecule inhibitors with reverse binding capabilities have been developed (e.g., imatinib strongly targets ABL without inhibiting SRC), this is the first case of a small molecule with subnanomolar IC50 for SRC that requires a concentration 3 orders of magnitude greater to reach the same level of inhibition in ABL.
In cell validation
Potency in cells:
EC50
EC50 (MDA-MB-231)= 9 nM; EC50 (MCF7)= 70 nM
Potency assay (cells):
Antiproliferative assays. The antiproliferative properties of eCF506 were tested against breast cancer MCF7 (ER+) and MDA-MB-231 (triple negative breast cancer) cells. Cell viability was measured using the PrestoBlue(R) reagent and analysed by spectrofluorometry. EC50 values were calculated using a 10-point half-log dose. response study (0.3-1000 nM).
Target engagement assay (cells):
Indirect. Inhibition of SRC kinase activity in cells was studied by Western blot. Upon activation, SRC undergoes autophosphorylation of the Y416 residue within its kinase domain. Study of p-SRC(Y416) levels can then serve both as evidence for the presence of active SRC and to evaluate direct inhibition of SRC kinase activity. Phosphorylation of the focal adhesion kinase (FAK), a downstream substrate of SRC with high relevance in cancer progression, was also studied in both MDA-MB-231 and MCF7 cells. Cell lysates were prepared following 24 h of serum starvation and 1.5 h exposure to each inhibitor and serum stimulation for 1 h. Analyses demonstrated that eCF506 inhibits phosphorylation of SRC and FAK at low nanomolar levels, with complete inhibition observed at 100 nM.
Potency in cells, off target:
IC50
Off target protein and potency (cells):
AKT >1000 nM
Potency assay, off target (cells):
Western blot
Toxicity
Cytoxicity assay:
Yes
Notes on cytotoxicity:
eCF506 activity was tested in cells that lack expression of SRC: SYF murine embryonic fibroblasts (SRC-/-, YES-/-, FYN-/-). EC50 values were calculated using a 10-point half-log dose.
EC50 in SYF cells =/>20 uM