Discovery of a broad spectrum antiproliferative agent with selectivity for DDR1 kinase: cell line-based assay, kinase panel, molecular docking, and toxicity studies

Figures & data

Figure 1. Quinazoline-based anticancer drugs and KST9046 chemical structure.

Figure 2. Dose-response curves (% growth versus sample concentration at NCI fixed protocol, µM) obtained from the NCI’s in vitro disease-oriented human tumor cells line of compound KST9046 on nine cancer disease. The different color and shape of NCI subpanel cell lines indicative of growth percentage inhibition with concentration of sample.

Table 1. % Growth inhibition at 10 µM, GI₅₀, TGI and LC₅₀ of compound KST9046 over the NCI cell-line panel.

Tumor cell lines	% Growth inhibition	GI50 (µM)	TGI (µM)	LC50 (µM)
Leukemia
CCRF-CEM	97.19	2.33	–	>100
HL-60(TB)	92.51	2.20	–	>100
K-562	91.78	2.52	>100	>100
MOLT-4	95.16	1.72	–	>100
RPMI-8226	L	1.30	–	>100
SR	L	1.98	–	>100
Non-small cell lung cancer
A549/ATCC	97.74	2.88	–	>100
HOP-62	L	2.10	5.60	>100
HOP-92	L	1.88	6.88	>100
NCI-H226	62.86	2.91	9.19	>100
NCI-H23	79.43	2.96	–	>100
NCI-H322M	84.46	2.79	–	>100
NCI-H460	95.64	2.48	–	>100
NCI-H522	L	1.68	3.81	–
Colon cancer
COLO 205	L	1.81	–	–
HCC-2998	64.30	3.90	>100	>100
HCT-116	91.37	2.61	>100	>100
HCT-15	99.23	2.72	>100	>100
HT29	99.26	2.93	–	>100
KM12	90.92	1.77	–	–
SW-620	76.07	2.79	–	>100
CNS cancer
SF-268	73.45	2.37	–	>100
SF-295	92.78	2.27	–	>100
SF-539	64.04	2.28	–	>100
SNB-19	77.06	2.91	7.42	>100
SNB-75	78.90	1.81	3.98	8.73
U251	93.01	3.28	>100	>100
Melanoma
LOX IMVI	78.59	2.93	–	>100
MALME-3 M	89.16	2.41	–	>100
M14	L	2.45	–	>100
MDA-MB-435	99.54	1.48	4.34	>100
SK-MEL-2	L	2.04	4.23	–
SK-MEL-28	79.13	2.20	–	>100
SK-MEL-5	L	1.61	2.98	–
UACC-257	L	2.44	–	>100
UACC-62	L	1.68	3.50	–
Ovarian cancer
IGROV1	81.01	2.59	–	>100
OVCAR-3	87.42	1.75	4.17	–
OVCAR-4	77.55	2.56	7.34	>100
OVCAR-5	70.37	2.72	>100	>100
OVCAR-8	96.48	2.76	7.98	>100
NCI/ADR-RES	86.36	2.97	7.71	>100
SK-OV-3	71.87	2.45	6.13	>100
Renal cancer
786-0	60.99	3.00	>100	>100
A498	L	1.75	5.96	>100
ACHN	96.53	2.58	–	>100
CAKI-1	85.36	3.03	>100	>100
RXF 393	68.53	–	–	>100
SN12C	78.26	2.53	–	>100
TK-10	L	2.63	7.98	>100
UO-31	90.63	2.17	–	>100
Prostate cancer
PC-3	90.43	2.22	–	>100
DU-145	81.09	3.38	>100	>100
Breast cancer
MCF7	93.96	2.02	–	>100
MDA-MB-231/ATCC	72.76	2.54	7.80	>100
HS 578T	54.14	2.62	7.02	>100
BT-549	55.22	2.34	7.41	>100
T-47D	L	1.75	4.37	>100
MDA-MB-468	L	2.31	–	>100

L: lethal, –: not tested.

Table 2. Summary of kinase inhibitory profile of the new agent KST9046 at 10 µM over a panel of 347 kinases.

Kinase	% Enzyme inhibition at 10 µM
ARAF	44
DDR1	76
FLT3	49
LIMK1	40
MLK2	53
Other 342 kinases*	Less than 25

*For more details, see supplementary material.

Figure 3. Structure similarity between KST9046 and type III DDR2 allosteric modulator.

Figure 4. Docking of compound KST9046 in the binding site of DDR1 kinase catalytic domain (PDB ID: 4BKJ) in 3D style.

Figure 5. Docking of Imatinib (A) and DDR1-1N-1 (B) (type II DDR1 inhibitors) in the binding site of DDR1 kinase catalytic domain in 3D style.

Scheme 1. Reagents and conditions: (i) 3-fluorobenzyl bromide, K₂CO₃, KI, CH₃CN, 75 °C, 8 h; (ii) H₂, 10% Pt/C, CH₃OH, rt, 6 h; (iii) Ethyl chloroformate, TEA, THF, rt, 2 h; (iv) (a) HMTA, TFA, rt, 1 h, (b) 10% KOH aqueous ethanolic (1:1), K₃Fe(CN)₆, 100 °C, 4 h; (v) 3-chlorophenyl isocyanate, THF, 85 °C, overnight.

Table 3. IC₅₀ values of compound KST9046 over four different isoforms of CYP450 comparing to positive control agents.

	CYP450 Inhibition, IC50 (μM)
Compound	2C9	2C19	2D6	3A4
KST9046	>10	>10	9.6	>10
Positive control IC50 (μM)	Sulfaphenazole (0.08)	Fluoxetine (0.04)	Quinidine (0.03)	Ketoconazole (0.06)