Design and synthesis of doublecortin-like kinase 1 inhibitors and their bioactivity evaluation

Figures & data

Figure 1. The role of DCLK1 in tumours.

Figure 2. Crystal structure of DCLK1-KD in complex with DCLK1-IN-1 (PDB: 7kxw) and molecular design.

Scheme 1. Synthesis of compounds A1–A10. Reagents and conditions: (a) NaY, 150 °C, dimethyl carbonate, 23–55%; (b) DIEA, 1,4-dioxane, 50 °C, 33–89%; (c) SnCl₂·2H₂O, EtOAc, 70 °C, 41–89%; (d) CH₃I, NaH, THF, 0 °C, 48–100%; (e) Pd(OAc)₂, XPhos, Cs₂CO₃, t-BuOH, 110 °C, 15–41%.

Scheme 2. Synthesis of compounds B1–B3. (a) DIEA, 1,4-dioxane, 50 °C, 70–85%; (c) SnCl₂·2H₂O, EtOAc, 70 °C, 43–95%; (d) R²I, NaH, THF, 0 °C, 57–100%; (e) Pd(OAc)₂, XPhos, Cs₂CO₃, t-BuOH, 110 °C, 15–41%.

Scheme 3. Synthesis of compounds C1, C2. (a) K₂CO₃, DMF, 50 °C, 80–96%; (b) SnCl₂·2H₂O, EtOAc, 70 °C, 52–78%; (c) Pd(OAc)₂, XPhos, Cs₂CO₃, t-BuOH, 110 °C, 35–46%.

Scheme 4. Synthesis of compounds D1–D16. (a) Pd(OAc)₂, XPhos, Cs₂CO₃, t-BuOH, 110 °C, 30–48%; (b)H₂, Pd/C, r.t., 100%; (c) Et₃N, CH₂Cl₂, r.t.; (d) LiOH (2 M), THF, 90% over two steps; (e) CH₃COSK, DMF, 100 °C, 38%; (f) K₂CO₃, DMF, 90 °C, 91%; (g) H₂O₂, AcOH, r.t., 95%; (h) TFA, CH₂Cl₂, r.t., 100%; (i) AcOH, EtOH, reflux, 82%.

Table 1. DCLK1 and LRRK2 inhibitory activities of the synthesised compounds at the concentration of 1 uM.

Entry	DCLK1 activity (%)	LRRK2 activity (%)	Selectivity (DCLK1 activity/LRRK2 activity)
XMD8-92	14	18	0.78
A1	25	8	3.13
A2	103	100	1.03
A3	85	88	0.97
A4	89	83	1.07
A5	87	89	0.98
A6	19	51	0.37
A7	109	109	1.00
A8	102	93	1.10
A9	17	50	0.34
A10	96	98	0.98
B1	102	76	1.34
B2	59	72	0.82
B3	28	70	0.40
C1	56	99	0.57
C2	15	7	2.14
D1	7	56	0.13
D2	10	49	0.20
D3	20	34	0.59
D4	18	33	0.55
D5	12	21	0.57
D6	9	19	0.47
D7	6	21	0.29
D8	8	22	0.36
D9	26	51	0.51
D10	51	81	0.63
D11	11	18	0.61
D12	5	10	0.50
D13	59	72	0.82
D14	7	16	0.44
D15	4	9	0.44
D16	15	33	0.45

Table 2. DCLK1 and LRRK2 inhibitory IC₅₀ values of the synthesised compounds.

Entry	IC50 of DCLK1 (nM)	IC50 of LRRK2 (nM)	Selectivity (IC50 of DCLK1/IC50 of LRRK2)
XMD8-92	161	219	0.74
A6	365	>1000	<0.37
A9	338	>1000	<0.34
B3	324	>1000	<0.32
D1	47	>1000	<0.05
D2	70	>1000	<0.07
D3	340	>1000	<0.34
D4	271	425	0.64
D5	146	320	0.46
D6	74	195	0.38
D7	46	154	0.30
D8	40	228	0.18
D11	100	266	0.38
D12	47	99	0.47
D14	53	132	0.40
D15	52	89	0.58

Figure 3. Structure–activity relationship analysis of DCLK1 inhibitors.

Figure 4. The antiproliferative effects of most compounds on HCT116.

Figure 5. Docking of compounds D1 and D8 to the residues of DCLK1 subunit (PDB ID: 5JZN).