Binding conformations and QSAR of CA-4 analogs as tubulin inhibitors

Figures & data

Figure 1.  Structural diagrams of CA-4 and CA-4P

Table 1.  Structures and experimental cytotoxicities (against the human T-lymphocyte Molt4/C8 cell line) of studied CA-4 analogs.

No.	X	R1	R2	R3	R4	R5	R6	IC50 (nM)	pIC50 (M)
1	NH	H	CH3	H	H	H	H	1400	5.854
2	NH	H	H	OCH3	H	H	H	6900	5.161
3	NH	H	OCH3	H	H	H	H	630	6.201
4	NH	OCH3	H	H	H	H	H	640	6.194
5	NH	H	OCH3	OCH3	H	H	H	8600	5.066
6	NCH3	H	H	H	H	H	H	2100	5.678
7	NCH3	H	H	CH3	H	H	H	1700	5.770
8	NCH3	H	CH3	H	H	H	H	110	6.959
9	NCH3	CH3	H	H	H	H	H	270	6.569
10	NCH3	H	H	OCH3	H	H	H	2100	5.678
11	NCH3	H	OCH3	H	H	H	H	57	7.244
12	NCH3	OCH3	H	H	H	H	H	3.8	8.420
13	NCH3	H	OCH3	OCH3	H	H	H	5000	5.301
14	NCH3	H	Cl	H	H	H	H	480	6.319
15	O	H	H	H	OCH3	H	H	1800	5.745
16	O	H	OCH3	H	H	H	H	140	6.854
17	O	OCH3	H	H	H	H	H	4400	5.357
18	O	H	H	OCH3	H	CH3	CH3	470	6.328
19	O	H	OCH3	H	H	CH3	CH3	48	7.319
20	O	OCH3	H	H	H	CH3	CH3	670	6.174
21	O	H	OCH3	H	H	H	COCH3	62	7.208
22	O	H	OCH3	H	H	H	COCH2Cl	310	6.509
23	O	H	OCH3	H	H	H	COCH2Br	240	6.620
24	O	H	OCH3	H	H	H	COCH2I	86	7.066
25	S	H	H	H	H	H	H	290	6.538
26	S	H	CH3	H	H	H	H	34	7.469
27	S	CH3	H	H	H	H	H	83	7.081
28	S	H	OCH3	H	H	H	H	10	8.000
29	S	OCH3	H	H	H	H	H	8.5	8.071
30	S	H	OCH3	OCH3	H	H	H	87	7.060
31	S	H	CH3	H	H	CH3	CH3	85	7.071
32	S	H	CH3	H	H	COCH3	COCH3	75	7.125

Figure 2.  Molecular structures and numbering of studied CA-4 analogs.

Figure 3.  Alignment of the 32 studied molecules.

Figure 4.  Binding conformations of the docked CN2 (cyan) and crystal CN2 (magenta) at the active site of tubulin.

Figure 5.  (a, b) Binding conformations of 32 docked compounds at the active site of tubulin.

Table 2.  CoMFA and docking results of the studied compounds.

Compound	Experimental pIC50 (M)	Calculated pIC50 (M)	Residual value	LOO-predicted pIC50 (M)	Docking E (kcal/mol)
1	5.854	6.273	0.419	6.673	−39.72
2	5.161	5.051	−0.110	4.894	−40.47
3	6.201	6.172	−0.029	6.164	−41.32
4	6.194	6.069	−0.125	6.078	−44.92
5	5.066	5.190	0.124	5.287	−40.59
6	5.678	5.714	0.036	6.182	−41.88
7	5.770	5.583	−0.187	5.919	−39.66
8	6.959	6.577	−0.382	6.085	−43.33
9	6.569	6.445	−0.124	6.276	−45.55
10	5.678	5.374	−0.304	5.089	−44.34
11	7.244	7.322	0.078	7.537	−45.56
12	8.420	8.463	0.043	7.439	−47.34
13	5.301	5.495	0.194	5.959	−47.63
14	6.319	6.177	−0.142	6.36	−43.56
15	5.745	5.804	0.059	5.957	−40.62
16	6.854	6.515	−0.339	6.143	−42.44
17	5.357	5.791	0.434	6.596	−44.09
18	6.328	6.487	0.159	6.33	−43.95
19	7.319	7.342	0.023	7.184	−44.06
20	6.174	6.072	−0.102	5.998	−44.35
21	7.208	7.189	−0.019	6.922	−40.44
22	6.509	6.602	0.093	6.841	−41.83
23	6.620	6.663	0.043	6.822	−45.2
24	7.066	7.010	−0.056	6.562	−41.34
25	6.538	6.738	0.200	7.178	−38.73
26	7.469	7.390	−0.079	7.062	−40.16
27	7.081	7.061	−0.020	7.196	−43.81
28	8.000	7.958	−0.042	7.43	−34.78
29	8.071	8.065	−0.006	7.521	−45.85
30	7.060	7.207	0.147	7.145	−47.53
31	7.071	7.132	0.061	7.401	−42.76
32	7.125	6.897	−0.228	6.921	−45.84

Figure 6.  (a) Docking conformation of the most potent inhibitor 12 and corresponding surface of tubulin at the colchicine-binding site, in which the red and blue regions represent oxygen and nitrogen atoms, respectively, whereas white regions represent carbon or hydrogen atoms. (b) Interactions between the colchicine-binding site and compound 12.

Table 3.  Statistical parameters of 3D-QSAR model from CoMFA.

Statistic index	N	R^2	q^2	SEE	F	R^2bs	SDbs	Contribution (%)
								Steric	Electrostatic
CoMFA	6	0.955	0.66	0.204	87.8	0.961	0.183	66.3	33.7

Note: N, optimal number of components; R², non-cross-validation coefficient; q², leave-one-out (LOO) cross-validation coefficient; SEE, standard error of estimation; F, F-test value; R²_bs, mean R² of bootstrapping analysis (100 runs); SD_bs, mean standard deviation by bootstrapping analysis.

Table 4.  Structures and computational results for 16 congeneric compounds as the test set.

No.	R	Experimental pIC50 (M)	Predicted pIC50 (M)	Residual value
T1	—	8.276	7.89	−0.386
T2	p-F	7.921	7.691	−0.23
T3	p-Cl	7.114	7.542	0.428
T4	o-Cl	7.77	7.385	−0.385
T5	m,p-2Cl	6.569	6.772	0.203
T6	p-Br	7.036	6.687	−0.349
T7	p-I	6.721	6.768	0.047
T8	p-CH3	7.796	7.584	−0.212
T9	p-OCH3	7.745	7.567	−0.178
T10	m-OCH3	7.77	7.111	−0.659
T11	m,p-2(OCH3)	7.699	7.084	−0.615
T12	m,m’,p-3(OCH3)	5.921	6.188	0.267
T13	p-OCH2CH3	6.62	6.827	0.207
T14	p-CF3	6.602	6.383	−0.219
T15	p-NO2	6.959	6.76	−0.199
T16	m-NO2	8.125	7.963	−0.162

Figure 7.  Plot of calculated (predicted) activities vs. experimental ones for CoMFA analysis, in which 32 compounds in the training set are expressed as dots and 16 compounds in the test set are expressed as triangles.

Figure 8.  A regression of observed vs. predicted activities for 16 compounds from the external test set, in which the red solid line is not through the origin and the black dotted line is through the origin.

Figure 9.  A regression of observed vs. LOO predicted activities for 32 compounds from the training set, in which the red solid line is not through the origin and the black dotted line is through the origin.

Figure 10.  A regression of observed vs. predicted activities for 48 compounds from the whole set, in which the red solid line is not through the origin and the black dotted line is through the origin.

Figure 11.  CoMFA steric contour map for compound 12 with the highest activity.

Figure 12.  CoMFA electrostatic contour map for compound 12 with the highest activity.