Use of Quantitative Structure–Activity Relationship (QSAR) and ADMET prediction studies as screening methods for design of benzyl urea derivatives for anti-cancer activity

Figures & data

Figure 1.  Flowchart of screening methods for new lead compounds.

Table 1.  Uni-Column statistics for training and test set of compounds.

	Column name	Average (mean)	Max*	Min*	Std Dev	Sum
Training set	pIC50	−1.1457	0.5690	−1.8760	0.6964	−22.9140
Test set	pIC50	−0.8125	−0.0790	−1.5490	0.6269	−3.2500

*Higher the value of pIC₅₀ (Greater +ve value), higher is the potency.

Figure 2.  Alignment of substituted benzyl urea derivatives using template based alignment method.

Table 2.  Statistical results of 2D-QSAR equation generated by MLR method and 3D-QSAR model generated by SA kNN–MFA for benzyl urea derivatives.

Sr. No.	Statistical parameter	Results
		2D-QSAR	3D-QSAR
1.	r^2	0.8787	—
2.	r^2SE	0.2411	—
3.	q^2	0.7215	0.6276
4.	q^2SE	0.2378	0.2843
5.	Pred_r^2	0.5728	0.9106
6.	Pred_r^2SE	0.2162	0.2199
7.	F-Test	19.914	—
8.	α q^2	0.0100	—
9.	Best-Rand q^2	0.2458	—
10.	Z-score q^2	2.6730	—
11	N	20	20
12	Nearest neighbour	—	4
11	Contributing descriptors	1. chiv1 (+ 0.6694) 2. MMFF_6 (−0.8569) 3. T_C_O_7 (−0.1222) 4. T_N_O_2 (+1.1713)	1. S_715(0.3304, 6.0782) 2. E_232 (-0.0255, 0.1432) 3. E_1064 (0.1346, 0.1345)

Table 3.  Structure of training and test sets of compounds along with observed and predicted activity.

Mol. No.	R	R1	R2	R3	Observed activity		SA kNN–MFA
					IC50 (µM)	PIC50	Predicted activity	Residual
1	-4-propylmorpholine	NO2	H	H	0.42	0.3768	0.4596	−0.0828
2	-4-ethylmorpholine	NO2	H	H	0.27	0.5686	0.5438	0.0248
3	-2-methylfuran	NO2	H	H	40.7	−1.6095	−1.4756	−0.1339
4	-ethylpiperidine-1-carboxylate	NO2	H	H	24.9	−1.3961	-1.7448	0.3487
5	-2-methylfuran	Cl	H	OH	71.3	−1.8530	−1.5958	−0.2572
6*	-4-ethylmorpholine	Cl	H	OH	3.88	−0.5888	−0.7637	0.1754
7	-4-propylmorpholine	Cl	H	OH	2.92	−0.4653	−0.7129	0.2476
8	-ethylpiperidine-1-carboxylate	Cl	H	OH	33.5	−1.5250	−1.3619	−0.1631
9	-4-ethylmorpholine	H	OH	H	11.8	−1.0718	−0.409	−0.662
10	-4-propylmorpholine	H	OH	H	7.5	−0.8750	−1.074	0.199
11	-2-methylfuran	H	OH	H	75.1	−1.8756	−1.5603	−0.3153
12	-ethylpiperidine-1-carboxylate	H	OH	H	67.2	−1.8273	−1.6452	−0.1821
13	-4-ethylmorpholine	H	NO2	H	2.24	−0.3504	−0.7603	0.4099
14*	-4-propylmorpholine	H	NO2	H	1.20	−0.0791	−0.4080	0.3289
15*	-2-methylfuran	H	NO2	H	35.4	−1.5490	−1.4951	−0.0539
16	-ethylpiperidine-1-carboxylate	H	NO2	H	26.0	−1.4149	−1.048	−0.366
17	-2-methylfuran	NO2	H	OH	28.6	−1.4563	−1.8394	0.3831
18*	-4-ethylmorpholine	NO2	H	OH	10.8	−1.0334	−1.0911	0.0577
19	-4-propylmorpholine	NO2	H	OH	8.5	−0.9294	−1.3932	0.4638
20	-ethylpiperidine-1-carboxylate	NO2	H	OH	38.4	−1.5843	−1.7281	0.1438
21	-2-methylfuran	Br	H	OH	40.5	−1.6074	−1.7168	0.1094
22	-4-ethylmorpholine	Br	H	OH	13.5	−1.1303	−1.7308	0.6005
23	-4-propylmorpholine	Br	H	OH	18.6	−1.2695	−1.6762	0.4067
24	-ethylpiperidine-1-carboxylate	Br	H	OH	41.8	−1.6211	−1.4703	−0.1514

*Compounds in test set.

Figure 3.  Comparison of observed activity vs predicted activity for training set (A) and test set (B) of compounds.

Figure 4.  Results of QSAR studies. (A) Contributions of 2D descriptors for biological activity developed using MLR equation (2D-QSAR). (B) Contributions of electrostatic and steric 3D data points towards biological activity developed using kNN–MFA method (3D-QSAR). (C) Pharmacophore requirement around benzyl urea.

Table 4.  Structure of designed NCEs along with predicted activity obtained by MLR equation generated by 2D-QSAR.

Sr. No.	Compound code	R1	R2	Screen result	Screen score	Predicted activity
1	E5	2-NO2	Benzyl	ADRXWS	6	0.413
2	A1	2-CH3	Nephthyl	ADRXWS	6	0.356
3	J2	2-C2H5	2,4-Dimethyphenyl	ADRXWS	6	0.291
4	E2	2-NO2	2,4-Dimethyphenyl	ADRXWS	6	0.146
5	A5	2-CH3	Benzyl	ADRXWS	6	−0.0198
6	J8	2-C2H5	1-Morpholine	ADRXWS	6	−0.0921
7	A8	2-CH3	1-Morpholine	ADRXWS	6	−0.1992
8	C1	3-OCH3 4-OH	Nephthyl	ADRXWS	6	−0.2112
9	J1	2-C2H5	Nephthyl	ADRXWS	6	−0.2214
10	E1	2-NO2	Nephthyl	ADRXWS	6	−0.2256
11	E8	2-NO2	1-Morpholine	ADRXWS	6	−0.2318
12	H1	2-Cl	Nephthyl	ADRXWS	6	−0.2377
13	A6	2-CH3	2-Furan	ADRXWS	6	−0.2412
14	H5	2-Cl	Benzyl	ADRXWS	6	−0.2489
15	J7	2-C2H5	2-Pyrrol	ADRXWS	6	−0.2801
16	A2	2-CH3	2,4-Dimethyphenyl	ADRXWS	6	−0.3125
17	H8	2-Cl	1-Morpholine	ADRXWS	6	−0.3890
18	E7	2-NO2	2-Pyrrol	ADRXWS	6	−0.4114
19	E6	2-NO2	2-Furan	ADRXWS	6	−0.4223
20	C2	3-OCH3 4-OH	2,4-Dimethyphenyl	ADRXWS	6	−0.4569
21	C5	3-OCH3 4-OH	Benzyl	ADRXWS	6	−0.4987
22	D8	2-OH	1-Morpholine	ADRXWS	6	−0.5239
23	C8	3-OCH3 4-OH	1-Morpholine	ADRXWS	6	−0.5673
24	D1	2-OH	Nephthyl	ADRXWS	6	−0.6166
25	F1	3-NO2	Nephthyl	ADRXWS	6	−0.7709
26	D5	2-OH	Benzyl	ADRXWS	6	−0.9876
27	H2	2-Cl	2,4-Dimethyphenyl	ADRXWS	6	−0.9943
28	D6	2-OH	2-Furan	ADRXWS	6	−1.2319
29	F5	3-NO2	Benzyl	ADRXWS	6	−1.2879
30	J6	2-C2H5	2-Furan	ADRXWS	6	−1.1341

Table 5.  Prediction of ADMET properties by using discovery studio, accelrys.

Sr. No.	Compound code	ADMET absorption level	ADMET PPB level	ADMET CYP2D6 probability	ADMET hepatotoxicity probability
1	C-1	0	2	0.772	0.655
2	E-5	0	2	0.455	0.456
3	E-2	0	0	0.297	0.529
4	E-7	0	0	0.435	0.357
5	F-1	0	2	0.772	0.596
6	J-2	0	1	0.584	0.589
7	D-6	0	0	0.415	0.357
8	H-5	0	2	0.366	0.317
9	H-1	0	2	0.841	0.609
10	F-5	0	2	0.455	0.43
11	J-1	0	2	0.841	0.642
12	C-5	0	2	0.613	0.602
13	C-2	0	1	0.485	0.609
14	A-8	0	2	0.405	0.072
15	E-1	0	2	0.782	0.682
16	Imatinib	0	1	0.514	0.655
17	Gefitinib	0	2	0.663	0.973
18	5-Flurouracil	1	0	0.019	0.834

Scheme 1.  Synthetic route for benzyl urea derivatives. Reagents & condition: (i) ethanol, reflux, 1–2 h (ii) NaBH₄, 50°C, 2–3 h (iii) dry CH₂Cl₂, 70°C, 4 h (iv) dry CH₂Cl₂, dry pyridine, 60°C, 5–6 h.

Table 6.  Anti-proliferative activity of compounds 7a–7g in cancer cell lines.

Compound code	R1	R2	Conc (µg/mL)	% Inhibition
				Molt-4 (%)	Jurkat J6 (%)	MCF-7 (%)	K562 (%)
7a (H-5)	-2-Cl	-Benzyl	25	0	3.9	8.85	—
			50	6.32	7.45	10.07	6.71
			100	10.42	7.78	10.07	9.59
			200	—	—	—	17.80
7b (E-5)	-2-NO2	-Benzyl	25	4.44	4.82	17.3	—
			50	6.5	4.6	9.22	0
			100	0.52	0.65	4.80	6.19
			200	—	—	—	16.66
7c (H-1)	-2-Cl	-1-Naphthyl	25	0	2.08	7.50	—
			50	4.66	3.61	5.54	14.92
			100	0.30	5.5	2.11	12.91
			200	—	—	—	7.94
7d (E-2)	-2-NO2	-2,4-dimethylphenyl	25	7.83	9.4	10.81	—
			50	3.91	18	11.91	13.08
			100	7.98	35	17.67	42.05
			200	—	—	—	45.37
7e (J-1)	-2-C2H5	-1-Naphthyl	25	0	4.82	0	—
			50	0.30	10.05	0	10.64
			100	3.46	11.73	7.99	13.78
			200	—	—	—	18.15
7f (C-1)	-3-OC2H5-4-OH	-1-Naphthyl	25	0	18.09	0.52	—
			50	4.59	10.05	17.79	9.773
			100	2.48	16.55	2.36	12.91
			200	—	—	—	18.67
7g (J-2)	-2-C2H5	-2,4-dimethylphenyl	25	6.6	14.36	0	—
			50	7.68	12.39	0	3.40
			100	0	14.3	0	11.43
			200	—	—	—	20.49
5-Flurouracil	—	—	25	65	40	4.93	—
			50	64	41	15.71	13.35
			100	61	37	21.59	7.76
			200	—	—	—	8.55

Figure 5.  Effect of compounds 7a–7g on (A) Molt-4, (B) Jurkat J6, (C) MCF-7, and (D) K562 cell lines on cell proliferation determined by MTT assay.