Biological evaluation, docking studies, and in silico ADME prediction of some pyrimidine and pyridine derivatives as potential EGFR^WT and EGFR^T790M inhibitors

Figures & data

Figure 1. Pyridine and pyrimidines-tethered antitumor drugs.

Figure 2. Some reported pyrazolopyridine derivatives and their IC₅₀ values as anticancer and kinase inhibitors.

Figure 3. The common pharmacophoric properties of the FDA-approved EGFRI (erlotinib).

Figure 4. Schematic illustration disclosing the pharmacophoric features of the afforded pyrimidine and pyridine derivatives as EGFRIs.

Scheme 1. The detailed synthesis of the afforded fused pyrimidine derivatives (7–11); Reagents and conditions: i) KOH, DMF, reflux; ii) Pyridine, reflux.

Scheme 3. The detailed synthesis of the afforded pyridine candidates (18–21); Reagents and conditions: i) DMF, K₂CO₃, reflux 8 h; ii) Ethanol, reflux 6 h; iii) Ethanol, Acetic acid, reflux 2 h (ii) Ethanol, reflux 2 h.

Scheme 2. The detailed synthesis of the pyridine derivatives (14–17); Reagents and conditions: i) Amm. acetate, Acetic acid, reflux 12 h; ii) Amm. acetate, butanol, reflux 5 h; iii) POCl₃, PCl₅, heating 10 h; iv) NaN₃, DMF, reflux 8 h; ii) NH₂NH₂, dioxane, reflux 12 h.

Table 1. Pyrimidine and pyridine IC₅₀ (µg/mL) on different cell lines.

Sample	MCF7		T47D		VERO		H460		FADU		HEP2		HEPG2		HCT116		CaCo2
	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD	IC50 (µg/mL)	SD
7	13.70	1.76	44.50	0.70	12.00	1.35	3.70	0.42	8.30	0.98	35.20	0.49	12.00	1.41	15.00	1.41	21.50	0.70
8	4.10	0.14	7.50	0.70	3.90	0.14	11.70	1.06	5.60	0.14	7.90	0.14	3.80	0.28	7.20	0.28	12.40	0.84
9	17.20	0.35	11.50	0.70	32.50	0.70	43.20	1.06	19.60	0.49	14.70	0.35	18.50	2.12	24.30	0.91	23.50	0.70
10	18.70	1.06	18.20	0.35	28.50	2.12	2.90	0.14	4.50	0.70	22.80	0.21	7.30	0.91	33.30	0.91	--	--
11	15.90	0.14	19.50	0.70	24.00	1.41	4.30	0.98	18.20	1.06	19.50	0.70	18.50	2.12	42.00	2.82	24.80	0.28
13	7.80	0.07	21.00	1.41	–	–	–	–	15.90	0.14	4.80	0.21	8.60	0.49	44.30	0.91	--	--
14	3.70	0.14	4.70	0.29	4.60	0.40	8.00	0.70	3.90	0.14	4.70	0.42	3.80	0.21	3.90	0.14	4.10	0.21
15	14.70	1.06	49.40	0.84	21.50	0.70	21.00	1.41	17.50	0.70	36.80	0.28	12.00	1.45	22.00	1.41	23.50	2.12
16	21.00	1.41	8.90	0.14	4.50	0.07	19.40	0.77	9.00	1.41	31.00	1.42	9.70	0.35	27.00	1.41	18.20	1.06
17	34.00	1.41	4.90	0.14	16.50	0.70	12.70	0.35	10.50	0.70	24.00	1.41	4.90	0.14	19.30	0.91	24.00	2.82
18	21.50	0.70	25.50	0.70	24.50	0.70	25.00	1.41	22.00	1.41	23.0	1.40	9.00	0.03	36.70	0.42	23.50	0.70
19	39.50	0.70	32.00	1.41	36.00	1.31	41.50	2.12	20.50	2.12	43.50	0.70	24.20	1.06	–	–	10.80	0.21
20	12.20	0.35	49.50	0.70	10.50	0.71	11.30	0.91	8.50	2.12	31.00	1.41	11.50	0.70	24.70	0.42	41.50	2.12
21	9.50	0.70	17.00	1.31	38.20	0.35	23.30	0.91	10.90	1.34	19.80	0.28	5.00	1.41	–	–	34.00	1.41
DOX	4.50	1.50	4.00	1.10	23.00	3.00	6.50	1.40	7.00	1.60	5.60	1.20	4.58	1.20	5.50	1.60	6.00	1.80

Figure 6. Results of compounds 8 and 14 on MDA in cell lyses of all tested cells following 48 h.

Figure 7. Results of compounds 8 and 14 on NO in culture media of all tested cells following 48 h.

Figure 8. Results of compounds 8 and 14 on GSH in cell lyses of all tested cells following 48 h.

Figure 9. Results of compounds 8 and 14 on SOD in cell lyses of all tested cells following 48 h.

Figure 10. Results of compounds 8 and 14 on apoptosis in HEPG2 cells following 48 h. (A) Control, (B) Compound 8, and (C) Compound 14.

Figure 11. Results of compounds 8 and 14 on the cell cycle of HEPG2 following 48 h. (A) Control, (B) Compound 8, and (C) Compound 14.

Figure 12. The bar chart representation reveals the inhibitory levels of the assessed derivatives against (A): EFGR Wild and (B): EGFR T790.

Table 2. The inhibitory potentials of the investigated 8 and 14 targets towards EGFR (Wild) and EGFR (T790M).

Compound	EGFR IC50 (µM)
	Wild	T790M
8	0.131 ± 0.008	0.027 ± 0.002
14	0.203 ± 0.012	0.156 ± 0.009
Erlotinib	0.042 ± 0.003	0.009 ± 0.001

Figure 13. 2D binding interactions of co-crystallised 5Q4 undocked ligand at EGFR-kinase domain.

Table 4. 3D interactions and positioning of the chemically synthesised compounds (8 and 14) and the docked 5Q4 reference at EGFR-Kinase target receptor.

Comp.	3D interactions	3D positioning
8
14
5Q4

Hydrogen bonds are represented in red and H-pi ones are represented in black.

Table 3. Receptor-binding energies and interactions of compounds 8, 14, and 5Q4 into the 5Q4 pocket of EGFR-kinase.

Comp.	S^a	Amino acid bond	Distance (Å)
8	−5.8756	Gln-791 (A) H-donor	2.92
		Met-793 (A) H-acceptor	3.13
		Leu-718 (A) pi-H	4.26
14	−5.5083	Cys-775 (A) H-donor	3.52
		Met-793 (A) H-acceptor	3.06
		Gly-796 (A) pi-H	4.02
5Q4	−7.0125	Gln-791 (A) H-donor	3.15
		Cys-775 (A) H-donor	4.13
		Met-793 (A) H-acceptor	3.04
		Leu-718 (A) pi-H	3.95

^aS: Score of a ligand into the binding pocket of 5Q4 (Kcal/mol).

Table 5. The physicochemical and pharmacokinetic characteristics of the examined derivatives (7–21).

Comp.	Log Po/w (WLOGP)	Log S (ESOL)	Water solubility	GI absorption	BBB permeability	P-gp substrate	Metabolic enzymes inhibition	Drug likeness matching
7	3.55	−4.93	Moderately soluble	Low	No	No	CYP2C19 inhibitor	Lipinski
8	3.65	−3.99	Soluble	High	No	Yes	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
9	3.11	−3.52	Soluble	High	No	No	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
10	1.81	−3.32	Soluble	High	No	No	CYP2C19 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
11	5.10	−5.27	Moderately soluble	High	No	Yes	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
							CYP2C9 inhibitor
							CYP3A4 inhibitor
13	6.09	−5.42	Moderately soluble	Low	No	Yes	CYP1A2 inhibitor	Lipinski, Veber, Muegge
							CYP2C19 inhibitor
							CYP2C9 inhibitor
							CYP2D6 inhibitor
							CYP3A4 inhibitor
14	3.24	−3.10	Soluble	High	No	No	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
							CYP2C9 inhibitor
							CYP2D6 inhibitor
15	4.60	−4.40	Moderately soluble	High	No	Yes	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
							CYP2C9 inhibitor
16	3.90	−4.42	Moderately soluble	High	No	No	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
17	3.04	−3.75	Soluble	High	No	Yes	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
							CYP2C9 inhibitor
							CYP2D6 inhibitor
							CYP3A4 inhibitor
18	3.88	−4.11	Moderately soluble	High	No	No	CYP1A2 inhibitor	Lipinski, Ghose, Veber, Egan, Muegge
							CYP2C19 inhibitor
							CYP2C9 inhibitor
							CYP3A4 inhibitor
19	2.31	−3.04	Soluble	Low	No	Yes	CYP1A2 inhibitor	Lipinski, Ghose, Muegge
							CYP2C9 inhibitor
							CYP3A4 inhibitor
20	4.38	−5.05	Moderately soluble	Low	No	No	CYP2C19 inhibitor	Lipinski, Ghose
							CYP2C9 inhibitor
21	3.22	−5.19	Moderately soluble	Low	No	No	CYP2C19 inhibitor	Lipinski, Ghose
							CYP2C9 inhibitor

Figure 14. The suggested SAR for the studied pyrimidine and pyridine derivatives.