One-pot synthesis of novel poly-substituted 3-cyanopyridines: Molecular docking, antimicrobial, cytotoxicity, and DFT/TD-DFT studies

Abstract

Novel pyridine-3-carbonitrile derivatives, denoted as (4a-j), were synthesized using a convergent synthetic approach that involved a one-pot four-component reaction. This was achieved by utilizing a combination of various aromatic aldehydes, acetophenone derivatives, malononitrile, and four different sodium alkoxide solutions. The synthesized compounds were characterized using various spectroscopic techniques such as IR, 1HNMR , 13CNMR , and elemental analysis. Molecular docking simulations were employed to investigate the binding affinity of compounds (4a-j) towards two proteins, DHFR and HT-hTS. The results revealed that 4-(4-chlorophenyl)-2-ethoxy-6-phenyl-pyridine-3-carbonitrile (4a) compound exhibited the highest binding affinity score (ΔG = -8.06 Kcal/mol) upon docking into the active site of DHFR, while 2-(4-nitrophenyl)-6-(4-chlorophenyl)-4-ethoxy-pyridine-3-carbonitrile (4d) compound displayed the strongest binding affinity score (ΔG = -4.17 Kcal/mol) when docked to the active site of HT-hTS. These results were supported by the cytotoxic activity of selected compounds (4a, 4b, 4e, and 4 h) against human cancer cell lines (MCF7, HT29, and A2780) as well as normal human fetal lung fibroblast (MRC5) using MTT assay. The cytotoxicity analyses revealed that compound (4a) displayed cytotoxic activity against all cancer cell lines, particularly human colorectal carcinoma (HT29) with an IC50 value of 2.243±0.217 μM, which is lower than that of the reference drug (Doxorubicin) with an IC50 value of 3.964±0.360 μM. Furthermore, compound (4a) exhibited a lower cytotoxic effect on normal human fetal lung fibroblast (MRC5) with an IC50 value of 2.222±0.137 μM, as compared to the IC50 value of the reference drug (Doxorubicin) which was 2.476±0.033 μM. The antimicrobial activity of selected compounds such as (4a, 4c, and 4f) was also evaluated against a panel of microorganisms, including two gram-positive strains (Staphylococcus aureus and Enterococcus faecalis) and two gram-negative strains (Escherichia coli and Pseudomonas aeruginosa). The zone of inhibition and minimum inhibition concentration (MIC) demonstrated the potency of these compounds. Specifically, compounds 4-(4-chlorophenyl)-2-ethoxy-6-phenyl-pyridine-3-carbonitrile (4a) and 4-(4-methoxyphenyl)-2‑methoxy-6-(4-nitrophenyl)-pyridine-3-carbonitrile (4f) exhibited MIC of 0.013 µM against E. coli strains, which is comparable to that of the reference drug amoxicillin (MIC=0.01 µM). Finally, Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT) studies were performed on compounds (4a-j) to obtain a more comprehensive understanding of the structure-activity relationship and solvatochromic behavior of these molecules. Overall, the results suggest that compound (4a) could potentially serve as a promising cytotoxic and antibacterial agent with a better safety profile and reduced side effects on normal cells.