Rationale design, synthesis and antimicrobial activity of benzimidazole-pyridinecarbonitrile conjugates: Insights into ROS-induced oxidative damage and molecular dynamics simulations

Abstract

A new series of Benzimidazole pyridinecarbonitrile scaffolds 4a-r have been designed and synthesized through a regioselective Michael addition interaction between 2-acetyl N-propyne-benzimidazole (1) and ylidenemalononitrile (2), facilitated by a freshly prepared sodium methoxide solution. All synthesized derivatives were assessed for their antimicrobial potential on S. aureus (Gram-positive), P. aeruginosa (Gram-negative), as well as C. albicans (unicellular fungal). Derivatives 4a, 4c, 4f, 4l, 4m and 4q showed promising antimicrobial properties against all the tested MDR pathogens. In particular, compounds 4c, 4f, 4l, and 4m demonstrated brilliant inhibitory activity on C. albicans with MIC = 10 μg/mL each, a 4-fold increase compared to Amphotericin B (MIC = 40 μg/mL). While compound 4a presented MIC = 10 μg/mL compared with ciprofloxacin (MIC = 20 μg/mL) against MRSA, the MIC recorded by 4c and 4f against P. aeruginosa was 20 μg/mL, which equals that of ciprofloxacin. Bacterial lipid peroxidation (LPO) and antibiofilm activity and evaluation of reactive oxygen species (ROS) induced by the most potent derivatives were evaluated, revealing that derivatives 4f and 4m demonstrated the best behavior among the tested compounds. Furthermore, molecular docking and molecular dynamics (MD) simulations validated the stability of compound 4f within the catalytic binding pocket of the DNA gyrase receptor. The molecules were geometrically optimized using DFT with the B3LYP 6–21 basis set, and their electronic properties were analyzed. The study also encompassed ADME predictions and drug-likeness assessments for the new compounds.