Influence of pyridyl nitrogen’s position and hydrogen bonding interactions on antibacterial activities investigated by in vitro and in silico

Pyridine derivatives are multifunctional materials with various biological activities viz., antibacterial, antiviral, anticancer, antihistamine, etc. and are also the building blocks in supramolecular chemistry. Schiff’s base compounds are known for their diversified applications / functionalities. A Schiff base with a pyridine moiety in its molecular structure is anticipated with potential biological activity. In order to study the effect of position of a pyridyl nitrogen on the antibacterial activity, two Schiff’s bases containing pyridine moiety viz., 3-chloro-4-fluoro-N-((pyridin-3-yl)methylene)benzenamine (3Py) and 3-chloro-4-fluoro-N-((pyridin-4-yl)methylene)benzenamine (4Py), were prepared by condensing 4-fluoro-3-chloro-aniline with 3-pyridinecarboxaldehyde and 4-pyridinecarboxaldehyde. Pyridine derivatives form a hetero synthon type intermolecular hydrogen bonding interactions with substituted benzoic acids. The lower homologues of 4-n-alkyloxybenzoic acids (nOBAs, ethyl, propyl and butyl homologues) were treated with the pyridine derivatives, 3Py and 4Py and were observed to be involved in intermolecular hydrogen bonding (HB) interactions. The pyridine derivatives (3Py and 4Py), benzoic acid derivatives and their 1:1 molar ratio complex were subjected to antibacterial activities through in vitro and in silico techniques. The antibacterial activities of the pristine compounds and their HB complexes against Gram-positive, Staphylococcus aureus and Gram-negative, Escherichia coli bacteria were studied by paper disc diffusion method. The antibacterial activity of the compounds is evaluated for their interactions with the key enzymes viz., E. coli MurB and S. aureus GyraseB by in silico technique. The pyridyl nitrogen at 4th position of the Schiff base (4Py) showed effective inhibition towards the S. aureus whereas the pyridyl nitrogen at 3rd position (3Py) of the Schiff base showed effective inhibition towards the E. coli. The increase in alkyl chain length of carboxylic acids was found to decrease the antimicrobial activity in the pristine homologues. The HB interactions between 3Py and nOBA showed different antibacterial activities compared to that between 4Py and nOBA against E. coli and S. aureus. The experimental results were supported by molecular docking, molecular dynamics simulation and ADME/T analysis. The findings are consistent with experimental data, demonstrating that Schiff base 4Py exhibits greater inhibitory efficacy against S.aureus, while 3Py shows superior activity agains E. coli, compared to their respective HB complexes.