Insights into bacterial interactions: Comparing fluorine-containing 1,2,4-triazoles to antibiotics using molecular docking and molecular dynamics approaches

Understanding the interactions between drugs and enzymes is crucial for designing effective therapeutics. This study employed a combination of molecular docking and molecular dynamics (MD) simulations to evaluate the binding affinity, stability, and dynamic behavior of two new compounds (compound <b>1</b> and compound <b>2</b>) compared to vancomycin and meropenem against <i>Staphylococcus aureus and Serratia marcescens</i> bacterial enzymes. Molecular docking studies provided insights into the binding interactions and affinities of these compounds, revealing that both compound <b>1</b> and compound <b>2</b> exhibit promising binding profiles. In particular, compound <b>1</b> demonstrated lower binding energies with key enzymes from <i>Staphylococcus aureus</i> compared to vancomycin, suggesting enhanced potential. MD simulations further elucidated the dynamic stability of these complexes. Results indicated that compound <b>1</b> maintains consistent binding modes with low RMSD and RMSF values, implying stable interactions. In contrast, vancomycin exhibited high RMSD and RMSF values in some enzyme complexes, reflecting potential instability. Compound <b>2</b> showed competitive stability and binding behavior compared to meropenem, with comparable RMSD and RMSF values across various enzyme targets. These findings highlight the potential of compound <b>1</b> and compound <b>2</b> as viable candidates for further development, offering insights into their stability and efficacy as new therapeutic agents.