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 1 and compound 2) compared to vancomycin and meropenem against Staphylococcus aureus and Serratia marcescens bacterial enzymes. Molecular docking studies provided insights into the binding interactions and affinities of these compounds, revealing that both compound 1 and compound 2 exhibit promising binding profiles. In particular, compound 1 demonstrated lower binding energies with key enzymes from Staphylococcus aureus compared to vancomycin, suggesting enhanced potential. MD simulations further elucidated the dynamic stability of these complexes. Results indicated that compound 1 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 2 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 1 and compound 2 as viable candidates for further development, offering insights into their stability and efficacy as new therapeutic agents.