All-atoms MD simulations study of newly designed ciprofloxacin derivatives as potential bacterial DHPS and DNA gyrase inhibitors

Abstract

The widespread use of antibiotics, particularly ciprofloxacin, has accelerated the emergence of antibiotic-resistant bacteria, posing a major public health challenge. Limited investment and declining pharmaceutical interest have slowed the discovery of new antibiotics, contributing to the increasing prevalence of multidrug-resistant (MDR) infections, especially those caused by ESKAPE pathogens. Uropathogenic Escherichia coli (UPEC), a leading cause of urinary tract infections (UTIs), develops multidrug resistance through mechanisms including drug target modification and reduced antibiotic susceptibility. In the present study, a series of ciprofloxacin-sulfonamide hybrid molecules (CIS1-CIS15) was designed, in which each pharmacophore retains its established mechanism of action. Ciprofloxacin inhibits DNA gyrase and topoisomerase IV, whereas sulfonamides inhibit dihydropteroate synthase (DHPS) by competing with para-aminobenzoic acid (PABA) in the bacterial folate biosynthetic pathway. Accordingly, the designed hybrids were computationally evaluated against both enzymatic targets to investigate their potential dual-target antibacterial activity. Molecular docking and molecular dynamics (MD) simulations were performed to assess the binding affinity and stability of the ciprofloxacin-bearing sulfonamide derivatives (CIS1-CIS15) against DNA gyrase and Staphylococcus aureus DHPS. Principal component analysis (PCA) and free-energy landscape (FEL) analysis were used to characterize the conformational flexibility and low-energy states of the protein–ligand complexes, while MD simulations validated the stability of the highest-scoring docked complexes. Among the designed derivatives, CIS4 (ciprofloxacin-sulfamethoxazole), CIS5 (ciprofloxacin–sulfaguanidine), and CIS12 (ciprofloxacin-sulfamerazine) exhibited the strongest binding affinity toward both targets while maintaining conformational stability throughout the simulations. Structural analysis of the pre- and post-MD trajectories identified Arg52, Lys39, Arg88, Lys94, Lys120, Glu201, and Lys203 as key residues involved in ligand recognition. Overall, CIS4, CIS5, and CIS12 emerged as the most promising dual-target inhibitor of bacterial DHPS and DNA gyrase. These findings provide valuable structural insights for the rational design of novel fluoroquinolone-based antibacterial agents and demonstrate the utility of computational approaches in identifying potential therapeutics against drug-resistant bacterial pathogens.