Understanding Experimentally Compatible Bactericidal Activity of Dicationic Ionic Liquids: A Mechanistic Insight into the Effect of Functional Groups by MD Simulations

Dicationic ionic liquids (DCILs) show a promising innovative potential as antibacterial agents to help overcome the antibiotic-resistant bacteria crisis worldwide. Changing ionic head groups, side chain lengthening, functionalizing, and modifying the hydrophobic/hydrophilic character of the IL structure influence their interaction strength with the bacterial cell wall. Nevertheless, deep molecular-level insights are a prerequisite in fully realizing the antibacterial mechanism of DCILs with varied functionalities and structures. Here, we selected three DCILs based on the recently investigated bis-imidazolium dibromide family, DCIL-1, DCIL-3, and DCIL-5, with the functional groups 2-hydroxybutyl, 2-hydroxy-3-(methacryloyloxy)propyl, and 2-hydroxy-3-phenoxypropyl, respectively. Current all-atom molecular dynamics (MD) simulations and free-energy calculations consistency with our earlier experimental assays confirmed the order of (DCIL-5 > DCIL-1 > DCIL-3) for their bactericidal activity against Escherichia coli (E. coli). The dication insertion is the dominant driving force for the bacterial bilayer disruption and rupture. The MD results revealed that the antibacterial activity of bulky DCILs was due to the interplay between the electrostatic and hydrophobic interactions. It further disclosed the antibacterial mechanism consisting of the dication adsorption on the bacterial membrane lipids through electrostatic attraction, the flip motion of dications for finding suitable orientation in close vicinity to the lipid bilayer’s surface, key hydrogen-bond forming simultaneously with the lipid’s head groups to promote the penetration of the adjacent hydrophobic group to the lipid bilayer center. The penetration process could increase the average surface area per lipid, decrease the lipid tail ordering and the bilayer thickness, and improve the lipid lateral diffusion and bilayer fluidity, resulting in lipid bilayer rupture and bacterial membrane lysis. The strongest antibacterial activity was demonstrated by DCIL-5, which had a 2-hydroxyl-3-phenoxypropyl functional group and a high relative hydrophobicity and lipophilicity that allowed it to permeate the bacterial cell walls efficiently. This research sheds light on the microscopic interactions between DCILs having various functional groups and Gram-negative bacterial membranes, providing crucial insights for screening and the rational design of new cationic agents as efficient antibacterial materials.