Chlorhexidine (CHX), a popular antibacterial drug, is widely used for oral health. Emerging
pieces of evidence suggest that commercially available chlorhexidine mouthwash formulations are
effective in suppressing the spread of SARS-CoV-2, possibly through destabilization of the viral lipid
envelope. CHX is known for its membrane-active properties; however, the molecular mechanism
revealing how it damages the viral lipid envelope is yet to be understood. Here we used extensive
conventional and umbrella sampling simulations to quantify the effects of CHX on model membranes
mimicking the composition of the SARS-CoV-2 outer lipid membrane as well as the host plasma
membrane. Our results show that the lipid composition and physical properties of the membrane
play an important role in binding and insertion, with CHX binding favorably to the viral membrane
over the plasma membrane. Among the simulated lipids, CHX preferentially binds to anionic lipids,
PS and PI, which are more concentrated in the viral membrane. The deeper and stable binding of
CHX to the viral membrane results in more pronounced swelling of the membrane laterally with a
thinning of the bilayer. The overall free energies of pore formation are strongly reduced for the viral
membrane compared to the plasma membrane; however, CHX has a larger concentration-dependent
effect on free energies of pore formation in the plasma membrane than the viral membrane. The
results indicate that CHX is less toxic to the human plasma membrane at low concentrations. Our
simulations reveal that CHX facilitates pore formation by the combination of thinning the membrane
and accumulation at the water defect. This study provides insights into the mechanism underlying
the anti-SARS-CoV-2 potency of CHX, supporting its potential for application as an effective and safe
oral rinse agent for preventing viral transmission