The ineffectiveness of antibiotics against bacteria can be caused by multidrug resistance (MDR) or by an outer membrane, which restricts the penetration of amphipathic compounds into Gram-negative bacteria. Remarkable activities of plant antimicrobials in the presence of MDR modulators have been observed against a series of MDR and Gram-negative bacteria (Tegos et al., Antimicrob Agents Chemother 46:3133, 2002). Assuming that modulators of MDR might form complexes with substrates of efflux pumps Zloh et al., Biogr Med Chem Lett 14:881, 2004), we have evaluated interaction energies between antimicrobials and MDR modulators reported in Tegos et al. (Antimicrob Agents Chemother 46:3133, 2002). In this paper, we can confirm that modulation activity against the efflux pump NorA in Staphylococcus aureus correlates with the interaction energies between MDR modulator INF271 and antibacterials. Additionally, the change of log P of complexes might be responsible for overcoming the membrane impermeability in Gram-negative bacteria and increasing the antibacterial activity in the presence of the modulator MC207110. This suggests that interactions between small molecules may play an important role in overcoming biological barriers in bacteria.