Figure 5. Molecular dynamics simulations of berberine and di-berberine conjugates reveal important characteristics for effective chemical probes of efflux function by MexY.

(a) 50 ns molecular dynamics simulation (Rep1) of berberine (top left) and di-berberine conjugates, Ber-C3 [5] (top right), and Ber-C12 [9] (bottom left), and Ber-pAr [10] (bottom right) in the MexY^PAO1 DBP and PBP. Conformations at the start (0 ns) and every 10 ns are shown as semi-transparent sticks (0 and 30 ns frames are indicated) and the final conformation (at 50 ns) is shown as solid sticks (orange). Parameters derived from MM/GBSA calculations: (b) binding affinity, (c) π-packing, and (d) ligand strain. Data shown are the individual calculated values for six frames (0 ns and one per 10 ns segment between 0–50 ns) with the average shown as a bar plot. Ber-C3 [5] was found to be an effective and specific efflux pump inhibitor for the MexXY-OprM efflux system compared to berberine, Ber-pAr [9] and Ber-C12 [10Statistical analysis was performed using one-way ANOVA on the mean for each ligand and a post-hoc Tukey test was used for pairwise comparison. Statistically significant results are shown (* p≤≤0.05, ** p≤0.01, *** p≤0.001, and **** p≤0.0001).].