Figure 1. HTVS identifies berberine analogs as potential probes of MexY.

(a) Homology model of the MexXY-OprM RND system comprising outer membrane (OM) protein OprM (blue), periplasmic (P) adaptor protein MexX (gold), and inner membrane (IM) transporter MexY (red). (b) Schematic of the MexY homotrimer in its three conformational states: access (dark grey), binding (red), and extrusion (light grey). The two putative main substrate entry channels (cleft and vestibule), primary substrate binding region (DBP and PBP), and path to MexX are indicated. A zoomed in view of the binding pocket structure (boxed) also highlights the MexX docking domain, DC (light green) and DN (pink), the porter domain, PN1 (blue), PN2 (teal), PC1 (purple), PC2 (orange), and the switch loop (lime green). (c) Checkerboard synergy assays in P. aeruginosa PAO1 with berberine and selected analogs from HTVS (Generation 1). Increased synergy is observed for Ber-Prop [3] and Ber-C6 [4] with Kan (top, orange) and Gen (bottom, teal) compared to berberine. Data are shown as the normalized mean of the optical density (OD₆₀₀) of two biological replicates (0 is no growth, and 1 is maximum growth). The lowest Fractional Inhibitory Concentration (FIC) score for each compound-antibiotic pair is given in the upper right corner.