New target for inhibition of bacterial RNA polymerase: 'switch region'

Abstract

A new drug target - the 'switch region' - has been identified within bacterial RNA polymerase (RNAP), the enzyme that mediates bacterial RNA synthesis. The new target serves as the binding site for compounds that inhibit bacterial RNA synthesis and kill bacteria. Since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. Since the new target is different from targets of other antibacterial agents, compounds that bind to the new target are not cross-resistant with other antibacterial agents. Four antibiotics that function through the new target have been identified: myxopyronin, corallopyronin, ripostatin, and lipiarmycin. This review summarizes the switch region, switch-region inhibitors, and implications for antibacterial drug discovery.

Figure 1. RNAP clamp and RNAP switch region

(A) Conformational states of the RNAP clamp (two orthogonal views) [11,12]. Structure of RNAP showing open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Circle, switch region; dashed circle, binding site for rifamycins; violet sphere, active-center Mg²⁺. (B) Conformational states of the RNAP switch region (stereoview) [11,12]. Structure of RNAP switch 1 and RNAP switch 2 (β’ residues 1304–1329 and β’ residues 330–349; residues numbered as in E. coli RNAP) showing conformational states associated with open (red), partly closed (yellow), and fully closed (green) clamp conformations, as observed in crystal structures (PDB 1I3Q, PDB 1HQM, PDB 1I6H). Gray squares, points of connection of switch 1 and switch 2 to the RNAP main mass. Colored circles, points of connection of switch 1 and switch 2 to the RNAP clamp.

Figure 2. Structures of inhibitors that function through the RNAP switch-region

(A) Myx A (R = n-propyl) and Myx B (R = n-butyl). (B) Cor A. (C) Rip A. (C) Lpm A3.

Figure 3. Targets of inhibitors that function through the RNAP switch-region

(A) Target of Myx [11,12]. (B) Target of Cor [11,12]. (C) Target of Rip [11,12]. (D) Target of Lpm [; D.D., R.Y.E., E.S., S.D., and R.H.E., unpublished]. Each panel shows two orthogonal views of RNAP. Red, sites of substitutions conferring moderate- to high-level resistance (≥4-fold resistance) to the specified inhibitor; blue, sites of substitutions conferring resistance to rifamycins; violet sphere, active-center Mg²⁺. The Myx, Cor, and Rip targets overlap essentially in toto. The Lpm target is adjacent to, but does not overlap, or only minimally overlaps, the Myx, Cor, and Rip targets (compare bottom subpanels of D to bottom subpanels of A–C).

Figure 4. Crystal structure of the RNAP-Myx complex (PDB 3DXJ)

(A) Binding pocket for Myx [12]. Cyan, surface representation of the binding pocket and the adjacent hydrophobic pocket. Gray, ribbon representation of RNAP backbone. Green, Myx carbon atoms; red, Myx oxygen atoms. RNAP residues are numbered as in T thermophilus RNAP and, in parentheses, as in E. coli RNAP. (B) Contacts between RNAP and Myx (stereoview) [12]. Gray, RNAP backbone (ribbon representation) and RNAP sidechain carbon atoms (stick representation); green, Myx carbon atoms; red, oxygen atoms; blue, nitrogen atoms. “W,” ordered bound water molecule. Dashed lines, H-bonds. (C) Schematic summary of contacts between RNAP and Myx [12]. “W”, ordered bound water molecule. Red dashed lines, H-bonds. Blue arcs, van der Waals interactions.