Fragment-based discovery of 6-azaindazoles as inhibitors of bacterial DNA ligase

Abstract

Herein we describe the application of fragment-based drug design to bacterial DNA ligase. X-ray crystallography was used to guide structure-based optimization of a fragment-screening hit to give novel, nanomolar, AMP-competitive inhibitors. The lead compound 13 showed antibacterial activity across a range of pathogens. Data to demonstrate mode of action was provided using a strain of S. aureus, engineered to overexpress DNA ligase.

Keywords: Bacterial DNA ligase; S. aureus; fragment-based drug design; structure-based optimization.

Figure 1

Inhibitors of DNA ligase described in the literature.^,

Figure 2

Fragment optimization and growth of 3 toward 13. Data presented as K_d (ITC) or IC₅₀ (biochemical assay) using DNA ligase from S. aureus.

Figure 3

(a) X-ray crystal structure of fragment 3 bound to LigA (S. aureus) showing key hydrogen bonds (purple dotted lines), a key water molecule (red sphere), and partially resected Connoly surface. (gray). Growth vectors toward the hydrophobic pocket, ribose binding region, and the protein backbone are shown by the red arrows. (b) X-ray crystal structure of 12 bound to LigA (S. aureus).

Figure 4

Illustration showing the alternative conformations of 12 (ethanolamine side chain removed for clarity). Electrostatic and steric clashes are shown in red, and positive interactions are shown in black.