Fragments vs bacterial DNA ligase: triumph of structure-based design

Fragment approaches have been used successfully against several anti-bacterial targets (see for example here, here, and here). In a recent issue of ACS Med. Chem. Lett., a team of researchers from Astex and GlaxoSmithKline report another potential weapon in the ongoing war against bugs.

The researchers were interested in bacterial DNA ligase (LigA), which is essential for DNA replication, is highly conserved among numerous types of bacteria, and is quite different from its human counterpart. They started by screening ~1500 fragments against S. aureus LigA using a combination of X-ray crystallography (soaking), ligand-observed NMR (WaterLOGSY), and thermal shift assays. Hits that made it through this gauntlet were then evaluated by isothermal titration calorimetry (ITC) and prioritized in part by ligand efficiency. One of the best molecules was compound 3.

The chlorine atom of compound 3 bound in a hydrophobic pocket of the enzyme. Wary of the potential reactivity of this motif, the researchers replaced it with a trifluoromethyl group; they also removed a nitrogen from the pyrazine ring to provide a vector for fragment growing. The resulting compound 10 had slightly improved potency.

Examining the structure of the initial fragment also revealed a water-mediated hydrogen bond, and by enlarging the triazole to a 6-azaindole 6-azaindazole (compound 12) the researchers were able to make this hydrogen bond directly while also more effectively filling the pocket, providing a satisfying 70-fold boost in affinity. However, close inspection of the crystal structure and computational modeling suggested that this molecule was binding in an energetically unfavorable conformation. Simply adding a nitrogen to the pyridine ring alleviated this problem, providing another 15-fold boost in potency (compound 13). This molecule also showed antibacterial activity against a number of Gram-positive pathogens.

This is a brief but elegant paper that demonstrates the power of crystallography and modeling to drive a fragment-derived medicinal chemistry effort. It will be fun to watch this story progress.