Virtual fragment screening for novel inhibitors of 6-phosphogluconate dehydrogenase

Abstract

The enzyme 6-phosphogluconate dehydrogenase is a potential drug target for the parasitic protozoan Trypanosoma brucei, the causative organism of human African trypanosomiasis. This enzyme has a polar active site to accommodate the phosphate, hydroxyl and carboxylate groups of the substrate, 6-phosphogluconate. A virtual fragment screen was undertaken of the enzyme to discover starting points for the development of inhibitors which are likely to have appropriate physicochemical properties for an orally bioavailable compound. A virtual screening library was developed, consisting of compounds with functional groups that could mimic the phosphate group of the substrate, but which have a higher pKa. Following docking, hits were clustered and appropriate compounds purchased and assayed against the enzyme. Three fragments were identified that had IC50 values in the low micromolar range and good ligand efficiencies. Based on these initial hits, analogues were procured and further active compounds were identified. Some of the fragments identified represent potential starting points for a medicinal chemistry programme to develop potent drug-like inhibitors of the enzyme.

Figure 1

Catalytic mechanism of 6PGDH enzyme.

Figure 2

T. brucei 6PGDH inhibitors reported previously.

Figure 3

(A) Ligand PEX in the active site of L. lactis 6PGDH. Putative hydrogen bonds are indicated by dashed lines. (B) Superposition of the ligand PEX (green carbon atoms) with the binding mode of the same ligand predicted by the docking calculations (grey carbon atoms). The RMSD between both posed is 1.16 Å.

Figure 4

Hits identified in the first screening with percentage of inhibition higher than 80% at 200 μM.

Figure 5

Docking poses for compound 1 (A), compound 2 (B) and compound 3 (C) in the active site of L. lactis.

Figure 6

IC₅₀ curves for the compounds 1–3.