Rational design of potent inhibitors of a metallohydrolase using a fragment-based approach.

Metallohydrolases form a large group of enzymes that play crucial roles in a broad range of biological functions. Among them purple acid phosphatases (PAPs) gained attention due to their crucial role in the acquisition of phosphate by plants and also as a promising target for novel treatments of bone-related disorders. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the Maybridge TM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.