Structural Basis for the Exceptional in vivo Efficacy of Bisphosphonate Drugs

To understand the structural basis for bisphosphonate therapy of bone diseases, we solved the crystal structures ofhuman f pyrophosphate synthase (FPPS) in its unliganded state, in complex with the nitrogen-containing bisphosphonate (N-BP) drugs zoledronate, pamidronate, alendronate, and ibandronate, and in the ternary complex with zoledronate and the substrate isopentenyl pyrophosphate (IPP). By revealing three structural snapshots ofthe enzyme catalytic cycle, each associated with a distinct conformational state, and details about the interactions with NBPs, these structures provide a novel understanding ofthe mechanism ofFPPS catalysis and inhibition. In particular, the accumulating substrate, IPP, was found to bind to and stabilize the FPPS–N-BP complexes rather than to compete with and displace the N-BP inhibitor. Stabilization ofthe FPPS–N-BP complex through IPP binding is supported by differential scanning calorimetry analyses ofa set ofrepresentative N-BPs. Among other factors such as high binding affinity for bone mineral, this particular mode ofFPPS inhibition contributes to the exceptional in vivo efficacy of N-BP drugs. Moreover, our data form the basis for structure-guided design of optimized N-BPs with improved pharmacological properties.