Structural Basis for the Exceptional in vivo Efficacy of Bisphosphonate Drugs

Abstract

To understand the structural basis for bisphosphonate therapy of bone diseases, we solved the crystal structures of human farnesyl 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 of the enzyme catalytic cycle, each associated with a distinct conformational state, and details about the interactions with N-BPs, these structures provide a novel understanding of the mechanism of FPPS 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 of the FPPS-N-BP complex through IPP binding is supported by differential scanning calorimetry analyses of a set of representative N-BPs. Among other factors such as high binding affinity for bone mineral, this particular mode of FPPS 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.

Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity

“…3B) binds to the FPP diphosphate site and, unlike the situation found with human and S. cerevisae GGPPS, is a potent inhibitor (IC 50 510 nM, versus approximately 100 μM) of Plasmodium GGPPS (Table S1) due to the fact that the zoledronate bisphosphonate group binds to 3 Mg 2þ in the PvGGPPS protein, just as in human FPPS (37,38). With the zoledronate analog BPH-703 (cyan in Fig.…”

Synthesis and preliminary pharmacological characterisation of a new class of nitrogen-containing bisphosphonates (N-BPs)

“…This radioactive fraction diminished by 50% in assays with 1 M ibandronate, while a In the attempt to rationalise the activity profile of the most active compounds 20, 20a compared to ibandronate, a molecular modelling investigation was carried out. Taking advantage of the existence of crystal structures of human FPPS, 24 SQS 25 and GGPPS, 26 flexible docking of the aforementioned bisphosphonates was accomplished in the active site of these three enzymes. In the case of FPPS, since a co-crystal with ibandronate has been obtained, 24 we had the opportunity to validate our approach, verifying that AutoDock 4.0 is able to reproduce the crystal pose of the reference inhibitor within the limits of experimental error (RMS deviation on heavy atoms 0.52 Å).…”

“…Taking advantage of the existence of crystal structures of human FPPS, 24 SQS 25 and GGPPS, 26 flexible docking of the aforementioned bisphosphonates was accomplished in the active site of these three enzymes. In the case of FPPS, since a co-crystal with ibandronate has been obtained, 24 we had the opportunity to validate our approach, verifying that AutoDock 4.0 is able to reproduce the crystal pose of the reference inhibitor within the limits of experimental error (RMS deviation on heavy atoms 0.52 Å). Additionally, the pose that reproduces the experimental binding mode also belongs to the most populated cluster, characterized by the best docking score (average G binding = -11.34 kcal mol -1 ).…”

“…In particular, each of the phosphonate moieties of ibandronate gives rise to electrostatic interactions with the metal ions present in the active site, in addition to chargeenhanced hydrogen bonds with Arg112, Lys200 and Lys257. 24 Instead, in the case of compounds 20 and 20a the bisphosphonate head is rotated, which results in only one of the phosphonate moieties coming into close contact with metal ions and Lys200, while Arg112 and Lys257 are not within hydrogenbonding distance. The loss of these interactions sums up to the lack of a protonated nitrogen atom capable of hydrogen bonding with the side chain of Thr201.…”

“…The loss of these interactions sums up to the lack of a protonated nitrogen atom capable of hydrogen bonding with the side chain of Thr201. 24 Finally, the phenylsulfonyl substituent on the oxadiazole ring protrudes out of the cavity, as evidenced by the representation of the solvent-excluded surface of the cavity in Figure 4a; the exposure to water of such a hydrophobic moiety further penalizes the binding of these inhibitors. Overall, this picture yields a reasonable interpretation of the lack of affinity for FPPS displayed by compounds 20, 20a.…”