Computational Insights into Binding of Bisphosphates to Farnesyl Pyrophosphate Synthase
Abstract:Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis and Paget's disease. Non-nitrogen containing BPs (non-N-BPs), namely etidronate, clodronate, tiludronate, as well as nitrogen-containing BPs (N-BPs), namely pamidronate, alendronate, ibandronate, risedronate, zoledronate and minodronate have been launched on the market to date. N-BPs act by inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS), and several crystal structures of complexes between FPPS and N-BPs have been revealed. Understanding the physical basis of the binding between protein and small molecules is an important goal in both medicinal chemistry and structural biology. In this review, we analyze in detail the energetic basis of molecular recognition between FPPS and N-BPs. First, we summarize the interactions between ligands and proteins observed in N-BPs-FPPS complexes in the Protein Data Bank (PDB). Second, we present an interaction energy analysis on the basis of full quantum mechanical calculation of FPPS and N-BP complexes using the fragment molecular orbital (FMO) method. The FMO result revealed that not only hydrogen bond and electrostatic interaction but also CH-O and -interaction with FPPS are important for N-BP's potency. Third, we describe a binding site analysis of FPPS on the basis of the inhomogeneous solvation theory which, by clustering the results from an explicit solvent molecular dynamics simulation (MD), is capable of describing the entropic and enthalpic contributions to the free energies of individual hydration sites. Finally, we also discuss the structure-activity relationship (SAR) of the series of minodronate derivatives.
Keywords: Bisphosphonate; Bisphosphonates (BPs); Charge transfer plus higher-order mixed terms; Farnesyl Pyrophosphate Synthase; Geranyl Pyrophosphate; Isopentenyl Pyrophosphate; Isothermal titration calorimetry; Minodronic acid; Nitrogen-containing BPs; Paget's disease; Protein Data Bank; adenosine triphosphate; alendronate; antiresoptive activity; bone resorption; dispersion; drug design; electrostatic; enthalpy-driven; farnesyl pyrophosphate synthase; fragment molecular; ibandronate; ibandronate model; imidazopyrizine; isopentenyl pyrophosphate; isoprenyl synthases; isothermal titration calorimetry; mevalonate pathway; minodronate; osteoclast; osteoporosis; pamidronate; protein-ligand binding; quantum mechanics; risedronate; tiludronate; zoledronate
Document Type: Research Article
Publication date: 2011-01-01
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