Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase–Bisphosphonate Interactions: A Crystallographic and Computational Analysis

Abstract

Geranylgeranyl diphosphate synthase (GGPPS) is a central metalloenzyme in the mevalonate pathway, crucial for the prenylation of small GTPases. As small GTPases are pivotal for cellular survival, GGPPS was highlighted as a potential target for treating human diseases, including solid and hematologic malignancies and parasitic infections. Most available GGPPS inhibitors are bisphosphonates, but the clinically available compounds demonstrate poor pharmacokinetic properties. Although the design of novel bisphosphonates with improved physicochemical properties is highly desirable, the structure of wild-type human GGPPS (hGGPPS) bound to a bisphosphonate has not been resolved. Moreover, various metalbisphosphonate-binding stoichiometries were previously reported in structures of yeast GGPPS (yGGPPS), hampering computational drug design with metal-binding pharmacophores (MBP). In this study, we report the 2.2 Å crystal structure of hGGPPS in complex with ibandronate, clearly depicting the involvement of three Mg 21 ions in bisphosphonate-protein interactions. Using drug-binding assays and computational docking, we show that the assignment of three Mg 21 ions to the binding site of both hGGPPS and yGGPPS greatly improves the correlation between calculated binding energies and experimentally measured affinities. This work provides a structural basis for future rational design of additional MBP-harboring drugs targeting hGGPPS. SIGNIFICANCE STATEMENT Bisphosphonates are inhibitors of geranylgeranyl diphosphate synthase (GGPPS), a metalloenzyme crucial for cell survival. Bisphosphonate binding depends on coordination by Mg 21 ions, but various Mg 21-bisphosphonate-binding stoichiometries were previously reported. In this study, we show that three Mg 21 ions are vital for drug binding and provide a structural basis for future computational design of GGPPS inhibitors.

Capturing Magnesium Ions via Microfluidic Hydrogel Microspheres for Promoting Cancellous Bone Regeneration

“…Furthermore, the incorporation of bioactive ions present in the natural bone matrix, such as copper ions, strontium ions, and magnesium ions, into bone substitutes stimulates vascularized bone regeneration. , Therefore, in our research, Mg 2+ is used as a key factor to achieve the enhancement of blood vessel formation and osteogenesis through the capture of composite microspheres. BP is an ideal tool for capturing Mg 2+ , because the BP molecule contains two adjacent phosphate groups, so it exhibits excellent efficiency when coordinating with various metal ions, especially Mg 2+ . − Therefore, energy dispersive X-ray spectroscopy (EDS) showed that GelMA-BP microspheres had uniform P element distribution and GelMA-BP-Mg microspheres had uniform magnesium element distribution (Figure B). In addition, for each group of composite microsphere samples, EDS revealed the presence of corresponding P elements and Mg elements in GelMA-BP and GelMA-BP-Mg observed by SEM (Figure C).…”

Geranylgeranyl diphosphate synthase: Role in human health, disease and potential therapeutic target

“… 17 They found each of the six monomers to associate with two Mg 2+ ions and one GGPP molecule. However, more recent studies suggested that three Mg 2+ are required for substrate binding 18 . Such discrepancies are most likely due to the low resolution at which the enzyme was characterised 18,19 .…”

“…However, more recent studies suggested that three Mg 2+ are required for substrate binding. 18 Such discrepancies are most likely due to the low resolution at which the enzyme was characterised. 18 , 19 Miyagi et al.…”

“…However, more recent studies suggested that three Mg 2+ are required for substrate binding. 18 Such discrepancies are most likely due to the low resolution at which the enzyme was characterised. 18,19 Miyagi et al also reported GGDPS to form an octamer in its active form, proving the need for more information on the quaternary structure of this enzyme.…”

“…18 Such discrepancies are most likely due to the low resolution at which the enzyme was characterised. 18,19 Miyagi et al also reported GGDPS to form an octamer in its active form, proving the need for more information on the quaternary structure of this enzyme. 20 Interestingly, sequence analysis found that this complex quaternary structure is specific to mammalian and insect GGDPS.…”