Human isoprenoid synthase enzymes as therapeutic targets

Abstract

In the human body, the complex biochemical network known as the mevalonate pathway is responsible for the biosynthesis of all isoprenoids, which consists of a vast array of metabolites that are vital for proper cellular functions. Two key isoprenoids, farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) are responsible for the post-translational prenylation of small GTP-binding proteins, and serve as the biosynthetic precursors to numerous other biomolecules. The down-stream metabolite of FPP and GGPP is squalene, the precursor to steroids, bile acids, lipoproteins, and vitamin D. In the past, interest in prenyl synthase inhibitors focused mainly on the role of the FPP in lytic bone diseases. More recently pre-clinical and clinical studies have strongly implicated high levels of protein prenylation in a plethora of human diseases, including non-skeletal cancers, the progression of neurodegenerative diseases and cardiovascular diseases. In this review, we focus mainly on the potential therapeutic value of down-regulating the biosynthesis of FPP, GGPP, and squalene. We summarize the most recent drug discovery efforts and the structural data available that support the current on-going studies.

Keywords: farnesyl pyrophosphate; geranylgeranyl pyrophosphate; isoprenoids; mevalonate pathway; squalene.

Figure 1

Schematic representation of the mevalonate pathway, indicating the major biochemical effects of isoprenoids. Classes of current drugs that modulate the function of key enzymes include Statins and Bisphosphonates (indicated ). FPPS, GGPS, and SQS enzymes are highlighted in green color boxes; other key enzymes are highlighted in gray color boxes.

Figure 2

Structures and sequence of steps involved in the biosynthesis of key isoprenoids.

Figure 3

Overall structures of human prenyl synthase enzymes. (A) Farnesyl pyrophosphate synthase (PDB ID: 2F7M); (B) geranylgeranyl pyrophosphate synthase (PDB ID: 2Q80), and (C) squalene synthase (PDB ID: 3WEG). The enzymes are shown in a blue-to-red rainbow color scheme. For hFPPS and hGGPPS, one monomeric subunit of the enzyme oligomer is represented in color. The conserved aspartic-acid rich motifs are shown in a stick representation and marked by arrows. The small domains composed of α₁ − α₃ in hFPPS and hGGPPS are indicated by elliptical circles; in this view, the α₁ in hFPPS is hidden behind the top portion of α_H.

Figure 4

Structure of human farnesyl pyrophosphate synthase. (A) Binding of zoledronate (1a) at the allylic site (PDB ID: 2ZW5). Mg²⁺ ions and water oxygen atoms are shown as yellow and red spheres, respectively. Yellow dashes indicate molecular interactions. (B) Binding of compound 8a (PDB ID: 4DEM). The hydrophobic channel accommodating the side chain of the inhibitor is rendered in a semi-transparent surface representation. (C) Binding of IPP at the homoallylic site (PDB ID: 4H5E). (D) Conformational changes responsible for structuring the C-terminal tail. (E) Binding of compound 13 at the allosteric site (PDB ID: 3N6K).

Figure 5

Structure of geranylgeranyl pyrophosphate synthase. (A) The inter-dimer interface in hGGPPS (PDB ID: 2Q80). (B) Binding of a bisphosphonate with a long alkyl side chain to yeast GGPPS (PDB ID: 2Z4X); the trinuclear metal cluster is similar to that in Figure 4A. (C) The product chain elongation channel in hGGPPS. (D) Binding of the substrate FPP in yeast GGPPS (PDB ID: 2E90); conformational changes of the key residues (as compared to the same residues in C) are evident; also Ala59 in hGGPPS is replaced with a serine in yeast GGPPS. (E) Binding of GGPP at the product inhibitory site in hGGPPS.

Figure 6

Structure of human squalene synthase. (A,B) Binding of the substrate mimic farnesyl thiopyrophosphate to hSQS (PDB ID: 3WEG). The Arg52 side chain is omitted for clear view of the two pyrophosphate groups in (A). The large hydrophobic cavity that accommodates the substrate tails is represented in (B). (C) Binding of the reaction intermediate PSPP shown in the same orientation as in (A) (PDB ID: 3WEH). For clarity of the view, residues (redundant with those in A) are not labeled. (D) Binding of a bisphosphonate inhibitor, compound 27 (PDB ID: 3LEE). (E) Binding of a benzoxazepine inhibitor, compound 49 (PDB ID: 3V66). (F) Binding of zaragozic acid A (38) (PDB ID: 3VJC).