Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

Abstract

Human farnesyl pyrophosphate synthase (hFPPS) is the gate-keeper of mammalian isoprenoids and the key target of bisphosphonate drugs. Bisphosphonates suffer from poor "drug-like" properties and are mainly effective in treating skeletal diseases. Recent investigations have implicated hFPPS in various nonskeletal diseases, including Alzheimer's disease (AD). Analysis of single nucleotide polymorphisms in the hFPPS gene and mRNA levels in autopsy-confirmed AD subjects was undertaken, and a genetic link between hFPPS and phosphorylated tau (P-Tau) levels in the human brain was identified. Elevated P-Tau levels are strongly implicated in AD progression. The development of nonbisphosphonate inhibitors can provide molecular tools for validating hFPPS as a therapeutic target for tauopathy-associated neurodegeneration. A multistage screening protocol led to the identification of a new monophosphonate chemotype that bind in an allosteric pocket of hFPPS. Optimization of these compounds could lead to human therapeutics that block tau metabolism and arrest the progression of neurodegeneration.

Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product

“…The one-site-binding pattern observed here is a consequence of the enzyme closure, which renders the allosteric pocket inaccessible to the substrates. Analogous results demonstrating the biased binding (that is, binding exclusively to the allylic substrate site in the presence of Mg 2+ ) have been confirmed crystallographically with allosteric BPs912. In contrast to the binding of DMAPP and GPP, FPP binding was not affected by Mg 2+ (Table 2).…”

“…Interestingly, the binding mode of FPP differs from those of the allosteric BPs reported earlier910. Their pyrophosphate/BP groups interact with the enzyme differently from one another and do not overlap when superimposed (Supplementary Fig.…”

“…2b). Direct interaction between anionic molecules at this site has been observed multiple times91011 and suggests that their charges are neutralized by surrounding protein residues. The tail of FPP extends deep into the allosteric pocket, making tight van der Waals contacts with the protein surface (Fig.…”

“…However, neither cholesterol and bile acids (downstream metabolites) nor nucleotides and their analogues inhibited the enzyme8. More recently, our own efforts identified a different series of non-BP inhibitors targeting the same pocket910. Here we discovered that certain BPs—all of them with bulky lipophilic side chains—could bind to this pocket.…”

Human isoprenoid synthase enzymes as therapeutic targets

“…Following these initial reports, in silico screening identified bisamidine-type inhibitors of hFPPS (e.g., 17 ) (Lindert et al, 2013), although the binding mode of these compounds has also not been reported. In our own efforts, multistage biochemical and structural screening led to the discovery of thienopyrimidine analogs (e.g., 18 ) that bind to the same allosteric pocket as compound 13 and exhibit equivalent in vitro potency (De Schutter et al, 2014). …”