Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase

Gritzalis, Dimitris; Park, Jaeok; Chiu, Wei Hang; Cho, Hyungjun; Lin, Yih‐Shyan; Schutter, Joris W. De; Lacbay, Cyrus M.; Zieliński, Michał; Berghuis, Albert M.; Tsantrizos, Youla S.

doi:10.1016/j.bmcl.2014.12.089

Cited by 16 publications

(14 citation statements)

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“…Earlier studies showed that ZOL, the third generation of nitrogen-containing bisphosphonates, was effective in inhibiting the proliferation, survival, and bone metastasis of PCa cells [17]. NMR and crystallography studies have further revealed that FDPS is a key target of nitrogen-containing bisphosphonates (N-BPs) [18]. Several preclinical and clinical studies have demonstrated the additive and synergistic effects of ZOL when combined with various cytotoxic agents in various cancers [19-22].…”

Section: Introductionmentioning

confidence: 99%

FDPS cooperates with PTEN loss to promote prostate cancer progression through modulation of small GTPases/AKT axis

et al. 2019

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Farnesyl Diphosphate Synthase (FDPS), a mevalonate pathway enzyme, is highly expressed in several cancers, including prostate cancer (PCa). To date, the mechanistic, functional and clinical significance of FDPS in cancer remains unexplored. We evaluated the FDPS expression and its cancer-associated phenotypes using in vitro and in vivo methods in PTEN deficient and sufficient human and mouse PCa cells and tumors. Interestingly, FDPS overexpression synergizes with PTEN deficiency in PTEN conditionally knockout mice (P<0.05) and expressed significantly higher in human (P<0.001) PCa tissues, cell lines and murine tumoroids compared to respective controls. In silico analysis revealed that FDPS is associated with increasing Gleason score, PTEN functionally deficient status and poor survival of PCa. Ectopic overexpression of FDPS promotes oncogenic phenotypes such as colony formation (P<0.01) and proliferation (P<0.01) through activation of AKT and ERK signaling by prenylating Rho A, Rho G and CDC42 small GTPases. Of interest, knockdown of FDPS in PCa cells exhibits decreased colony growth and proliferation (P<0.001) by modulating AKT and ERK pathways. Further, genetic and pharmacological inhibition of PI3K but not AKT reduced FDPS expression. Pharmacological targeting of FDPS by zoledronic acid (ZOL), which is already in clinics exhibit reduced growth and clonogenicity of human and murine PCa cells (P<0.01) and 3D tumoroids (P<0.02) by disrupting AKT and ERK signaling through direct interference of small GTPases protein prenylation. Thus, FDPS plays an oncogenic role in PTEN-deficient PCa through GTPase/AKT axis. Identifying mevalonate pathway proteins could serve as a therapeutic target in PTEN dysregulated tumors.

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Section: Introductionmentioning

confidence: 99%

FDPS cooperates with PTEN loss to promote prostate cancer progression through modulation of small GTPases/AKT axis

et al. 2019

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“…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.…”

Section: Resultsmentioning

confidence: 83%

“…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.…”

Section: Resultsmentioning

confidence: 94%

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Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product

et al. 2017

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Farnesyl pyrophosphate synthase (FPPS) is an enzyme of the mevalonate pathway and a well-established therapeutic target. Recent research has focused around a newly identified druggable pocket near the enzyme's active site. Pharmacological exploitation of this pocket is deemed promising; however, its natural biological function, if any, is yet unknown. Here we report that the product of FPPS, farnesyl pyrophosphate (FPP), can bind to this pocket and lock the enzyme in an inactive state. The Kd for this binding is 5–6 μM, within a catalytically relevant range. These results indicate that FPPS activity is sensitive to the product concentration. Kinetic analysis shows that the enzyme is inhibited through FPP accumulation. Having a specific physiological effector, FPPS is a bona fide allosteric enzyme. This allostery offers an exquisite mechanism for controlling prenyl pyrophosphate levels in vivo and thus contributes an additional layer of regulation to the mevalonate pathway.

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“…A stereo-view of the SaSES2/FPP and digeranyl bisphosphonate structures is shown in Figure 9f, and clearly indicates that the "FPPS" substrate site is not occupied. The isoprenoid side-chain in the HT proteins can thus occupy two sites: one is located between helices D and F and is involved in regulating product chain length 47 while the second occupies the product 48 site and may be involved in feedback inhibition (as shown for FPP binding to the allosteric site in FPPS 49 and it is this second , ad site (between helices C and G) into which cyclase substrates bind (and where amino-acid side-chains control substrate/product conformations). So, while there are many similarities in the AC, B and D domains between the C cyclases and the HT prenyltransferases, the ligand side-chain positions differ with allylic HT prenyltransferase substrates binding to ab (helices D, F), while the C cyclase substrates bind to a site that is very similar to the ad site seen in GGPPS which is contoured, in most cases, to facilitate cyclization although in SaSES (product or inhibitor), the chains are quite extended.…”

Section: Resultsmentioning

confidence: 99%

The ABCs (and Ds) of Class I Terpene Cyclase (αC), Trans- Head-to-Tail (αHT) and Head-to-Head (αHH) Prenyltransferase Structures and Mechanisms of Action

Chen¹,

Malwal²,

Han³

et al. 2019

Preprint

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We report the structures of the terpene cyclases Santalum album L. sesquisabinene synthases 1 and 2 and of santalene synthase, in apo forms, and with the sesquisabinene synthases, bound to either farnesyl diphosphate (FPP), farnesyl S-thiolo-diphosphate, FPP containing a POP bridging O-to-CCl2 substitution, or to sabinene, leading to a sequential mechanism for substrate binding and catalysis. We trapped early pre-catalytic inactive open forms that show how ligands initially bind to the apo-proteins, then when the pocket closes, catalysis can proceed. We also show that there are strong structural similarities between the most highly conserved residues in class I cyclases and those in head-to-tail (aHT) trans-prenyl transferases—outside the well-known DDXXD-like and NSE/DTE-like domains. In the aHT prenyltransferases there is a highly conserved Thr>Gln>Asp>Tyr motif and in the cyclases, a similar Thr>Arg>Asp>Tyr domain, these residues forming very similar, extended H-bond networks (rmsd ~1.4 Å) that are involved in catalysis, leading to the proposal that there are 3 key domains in both the cyclases and the aHT prenyltransferases: The AC-domain that binds MgA and MgC; the B domain that binds MgB and leads to pocket closure, ionization, and condensation or cyclization; and the D-domain H-bond network, involved in H+ elimination. In aHH prenyltransferases the overall folds and MgABC motifs are similar to those found in the cyclase and aHT proteins, but the full Thr>Arg/Gln>Asp>Tyr domain is absent and instead there are Tyr/Asp or Tyr/Glu residues that bind to MgC and are highly conserved. Overall, the results are of general interest since they show unexpected similarities between the enzymes that produce the most diverse molecules on Earth: aHT and aHH prenyltransferases, and terpenoid cyclases.

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Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase

Cited by 16 publications

References 16 publications

FDPS cooperates with PTEN loss to promote prostate cancer progression through modulation of small GTPases/AKT axis

FDPS cooperates with PTEN loss to promote prostate cancer progression through modulation of small GTPases/AKT axis

Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product

The ABCs (and Ds) of Class I Terpene Cyclase (αC), Trans- Head-to-Tail (αHT) and Head-to-Head (αHH) Prenyltransferase Structures and Mechanisms of Action

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