Farnesyl diphosphate synthase

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Introduction

Contents

Farnesyl pyrophosphate synthase or Farnesyl diphosphate synthase or geranyltranstransferase (FPPS) is a chain elongation enzyme that catalyzes carbon-carbon formation in two consecutive condensation reactions that convert one equivalent of dimethylallyl diphosphate (DMAPP) and two equivalents of isopentyl diphosphates (IPP) into one equivalent of Farnesyl pyrophosphate (FPP). [1]In the first step, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second step, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). It is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FFPS has been studied in conjunction with different parasites. Bisphosphonates have been shown to inhibit FPPS and are currently being used for osteoporosis and the treatment of various bone diseases. Inhibition of FPPS in parasites such Trypanosoma cruzi (Tc), Trypanosoma brucei (Tb), Toxoplasma gondii and Leishmania major (Lm) displays antiparasitic activity which is being evaluated as putative therapeutics. [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13]

Function

In the first condensation reaction, IPP and its isomer DMAPP react to form a ten-carbon geranyl diphosphate (GPP), while in the second condensation reaction, the product geranyl diphosphate from the first step and an additional IPP molecule react to make FPP (see diagram). FPP is an essential enzyme in the biosynthesis of mevalonate, isoprenoids, and sterols in a variety of organisms. FPPS has been studied in conjunction with different parasites. TcFPPS refers to FPPS in the Typanosoma cruzi parasite while LmFPPS refers to FPPS in the Leishmania major parasite. Bisphosphonates have been shown to inhibit FPPS and are currently being used as antiparasitic drugs as well as a treatment for various bone diseases.

Structure

FPPS exists as a homodimer, with each monomer having an active site. The monomers have the characteristic FPPS fold of a ten-helix bundle and four other helices that run perpendicular to the bundle. There are two substrate sites, one is allylic and the other is homoallylic. GPP and DMAPP bind to the allylic site, while IPP binds to the homoallylic site. These two sites are connected to the top of the bundle and exist as part of a cavity[14]. Another characteristic feature of all FPPS enzymes are two highly conserved aspartate rich motifs. These motifs are called First Aspartate Rich Motif (FARM) and Second Aspartate Rich Motif (SARM), and have sequences of DDXX(XX)D and DDXXD respectively. FARM and SARM are found on opposite sides on the active site cavity facing one another[15].

When FPPS interacts with bisphosphonates, the bisphosphonates bind in the homoallylic binding sites and are coordinated by three divalent cations (Ca2+ or Mg2+). The identity of the bisphosphonate influences which divalent cations bind, as well as whether IPP binds. In the structure of LmFPPS with 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium, three Ca 2+ ions and IPP are present.

FPS active site contains Mg+2 ions coordination sites and binds bisphosphonate inhibitors; see also phosphates coordination sites, (PDB code 2opm)[16], water molecules are shown as red spheres.

Relevance

FPS bisphosphonate inhibitors (like zoledronic acid) are used as drugs for treatment of bone resorption diseases[17]. FPS inhibitor Alendronate or Fosamax is used in treatment of osteoporosis[18]. Bisphosphonates have been explored as antiparasitic drugs with FPPS because current treatments are expensive, have low efficacy, and have dangerous side effects. FPPS is important in the lengthening of hydrophobic chains and determination of their specificity.

Published 3D structures of FPPS

Farnesyl diphosphate synthase 3D structures


Human farnesyl diphosphate synthase complex with lipophylic bisphosphonate inhibitor and Mg+2 ions (green) (PDB code 2opm)

Drag the structure with the mouse to rotate

References

  1. ↑ Schulbach MC, Mahapatra S, Macchia M, Barontini S, Papi C, Minutolo F, Bertini S, Brennan PJ, Crick DC. Purification, enzymatic characterization, and inhibition of the Z-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J Biol Chem. 2001 Apr 13;276(15):11624-30. Epub 2001 Jan 4. PMID:11152452 doi:http://dx.doi.org/10.1074/jbc.M007168200
  2. ↑ Aripirala S, Gonzalez-Pacanowska D, Oldfield E, Kaiser M, Amzel LM, Gabelli SB. Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates. Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):802-10. doi:, 10.1107/S1399004713033221. Epub 2014 Feb 22. PMID:24598749 doi:http://dx.doi.org/10.1107/S1399004713033221
  3. ↑ Mukherjee S, Basu S, Zhang K. Farnesyl pyrophosphate synthase is essential for the promastigote and amastigote stages in Leishmania major. Mol Biochem Parasitol. 2019 Jun;230:8-15. doi: 10.1016/j.molbiopara.2019.03.001. , Epub 2019 Mar 26. PMID:30926449 doi:http://dx.doi.org/10.1016/j.molbiopara.2019.03.001
  4. ↑ Ortiz-Gomez A, Jimenez C, Estevez AM, Carrero-Lerida J, Ruiz-Perez LM, Gonzalez-Pacanowska D. Farnesyl diphosphate synthase is a cytosolic enzyme in Leishmania major promastigotes and its overexpression confers resistance to risedronate. Eukaryot Cell. 2006 Jul;5(7):1057-64. doi: 10.1128/EC.00034-06. PMID:16835450 doi:http://dx.doi.org/10.1128/EC.00034-06
  5. ↑ Rodriguez N, Bailey BN, Martin MB, Oldfield E, Urbina JA, Docampo R. Radical cure of experimental cutaneous leishmaniasis by the bisphosphonate pamidronate. J Infect Dis. 2002 Jul 1;186(1):138-40. doi: 10.1086/341074. Epub 2002 Jun 5. PMID:12089677 doi:http://dx.doi.org/10.1086/341074
  6. ↑ Galaka T, Falcone BN, Li C, Szajnman SH, Moreno SNJ, Docampo R, Rodriguez JB. Synthesis and biological evaluation of 1-alkylaminomethyl-1,1-bisphosphonic acids against Trypanosoma cruzi and Toxoplasma gondii. Bioorg Med Chem. 2019 Aug 15;27(16):3663-3673. doi: 10.1016/j.bmc.2019.07.004., Epub 2019 Jul 4. PMID:31296439 doi:http://dx.doi.org/10.1016/j.bmc.2019.07.004
  7. ↑ Garzoni LR, Caldera A, Meirelles Mde N, de Castro SL, Docampo R, Meints GA, Oldfield E, Urbina JA. Selective in vitro effects of the farnesyl pyrophosphate synthase inhibitor risedronate on Trypanosoma cruzi. Int J Antimicrob Agents. 2004 Mar;23(3):273-85. doi:, 10.1016/j.ijantimicag.2003.07.020. PMID:15164969 doi:http://dx.doi.org/10.1016/j.ijantimicag.2003.07.020
  8. ↑ Montalvetti A, Bailey BN, Martin MB, Severin GW, Oldfield E, Docampo R. Bisphosphonates are potent inhibitors of Trypanosoma cruzi farnesyl pyrophosphate synthase. J Biol Chem. 2001 Sep 7;276(36):33930-7. doi: 10.1074/jbc.M103950200. Epub 2001, Jul 2. PMID:11435429 doi:http://dx.doi.org/10.1074/jbc.M103950200
  9. ↑ Yardley V, Khan AA, Martin MB, Slifer TR, Araujo FG, Moreno SN, Docampo R, Croft SL, Oldfield E. In vivo activities of farnesyl pyrophosphate synthase inhibitors against Leishmania donovani and Toxoplasma gondii. Antimicrob Agents Chemother. 2002 Mar;46(3):929-31. doi:, 10.1128/aac.46.3.929-931.2002. PMID:11850291 doi:http://dx.doi.org/10.1128/aac.46.3.929-931.2002
  10. ↑ Ling Y, Sahota G, Odeh S, Chan JM, Araujo FG, Moreno SN, Oldfield E. Bisphosphonate inhibitors of Toxoplasma gondi growth: in vitro, QSAR, and in vivo investigations. J Med Chem. 2005 May 5;48(9):3130-40. doi: 10.1021/jm040132t. PMID:15857119 doi:http://dx.doi.org/10.1021/jm040132t
  11. ↑ Martin MB, Grimley JS, Lewis JC, Heath HT 3rd, Bailey BN, Kendrick H, Yardley V, Caldera A, Lira R, Urbina JA, Moreno SN, Docampo R, Croft SL, Oldfield E. Bisphosphonates inhibit the growth of Trypanosoma brucei, Trypanosoma cruzi, Leishmania donovani, Toxoplasma gondii, and Plasmodium falciparum: a potential route to chemotherapy. J Med Chem. 2001 Mar 15;44(6):909-16. doi: 10.1021/jm0002578. PMID:11300872 doi:http://dx.doi.org/10.1021/jm0002578
  12. ↑ Martin MB, Sanders JM, Kendrick H, de Luca-Fradley K, Lewis JC, Grimley JS, Van Brussel EM, Olsen JR, Meints GA, Burzynska A, Kafarski P, Croft SL, Oldfield E. Activity of bisphosphonates against Trypanosoma brucei rhodesiense. J Med Chem. 2002 Jul 4;45(14):2904-14. doi: 10.1021/jm0102809. PMID:12086478 doi:http://dx.doi.org/10.1021/jm0102809
  13. ↑ Yang G, Zhu W, Kim K, Byun SY, Choi G, Wang K, Cha JS, Cho HS, Oldfield E, No JH. In Vitro and In Vivo Investigation of the Inhibition of Trypanosoma brucei Cell Growth by Lipophilic Bisphosphonates. Antimicrob Agents Chemother. 2015 Dec;59(12):7530-9. doi: 10.1128/AAC.01873-15., Epub 2015 Sep 21. PMID:26392508 doi:http://dx.doi.org/10.1128/AAC.01873-15
  14. ↑ Aripirala S, Gonzalez-Pacanowska D, Oldfield E, Kaiser M, Amzel LM, Gabelli SB. Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates. Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):802-10. doi:, 10.1107/S1399004713033221. Epub 2014 Feb 22. PMID:24598749 doi:http://dx.doi.org/10.1107/S1399004713033221
  15. ↑ Maheshwari S, Kim YS, Aripirala S, Murphy M, Amzel LM, Gabelli SB. Identifying Structural Determinants of Product Specificity in Leishmania major Farnesyl Diphosphate Synthase. Biochemistry. 2020 Jul 12. doi: 10.1021/acs.biochem.0c00432. PMID:32584028 doi:http://dx.doi.org/10.1021/acs.biochem.0c00432
  16. ↑ Zhang Y, Cao R, Yin F, Hudock MP, Guo RT, Krysiak K, Mukherjee S, Gao YG, Robinson H, Song Y, No JH, Bergan K, Leon A, Cass L, Goddard A, Chang TK, Lin FY, Van Beek E, Papapoulos S, Wang AH, Kubo T, Ochi M, Mukkamala D, Oldfield E. Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. J Am Chem Soc. 2009 Apr 15;131(14):5153-62. PMID:19309137 doi:10.1021/ja808285e
  17. ↑ Das S, Edwards PA, Crockett JC, Rogers MJ. Upregulation of endogenous farnesyl diphosphate synthase overcomes the inhibitory effect of bisphosphonate on protein prenylation in Hela cells. Biochim Biophys Acta. 2014 Apr 4;1841(4):569-73. doi:, 10.1016/j.bbalip.2013.12.010. Epub 2013 Dec 22. PMID:24369118 doi:http://dx.doi.org/10.1016/j.bbalip.2013.12.010
  18. ↑ Selby P. Alendronate treatment for osteoporosis: a review of the clinical evidence. Osteoporos Int. 1996;6(6):419-26. doi: 10.1007/bf01629572. PMID:9116385 doi:http://dx.doi.org/10.1007/bf01629572
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