51
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Ali N, Jurczyluk J, Shay G, Tnimov Z, Alexandrov K, Munoz MA, Skinner OP, Pavlos NJ, Rogers MJ. A highly sensitive prenylation assay reveals in vivo effects of bisphosphonate drug on the Rab prenylome of macrophages outside the skeleton. Small GTPases 2015; 6:202-11. [PMID: 26399387 PMCID: PMC4905276 DOI: 10.1080/21541248.2015.1085485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bisphosphonate drugs such as zoledronic acid (ZOL), used for the treatment of common bone disorders, target the skeleton and inhibit bone resorption by preventing the prenylation of small GTPases in bone-destroying osteoclasts. Increasing evidence indicates that bisphosphonates also have pleiotropic effects outside the skeleton, most likely via cells of the monocyte/macrophage lineage exposed to nanomolar circulating drug concentrations. However, no effects of such low concentrations of ZOL have been reported using existing approaches. We have optimized a highly sensitive in vitro prenylation assay utilizing recombinant geranylgeranyltransferases to enable the detection of subtle effects of ZOL on the prenylation of Rab- and Rho-family GTPases. Using this assay, we found for the first time that concentrations of ZOL as low as 10nM caused inhibition of Rab prenylation in J774 macrophages following prolonged cell culture. By combining the assay with quantitative mass spectrometry we identified an accumulation of 18 different unprenylated Rab proteins in J774 cells after nanomolar ZOL treatment, with a >7-fold increase in the unprenylated form of Rab proteins associated with the endophagosome pathway (Rab1, Rab5, Rab6, Rab7, Rab11, Rab14 and Rab21). Finally, we also detected a clear effect of subcutaneous ZOL administration in vivo on the prenylation of Rab1A, Rab5B, Rab7A and Rab14 in mouse peritoneal macrophages, confirming that systemic treatment with bisphosphonate drug can inhibit prenylation in myeloid cells in vivo outside the skeleton. These observations begin a new era in defining the precise pharmacological actions of bisphosphonate drugs on the prenylation of small GTPases in vivo.
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Affiliation(s)
- Naveid Ali
- a Garvan Institute of Medical Research and St Vincent's Clinical School; UNSW Australia ; Sydney , Australia
| | - Julie Jurczyluk
- a Garvan Institute of Medical Research and St Vincent's Clinical School; UNSW Australia ; Sydney , Australia
| | - Gemma Shay
- b Institute of Medical Sciences; University of Aberdeen ; Aberdeen , UK.,e H. Lee Moffitt Cancer Center ; Tampa , FL USA
| | - Zakir Tnimov
- c Institute for Molecular Bioscience; The University of Queensland ; Queensland , Australia
| | - Kirill Alexandrov
- c Institute for Molecular Bioscience; The University of Queensland ; Queensland , Australia
| | - Marcia A Munoz
- a Garvan Institute of Medical Research and St Vincent's Clinical School; UNSW Australia ; Sydney , Australia
| | - Oliver P Skinner
- a Garvan Institute of Medical Research and St Vincent's Clinical School; UNSW Australia ; Sydney , Australia
| | | | - Michael J Rogers
- a Garvan Institute of Medical Research and St Vincent's Clinical School; UNSW Australia ; Sydney , Australia
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52
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Marzinzik AL, Amstutz R, Bold G, Bourgier E, Cotesta S, Glickman JF, Götte M, Henry C, Lehmann S, Hartwieg JCD, Ofner S, Pellé X, Roddy TP, Rondeau JM, Stauffer F, Stout SJ, Widmer A, Zimmermann J, Zoller T, Jahnke W. Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding. ChemMedChem 2015; 10:1884-91. [PMID: 26381451 DOI: 10.1002/cmdc.201500338] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 12/27/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS) is an established target for the treatment of bone diseases, but also shows promise as an anticancer and anti-infective drug target. Currently available anti-FPPS drugs are active-site-directed bisphosphonate inhibitors, the peculiar pharmacological profile of which is inadequate for therapeutic indications beyond bone diseases. The recent discovery of an allosteric binding site has paved the way toward the development of novel non-bisphosphonate FPPS inhibitors with broader therapeutic potential, notably as immunomodulators in oncology. Herein we report the discovery, by an integrated lead finding approach, of two new chemical classes of allosteric FPPS inhibitors that belong to the salicylic acid and quinoline chemotypes. We present their synthesis, biochemical and cellular activities, structure-activity relationships, and provide X-ray structures of several representative FPPS complexes. These novel allosteric FPPS inhibitors are devoid of any affinity for bone mineral and could serve as leads to evaluate their potential in none-bone diseases.
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Affiliation(s)
| | - René Amstutz
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Conim AG, Oberwiler Kirchweg 4c, 6300, Zug, Switzerland
| | - Guido Bold
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | | | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - J Fraser Glickman
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,High Throughput and Spectroscopy Resource Center, Rockefeller University, New York, NY, 10065, USA
| | - Marjo Götte
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Christelle Henry
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | | | - Silvio Ofner
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Thomas P Roddy
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Agios, Cambridge, MA, 02139-4169, USA
| | | | - Frédéric Stauffer
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Steven J Stout
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Armin Widmer
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Johann Zimmermann
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Polyphor, Hegenheimermattweg 125, 4123, Allschwil, Switzerland
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.
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53
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Yokoyama T, Mizuguchi M, Ostermann A, Kusaka K, Niimura N, Schrader TE, Tanaka I. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase. J Med Chem 2015; 58:7549-56. [PMID: 26314394 DOI: 10.1021/acs.jmedchem.5b01147] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS) catalyzes the condensation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate to FPP and is known to be a molecular target of osteoporosis drugs, such as risedronate (RIS), which is a nitrogen-containing bisphosphonate. The protonation states and hydration structure of RIS bound to FPPS were determined by neutron protein crystallography, which allows direct visualization of hydrogens and deuteriums. The structure analysis revealed that the phosphate groups of RIS were fully deprotonated with the abnormally decreased pKa, and that the roles of E93 and D264 consisted of canceling the extra negative charges upon the binding of ligands. Collectively, our neutron structures provided insights into the physicochemical properties during the bisphosphonate binding event.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München , Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Tabias E Schrader
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, 85747 Garching, Germany
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan.,College of Engineering, Ibaraki University , Naka-Narusawa 4-12-1, Hitachi, Ibaraki 316-8511, Japan
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54
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Sen SE, Wood L, Jacob R, Xhambazi A, Pease B, Jones A, Horsfield T, Lin A, Cusson M. Disruption of insect isoprenoid biosynthesis with pyridinium bisphosphonates. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 63:113-123. [PMID: 26073627 DOI: 10.1016/j.ibmb.2015.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 06/04/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) catalyzes the condensation of the non-allylic diphosphate, isopentenyl diphosphate (IPP; C5), with the allylic diphosphate primer dimethylallyl diphosphate (DMAPP; C5) to generate the C15 prenyl chain (FPP) used for protein prenylation as well as sterol and terpene biosynthesis. Here, we designed and prepared a series of pyridinium bisphosphonate (PyrBP) compounds, with the aim of selectively inhibiting FPPS of the lepidopteran insect order. FPPSs of Drosophila melanogaster and the spruce budworm, Choristoneura fumiferana, were inhibited by several PyrBPs, and as hypothesized, larger bisphosphonates were more selective for the lepidopteran protein and completely inactive towards dipteran and vertebrate FPPSs. Cell growth of a D. melanogaster cell line was adversely affected by exposure to PyrPBs that were strongly inhibitory to insect FPPS, although their effect was less pronounced than that observed upon exposure to the electron transport disrupter, chlorfenapyr. To assess the impact of PyrBPs on lepidopteran insect growth and development, we performed feeding and topical studies, using the tobacco hornworm, Manduca sexta, as our insect model. The free acid form of a PyrBP and a known bisphosphonate inhibitor of vertebrate FPPS, alendronate, had little to no effect on larval M. sexta; however, the topical application of more lipophilic ester PyrBPs caused decreased growth, incomplete larval molting, cuticle darkening at the site of application, and for those insects that survived, the formation of larval-pupal hybrids. To gain a better understanding of the structural differences that produce selective lepidopteran FPPS inhibition, homology models of C. fumiferana and D. melanogaster FPPS (CfFPPS2, and DmFPPS) were prepared. Docking of substrates and PyrBPs demonstrates that differences at the -3 and -4 positions relative to the first aspartate rich motif (FARM) are important factors in the ability of the lepidopteran enzyme to produce homologous isoprenoid structure and to be selectively inhibited by larger PyrBPs.
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Affiliation(s)
- Stephanie E Sen
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA.
| | - Lyndsay Wood
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Reshma Jacob
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Alisa Xhambazi
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Britanny Pease
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Alexis Jones
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Taylor Horsfield
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Alice Lin
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Michel Cusson
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Stn. Sainte-Foy, Quebec City, QC G1V 4C7, Canada
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55
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Fernández D, Ortega-Castro J, Mariño L, Perelló J, Frau J. Mechanistic insights into protonation state as a critical factor in hFPPS enzyme inhibition. J Comput Aided Mol Des 2015; 29:667-80. [PMID: 26081258 DOI: 10.1007/s10822-015-9853-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
Zoledronate and risedronate are the most powerful available nitrogen-containing bisphosphonates used in the treatment of bone-resorption disorders. Knowledge about inhibition mechanisms of these molecules is based on available crystallographic structures of human farnesyl pyrophosphate synthase (hFPPS). However, there is a lack of information explaining the inhibition potency of these two molecules compared to the natural substrate, dimethylallyl pyrophosphate. We carried out a molecular dynamics study that shown: (1) that NBPs potency is related to higher electrostatic interactions with the metallic cluster of the active site than to the natural substrate, and (2) the protonation of the R2 side chain is a critical factor to stabilize the NBPs into a closely irreversible ternary complex with the hFPPS.
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Affiliation(s)
- David Fernández
- Department de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, 07122, Palma de Mallorca, Spain
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56
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Ge H, Liu J, Zhao W, Wang Y, He Q, Wu R, Li D, Xu J. Mechanistic studies for tri-targeted inhibition of enzymes involved in cholesterol biosynthesis by green tea polyphenols. Org Biomol Chem 2015; 12:4941-51. [PMID: 24879560 DOI: 10.1039/c4ob00589a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, we found that three enzymes, MVK, MDD and FPPS, in the mevalonate pathway (MVP) of cholesterol biosynthesis, can be simultaneously inhibited by two green tea polyphenols ((-)-epicatechin-3-gallate, ECG; (-)-epigallocatechin-3-gallate, EGCG). Molecular dynamics simulations and pharmacophore studies were carried out to elucidate the tri-targeted inhibition mechanisms. Our results indicate that similar triangular binding pockets exist in all three enzymes, which is essential for their binding with polyphenols. Two distinct binding poses for ECG and EGCG were observed in our MD simulations. These results shed light on the potential for further selective and multi-targeted inhibitor design for the treatment of hyperlipidemia.
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Affiliation(s)
- Hu Ge
- School of Pharmaceutical Sciences & Institute of Human Virology, Sun Yat-Sen University, 132 East Circle Road at University City, Guangzhou, 510006, China.
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57
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Liu YL, Cao R, Wang Y, Oldfield E. Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries. ACS Med Chem Lett 2015; 6:349-54. [PMID: 25815158 DOI: 10.1021/ml500528x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/29/2015] [Indexed: 11/28/2022] Open
Abstract
Farnesyl diphosphate synthase (FPPS) is an important drug target for bone resorption, cancer, and some infectious diseases. Here, we report five new structures including two having unique bound ligand geometries. The diamidine inhibitor 7 binds to human FPPS close to the homoallylic (S2) and allosteric (S3) sites and extends into a new site, here called S4. With the bisphosphonate inhibitor 8, two molecules bind to Trypanosoma brucei FPPS, one molecule in the allylic site (S1) and the other close to S2, the first observation of two bisphosphonate molecules bound to FPPS. We also report the structures of apo-FPPS from T. brucei, together with two more bisphosphonate-bound structures (2,9), for purposes of comparison. The diamidine structure is of particular interest because 7 could represent a new lead for lipophilic FPPS inhibitors, while 8 has low micromolar activity against T. brucei, the causative agent of human African trypanosomiasis.
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Affiliation(s)
- Yi-Liang Liu
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rong Cao
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yang Wang
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Eric Oldfield
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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58
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Schmidberger JW, Schnell R, Schneider G. Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:721-31. [PMID: 25760619 PMCID: PMC4356374 DOI: 10.1107/s1399004715001121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022]
Abstract
Locus PA4043 in the genome of Pseudomonas aeruginosa PAO1 has been annotated as coding for a farnesyl pyrophosphate synthase (FPPS). This open reading frame was cloned and expressed recombinantly in Escherichia coli. The dimeric enzyme shows farnesyl pyrophosphate synthase activity and is strongly inhibited by ibandronate and zoledronate, drugs that are presently in clinical use. The structures of the unliganded enzyme and complexes with the substrate geranyl diphosphate (GPP), the inhibitor ibandronate and two compounds obtained from a differential scanning fluorimetry-based screen of a fragment library were determined by X-ray crystallography to resolutions of better than 2.0 Å. The enzyme shows the typical α-helical fold of farnesyl pyrophosphate synthases. The substrate GPP binds in the S1 substrate site in an open conformation of the enzyme. In the enzyme-ibandronate complex three inhibitor molecules are bound in the active site of the enzyme. One inhibitor molecule occupies the allylic substrate site (S1) of each subunit, as observed in complexes of nitrogen-containing bisphosphonate inhibitors of farnesyl synthases from other species. Two (in subunit A) and one (in subunit B) additional ibandronate molecules are bound in the active site. The structures of the fragment complexes show two molecules bound in a hydrophobic pocket adjacent to the active site. This allosteric pocket, which has previously only been described for FPPS from eukaryotic organisms, is thus also present in enzymes from pathogenic prokaryotes and might be utilized for the design of inhibitors of bacterial FPPS with a different chemical scaffold to the highly charged bisphosphonates, which are less likely to pass bacterial membranes.
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Affiliation(s)
- Jason W. Schmidberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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59
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Construction of 1H-pyrrol-2-ylphosphonates via [3+2] cycloaddition of phosphate azomethine ylides with ynones. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.091] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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60
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Arkko S, Zlatev H, Mönkkönen H, Räikkönen J, Benzaïd I, Clézardin P, Mönkkönen J, Määttä J. Upregulation of the mevalonate pathway by cholesterol depletion abolishes tolerance to N-bisphosphonate induced Vγ9Vδ2 T cell cytotoxicity in PC-3 prostate cancer cells. Cancer Lett 2015; 357:279-285. [DOI: 10.1016/j.canlet.2014.11.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/14/2014] [Accepted: 11/14/2014] [Indexed: 12/14/2022]
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61
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Gritzalis D, Park J, Chiu W, Cho H, Lin YS, De Schutter JW, Lacbay CM, Zielinski M, Berghuis AM, Tsantrizos YS. Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase. Bioorg Med Chem Lett 2015; 25:1117-23. [PMID: 25630225 DOI: 10.1016/j.bmcl.2014.12.089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/26/2014] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
In order to explore the interactions of bisphosphonate ligands with the active site and an allosteric pocket of the human farnesyl pyrophosphate synthase (hFPPS), substituted indole and azabenzimidazole bisphosphonates were designed as chameleon ligands. NMR and crystallographic studies revealed that these compounds can occupy both sub-pockets of the active site cavity, as well as the allosteric pocket of hFPPS in the presence of the enzyme's Mg(2+) ion cofactor. These results are consistent with the previously proposed hypothesis that the allosteric pocket of hFPPS, located near the active site, plays a feed-back regulatory role for this enzyme.
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Affiliation(s)
- Dimitrios Gritzalis
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Wei Chiu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Hyungjun Cho
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Joris W De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Cyrus M Lacbay
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Michal Zielinski
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Department of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, QC H3A 2B4, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada; Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada.
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62
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Han X, Chen CC, Kuo CJ, Huang CH, Zheng Y, Ko TP, Zhu Z, Feng X, Wang K, Oldfield E, Wang AHJ, Liang PH, Guo RT, Ma Y. Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms. Proteins 2015; 83:37-45. [PMID: 24895191 PMCID: PMC4256133 DOI: 10.1002/prot.24618] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 05/12/2014] [Accepted: 05/27/2014] [Indexed: 01/07/2023]
Abstract
Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, which serves as a side chain of ubiquinone and menaquinone. OPPs belongs to the trans-prenyltransferase class of proteins. The structures of OPPs from Escherichia coli were solved in the apo-form as well as in complexes with IPP and a FPP thio-analog, FsPP, at resolutions of 2.2-2.6 Å, and revealed the detailed interactions between the ligands and enzyme. At the bottom of the active-site tunnel, M123 and M135 act in concert to form a wall which determines the final chain length. These results represent the first ligand-bound crystal structures of a long-chain trans-prenyltransferase and provide new information on the mechanisms of catalysis and product chain elongation.
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Affiliation(s)
- Xu Han
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Zhen Zhu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xinxin Feng
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Ke Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
| | - Yanhe Ma
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
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Itzstein C, Coxon FP, Rogers MJ. The regulation of osteoclast function and bone resorption by small GTPases. Small GTPases 2014; 2:117-130. [PMID: 21776413 DOI: 10.4161/sgtp.2.3.16453] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/22/2011] [Accepted: 05/10/2011] [Indexed: 01/11/2023] Open
Abstract
Osteoclasts are multinucleated cells that are responsible for resorption of bone, and increased activity of these cells is associated with several common bone diseases, including postmenopausal osteoporosis. Upon adhesion to bone, osteoclasts become polarized and reorganise their cytoskeleton and membrane to form unique domains including the sealing zone (SZ), which is a dense ring of F-actin-rich podosomes delimiting the ruffled border (RB), where protons and proteases are secreted to demineralise and degrade the bone matrix, respectively. These processes are dependent on the activity of small GTPases. Rho GTPases are well known to control the organization of F-actin and adhesion structures of different cell types, affecting subsequently their migration. In osteoclasts, RhoA, Rac, Cdc42, RhoU and also Arf6 regulate podosome assembly and their organization into the SZ. By contrast, the formation of the RB involves vesicular trafficking pathways that are regulated by the Rab family of GTPases, in particular lysosomal Rab7. Finally, osteoclast survival is dependent on the activity of Ras GTPases. The correct function of almost all these GTPases is absolutely dependent on post-translational prenylation, which enables them to localize to specific target membranes. Bisphosphonate drugs, which are widely used in the treatment of bone diseases such as osteoporosis, act by preventing the prenylation of small GTPases, resulting in the loss of the SZ and RB and therefore inhibition of osteoclast activity, as well as inducing osteoclast apoptosis. In this review we summarize current understanding of the role of specific prenylated small GTPases in osteoclast polarization, function and survival.
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Affiliation(s)
- Cecile Itzstein
- Musculoskeletal Research Programme; Institute of Medical Sciences; University of Aberdeen; Aberdeen, Scotland UK
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64
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Guggisberg AM, Amthor RE, Odom AR. Isoprenoid biosynthesis in Plasmodium falciparum. EUKARYOTIC CELL 2014; 13:1348-59. [PMID: 25217461 PMCID: PMC4248697 DOI: 10.1128/ec.00160-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Malaria kills nearly 1 million people each year, and the protozoan parasite Plasmodium falciparum has become increasingly resistant to current therapies. Isoprenoid synthesis via the methylerythritol phosphate (MEP) pathway represents an attractive target for the development of new antimalarials. The phosphonic acid antibiotic fosmidomycin is a specific inhibitor of isoprenoid synthesis and has been a helpful tool to outline the essential functions of isoprenoid biosynthesis in P. falciparum. Isoprenoids are a large, diverse class of hydrocarbons that function in a variety of essential cellular processes in eukaryotes. In P. falciparum, isoprenoids are used for tRNA isopentenylation and protein prenylation, as well as the synthesis of vitamin E, carotenoids, ubiquinone, and dolichols. Recently, isoprenoid synthesis in P. falciparum has been shown to be regulated by a sugar phosphatase. We outline what is known about isoprenoid function and the regulation of isoprenoid synthesis in P. falciparum, in order to identify valuable directions for future research.
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Affiliation(s)
- Ann M Guggisberg
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rachel E Amthor
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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65
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Lacbay CM, Mancuso J, Lin YS, Bennett N, Götte M, Tsantrizos YS. Modular Assembly of Purine-like Bisphosphonates as Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2014; 57:7435-49. [DOI: 10.1021/jm501010f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Cyrus M. Lacbay
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - John Mancuso
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Yih-Shyan Lin
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Nicholas Bennett
- Department
of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
- Department
of Medicine, Division of Experimental Medicine, McGill University, 1110
Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Youla S. Tsantrizos
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
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66
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Park J, Matralis AN, Berghuis AM, Tsantrizos YS. Human isoprenoid synthase enzymes as therapeutic targets. Front Chem 2014; 2:50. [PMID: 25101260 PMCID: PMC4106277 DOI: 10.3389/fchem.2014.00050] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 06/25/2014] [Indexed: 12/14/2022] Open
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.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University Montreal, QC, Canada
| | | | - Albert M Berghuis
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology, McGill University Montreal, QC, Canada
| | - Youla S Tsantrizos
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Department of Chemistry, McGill University Montreal, QC, Canada
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67
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De Schutter JW, Park J, Leung CY, Gormley P, Lin YS, Hu Z, Berghuis AM, Poirier J, Tsantrizos YS. Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases. J Med Chem 2014; 57:5764-76. [DOI: 10.1021/jm500629e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Joris W. De Schutter
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Jaeok Park
- Department
of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Chun Yuen Leung
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Patrick Gormley
- Douglas Mental Health University Institute, 6825 Lasalle, Verdun, Quebec, H4H 1R3, Canada
| | - Yih-Shyan Lin
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Zheping Hu
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Albert M. Berghuis
- Department
of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
- Department
of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
- Groupe
de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada
| | - Judes Poirier
- Douglas Mental Health University Institute, 6825 Lasalle, Verdun, Quebec, H4H 1R3, Canada
| | - Youla S. Tsantrizos
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Department
of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
- Groupe
de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada
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68
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Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc Natl Acad Sci U S A 2014; 111:E2530-9. [PMID: 24927548 DOI: 10.1073/pnas.1409061111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We used in silico methods to screen a library of 1,013 compounds for possible binding to the allosteric site in farnesyl diphosphate synthase (FPPS). Two of the 50 predicted hits had activity against either human FPPS (HsFPPS) or Trypanosoma brucei FPPS (TbFPPS), the most active being the quinone methide celastrol (IC50 versus TbFPPS ∼ 20 µM). Two rounds of similarity searching and activity testing then resulted in three leads that were active against HsFPPS with IC50 values in the range of ∼ 1-3 µM (as compared with ∼ 0.5 µM for the bisphosphonate inhibitor, zoledronate). The three leads were the quinone methides taxodone and taxodione and the quinone arenarone, compounds with known antibacterial and/or antitumor activity. We then obtained X-ray crystal structures of HsFPPS with taxodione+zoledronate, arenarone+zoledronate, and taxodione alone. In the zoledronate-containing structures, taxodione and arenarone bound solely to the homoallylic (isopentenyl diphosphate, IPP) site, not to the allosteric site, whereas zoledronate bound via Mg(2+) to the same site as seen in other bisphosphonate-containing structures. In the taxodione-alone structure, one taxodione bound to the same site as seen in the taxodione+zoledronate structure, but the second located to a more surface-exposed site. In differential scanning calorimetry experiments, taxodione and arenarone broadened the native-to-unfolded thermal transition (Tm), quite different to the large increases in ΔTm seen with biphosphonate inhibitors. The results identify new classes of FPPS inhibitors, diterpenoids and sesquiterpenoids, that bind to the IPP site and may be of interest as anticancer and antiinfective drug leads.
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69
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Yokoyama T, Ostermann A, Mizuguchi M, Niimura N, Schrader TE, Tanaka I. Crystallization and preliminary neutron diffraction experiment of human farnesyl pyrophosphate synthase complexed with risedronate. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:470-2. [PMID: 24699741 DOI: 10.1107/s2053230x14004087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/21/2014] [Indexed: 11/10/2022]
Abstract
Nitrogen-containing bisphosphonates (N-BPs), such as risedronate and zoledronate, are currently used as a clinical drug for bone-resorption diseases and are potent inhibitors of farnesyl pyrophosphate synthase (FPPS). X-ray crystallographic analyses of FPPS with N-BPs have revealed that N-BPs bind to FPPS with three magnesium ions and several water molecules. To understand the structural characteristics of N-BPs bound to FPPS, including H atoms and hydration by water, neutron diffraction studies were initiated using BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ). FPPS-risedronate complex crystals of approximate dimensions 2.8 × 2.5 × 1.5 mm (∼3.5 mm(3)) were obtained by repeated macro-seeding. Monochromatic neutron diffraction data were collected to 2.4 Å resolution with 98.4% overall completeness. Here, the first successful neutron data collection from FPPS in complex with N-BPs is reported.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Tobias E Schrader
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH Outstation at MLZ, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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70
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Park J, Lin YS, Tsantrizos YS, Berghuis AM. Structure of human farnesyl pyrophosphate synthase in complex with an aminopyridine bisphosphonate and two molecules of inorganic phosphate. Acta Crystallogr F Struct Biol Commun 2014; 70:299-304. [PMID: 24598914 PMCID: PMC3944689 DOI: 10.1107/s2053230x14002106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/29/2014] [Indexed: 12/12/2022] Open
Abstract
Human farnesyl pyrophosphate synthase (hFPPS) produces farnesyl pyrophosphate, an isoprenoid essential for a variety of cellular processes. The enzyme has been well established as the molecular target of the nitrogen-containing bisphosphonates (N-BPs), which are best known for their antiresorptive effects in bone but are also known for their anticancer properties. Crystal structures of hFPPS in ternary complexes with a novel bisphosphonate, YS0470, and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi) and isopentenyl pyrophosphate (IPP) have recently been reported. Only the co-binding of the bisphosphonate with either PPi or IPP resulted in the full closure of the C-terminal tail of the enzyme, a conformational change that is required for catalysis and that is also responsible for the potent in vivo efficacy of N-BPs. In the present communication, a co-crystal structure of hFPPS in complex with YS0470 and two molecules of Pi is reported. The unusually close proximity between these ligands, which was confirmed by anomalous diffraction data, suggests that they interact with one another, with their anionic charges neutralized in their bound state. The structure also showed the tail of the enzyme to be fully disordered, indicating that simultaneous binding of two Pi molecules with a bisphosphonate cannot induce the tail-closing conformational change in hFPPS. Examination of homologous FPPSs suggested that this ligand-dependent tail closure is only conserved in the mammalian proteins. The prevalence of Pi-bound hFPPS structures in the PDB raises a question regarding the in vivo relevance of Pi binding to the function of the enzyme.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Ouest, Montreal, QC H3A 0B8, Canada
| | - Youla S. Tsantrizos
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Ouest, Montreal, QC H3A 0B8, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
- Department of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, QC H3A 2B4, Canada
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71
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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 CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:802-10. [PMID: 24598749 PMCID: PMC3949514 DOI: 10.1107/s1399004713033221] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/08/2013] [Indexed: 11/10/2022]
Abstract
Farnesyl diphosphate synthase (FPPS) is an essential enzyme involved in the biosynthesis of sterols (cholesterol in humans and ergosterol in yeasts, fungi and trypanosomatid parasites) as well as in protein prenylation. It is inhibited by bisphosphonates, a class of drugs used in humans to treat diverse bone-related diseases. The development of bisphosphonates as antiparasitic compounds targeting ergosterol biosynthesis has become an important route for therapeutic intervention. Here, the X-ray crystallographic structures of complexes of FPPS from Leishmania major (the causative agent of cutaneous leishmaniasis) with three bisphosphonates determined at resolutions of 1.8, 1.9 and 2.3 Å are reported. Two of the inhibitors, 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium (300B) and 3-butyl-1-(2,2-diphosphonoethyl)pyridinium (476A), co-crystallize with the homoallylic substrate isopentenyl diphosphate (IPP) and three Ca(2+) ions. A third inhibitor, 3-fluoro-1-(2-hydroxy-2,2-diphosphonoethyl)pyridinium (46I), was found to bind two Mg(2+) ions but not IPP. Calorimetric studies showed that binding of the inhibitors is entropically driven. Comparison of the structures of L. major FPPS (LmFPPS) and human FPPS provides new information for the design of bisphosphonates that will be more specific for inhibition of LmFPPS. The asymmetric structure of the LmFPPS-46I homodimer indicates that binding of the allylic substrate to both monomers of the dimer results in an asymmetric dimer with one open and one closed homoallylic site. It is proposed that IPP first binds to the open site, which then closes, opening the site on the other monomer, which closes after binding the second IPP, leading to the symmetric fully occupied FPPS dimer observed in other structures.
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Affiliation(s)
- Srinivas Aripirala
- Institute for Multiscale Modeling of Biological Interactions and Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, 725 North Wolfe Street WBSB 605, Baltimore, MD 21210, USA
| | | | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcel Kaiser
- University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street WBSB 604, Baltimore, MD 21205, USA
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street WBSB 604, Baltimore, MD 21205, USA
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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72
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Salcius M, Bauer AJ, Hao Q, Li S, Tutter A, Raphael J, Jahnke W, Rondeau JM, Bourgier E, Tallarico J, Michaud GA. SEC-TID: A Label-Free Method for Small-Molecule Target Identification. ACTA ACUST UNITED AC 2014; 19:917-27. [PMID: 24554445 DOI: 10.1177/1087057114522691] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/08/2014] [Indexed: 11/16/2022]
Abstract
Bioactive small molecules are an invaluable source of therapeutics and chemical probes for exploring biological pathways. Yet, significant hurdles in drug discovery often come from lacking a comprehensive view of the target(s) for both early tool molecules and even late-stage drugs. To address this challenge, a method is provided that allows for assessing the interactions of small molecules with thousands of targets without any need to modify the small molecule of interest or attach any component to a surface. We describe size-exclusion chromatography for target identification (SEC-TID), a method for accurately and reproducibly detecting ligand-macromolecular interactions for small molecules targeting nucleic acid and several protein classes. We report the use of SEC-TID, with a library consisting of approximately 1000 purified proteins derived from the protein databank (PDB), to identify the efficacy targets tankyrase 1 and 2 for the Wnt inhibitor XAV939. In addition, we report novel interactions for the tumor-vascular disrupting agent vadimezan/ASA404 (interacting with farnesyl pyrophosphate synthase) and the diuretic mefruside (interacting with carbonic anhydrase XIII). We believe this method can dramatically enhance our understanding of the mechanism of action and potential liabilities for small molecules in drug discovery pipelines through comprehensive profiling of candidate druggable targets.
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Affiliation(s)
- Michael Salcius
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Andras J Bauer
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Qin Hao
- Analytical Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Shu Li
- Analytical Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Antonin Tutter
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jacob Raphael
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Wolfgang Jahnke
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jean-Michel Rondeau
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Emmanuelle Bourgier
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - John Tallarico
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory A Michaud
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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73
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Liu CI, Jeng WY, Chang WJ, Shih MF, Ko TP, Wang AHJ. Structural insights into the catalytic mechanism of human squalene synthase. ACTA ACUST UNITED AC 2014; 70:231-41. [PMID: 24531458 DOI: 10.1107/s1399004713026230] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/23/2013] [Indexed: 11/11/2022]
Abstract
Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step reductive `head-to-head' condensation of two molecules of farnesyl pyrophosphate to form squalene using presqualene diphosphate (PSPP) as an intermediate. In this paper, the structures of human SQS and its mutants in complex with several substrate analogues and intermediates coordinated with Mg2+ or Mn2+ are presented, which stepwise delineate the biosynthetic pathway. Extensive study of the SQS active site has identified several critical residues that are involved in binding reduced nicotinamide dinucleotide phosphate (NADPH). Based on mutagenesis data and a locally closed (JK loop-in) structure observed in the hSQS-(F288L)-PSPP complex, an NADPH-binding model is proposed for SQS. The results identified four major steps (substrate binding, condensation, intermediate formation and translocation) of the ordered sequential mechanisms involved in the `1'-1' isoprenoid biosynthetic pathway. These new findings clarify previous hypotheses based on site-directed mutagenesis and biochemical analysis.
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Affiliation(s)
- Chia-I Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Yih Jeng
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wei-Jung Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Min-Fang Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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74
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Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. Farnesyl diphosphate synthase inhibitors from in silico screening. Chem Biol Drug Des 2014; 81:742-8. [PMID: 23421555 PMCID: PMC3671582 DOI: 10.1111/cbdd.12121] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/16/2013] [Accepted: 02/09/2013] [Indexed: 12/24/2022]
Abstract
The relaxed complex scheme is an in silico drug screening method that accounts for receptor flexibility using molecular dynamics simulations. Here, we used this approach combined with similarity searches and experimental inhibition assays to identify several low micromolar, non-bisphosphonate inhibitors, bisamidines, of farnesyl diphosphate synthase (FPPS), an enzyme targeted by some anticancer and antimicrobial agents and for the treatment of bone resorption diseases. This novel class of farnesyl diphosphate synthase inhibitors have more drug-like properties than existing bisphosphonate inhibitors, making them interesting pharmaceutical leads.
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Affiliation(s)
- Steffen Lindert
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA.
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75
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Kawasaki Y, Sekiguchi M, Kawasaki M, Hirakura Y. Thermodynamic Evaluation of the Binding of Bisphosphonates to Human Farnesyl Pyrophosphate Synthase. Chem Pharm Bull (Tokyo) 2014; 62:77-83. [DOI: 10.1248/cpb.c13-00710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yuko Kawasaki
- Institute for Drug Discovery Research, Astellas Pharma Inc
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76
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Zhou Y, Liu S, Song J, Zhang Z. Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation. PLoS One 2013; 8:e83167. [PMID: 24349449 PMCID: PMC3859641 DOI: 10.1371/journal.pone.0083167] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/30/2013] [Indexed: 12/03/2022] Open
Abstract
The existence and function of most proteins in the human proteome are regulated by the ubiquitination process. To date, tens of thousands human ubiquitination sites have been identified from high-throughput proteomic studies. However, the mechanism of ubiquitination site selection remains elusive because of the complicated sequence pattern flanking the ubiquitination sites. In this study, we perform a systematic analysis of 1,330 ubiquitination sites in 505 protein structures and quantify the significantly high accessibility and unexpectedly high centrality of human ubiquitination sites. Further analysis suggests that the higher centrality of ubiquitination sites is associated with the multi-functionality of ubiquitination sites, among which protein-protein interaction sites are common targets of ubiquitination. Moreover, we demonstrate that ubiquitination sites are flanked by residues with non-random local conformation. Finally, we provide quantitative and unambiguous evidence that most of the structural propensities contain specific information about ubiquitination site selection that is not represented by the sequence pattern. Therefore, the hypothesis about the structural level of the ubiquitination site selection mechanism has been substantially approved.
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Affiliation(s)
- Yuan Zhou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sixue Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiangning Song
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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77
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Liu J, Liu W, Ge H, Gao J, He Q, Su L, Xu J, Gu LQ, Huang ZS, Li D. Syntheses and characterization of non-bisphosphonate quinoline derivatives as new FPPS inhibitors. Biochim Biophys Acta Gen Subj 2013; 1840:1051-62. [PMID: 24246954 DOI: 10.1016/j.bbagen.2013.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/11/2013] [Accepted: 11/08/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND Farnesyl pyrophosphate synthase (FPPS) is a key regulatory enzyme in the biosynthesis of cholesterol and in the post-translational modification of signaling proteins. It has been reported that non-bisphosphonate FPPS inhibitors targeting its allosteric binding pocket are potentially important for the development of promising anti-cancer drugs. METHODS The following methods were used: organic syntheses of non-bisphosphonate quinoline derivatives, enzyme inhibition studies, fluorescence titration assays, synergistic effect studies of quinoline derivatives with zoledronate, ITC studies for the binding of FPPS with quinoline derivatives, NMR-based HAP binding assays, molecular modeling studies, fluorescence imaging assay and MTT assays. RESULTS We report our syntheses of a series of quinoline derivatives as new FPPS inhibitors possibly targeting the allosteric site of the enzyme. Compound 6b showed potent inhibition to FPPS without significant hydroxyapatite binding affinity. The compound showed synergistic inhibitory effect with active-site inhibitor zoledronate. ITC experiment confirmed the good binding effect of compound 6b to FPPS, and further indicated the binding ratio of 1:1. Molecular modeling studies showed that 6b could possibly bind to the allosteric binding pocket of the enzyme. The fluorescence microscopy indicated that these compounds could get into cancer cells. CONCLUSIONS Our results showed that quinoline derivative 6b could become a new lead compound for further optimization for cancer treatment. GENERAL SIGNIFICANCE The traditional FPPS active-site inhibitors bisphosphonates show poor membrane permeability to tumor cells, due to their strong polarity. The development of new non-bisphosphonate FPPS inhibitors with good cell membrane permeability is potentially important.
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78
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Leung CY, Park J, De Schutter JW, Sebag M, Berghuis AM, Tsantrizos YS. Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition. J Med Chem 2013; 56:7939-50. [PMID: 23998921 DOI: 10.1021/jm400946f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Chun Yuen Leung
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Jaeok Park
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
| | - Joris W. De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Michael Sebag
- Division
of Haematology, McGill University Health Center, Royal Victoria Hospital, C6.80,
687 Pine Avenue West, Montreal, Quebec, Canada H3A 1A1
| | - Albert M. Berghuis
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
- Department of Microbiology and Immunology, McGill University, 801 Sherbrooke Street
West, Montreal, Quebec, Canada H3A 0B8
| | - Youla S. Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
- Groupe de Recherche
Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir
William Osler, Montreal, Quebec, Canada H3G 0B1
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79
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Fernández D, Ortega-Castro J, Frau J. Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates: a 3D-QSAR study. J Comput Aided Mol Des 2013; 27:739-54. [PMID: 23979193 DOI: 10.1007/s10822-013-9674-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 08/08/2013] [Indexed: 01/06/2023]
Abstract
We report the results of a comparative molecular field analysis and comparative molecular similarity index analysis of the human farnesyl pyrophosphate synthase (FPPS) inhibition by nitrogen bisphosphonates (NBPs) taking into account their time-dependent inhibition efficacies. The 3D-QSAR models obtained provide steric, electrostatic and hydrophobic contour maps consistent with the interactions into the active site of human FPPS observed in available crystallographic structures. Furthermore, the 3D-QSAR models obtained provide accurately IC50 values of the NBPs of the training set. The predictive ability of these 3D-QSAR models was found to rely on the choice of biologically active conformations of the target molecules and on a careful examination of the protonation status of the NBPs in the training set. The best models obtained can be useful to predict biological values of a high number of NBPs that have been used for the treatment of different diseases as potential inhibitors of the activity of the FPPS enzyme.
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Affiliation(s)
- David Fernández
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, 07122, Spain
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80
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Low toxicity and unprecedented anti-osteoclast activity of a simple sulfur-containing gem-bisphosphonate: a comparative study. Eur J Med Chem 2013; 65:448-55. [PMID: 23748153 DOI: 10.1016/j.ejmech.2013.04.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/08/2013] [Accepted: 04/11/2013] [Indexed: 11/22/2022]
Abstract
Bisphosphonates (BPs) are key drugs for the treatment of bone resorption diseases like osteoporosis, Paget's disease and some forms of tumors. Recent findings underlined the importance of lipophilic N-containing BPs to ensure high biological activity. Herein we present some unprecedented results concerning the low toxicity and good anti-osteoclast activity of low molecular weight hydrophilic S-containing BPs. A series of S and N-containing BPs bearing aromatic and aliphatic substitution were prepared through Michael addition reaction between vinylidenebisphosphonate tetraethyl ester and the proper nucleophile under basic catalysis. S-containing BPs showed a generally low toxicity, determined with the neutral-red assay using the L929 cell line, and, in particular for an aliphatic one, a good biological activity assessed on primary cultures of human osteoclasts.
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81
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Zhang Y, Zhu W, Liu YL, Wang H, Wang K, Li K, No JH, Ayong L, Gulati A, Pang R, Freitas-Junior L, Morita CT, Oldfield E. Chemo-Immunotherapeutic Anti-Malarials Targeting Isoprenoid Biosynthesis. ACS Med Chem Lett 2013; 4:423-427. [PMID: 23610597 DOI: 10.1021/ml4000436] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We synthesized 30 lipophilic bisphosphonates and tested them in malaria parasite killing (targeting parasite geranylgeranyl diphosphate synthase, GGPPS) as well in human γδ T cell activation (targeting human farnesyl diphosphate synthase, FPPS). Similar patterns of activity were seen in inhibiting human FPPS and Plasmodium GGPPS, with short to medium chain-length species having most activity. In cells, shorter chain-length species had low activity, due to poor membrane permeability, and longer chain length species were poor enzyme inhibitors. Optimal activity was thus seen with ~C10 side-chains, which have the best combination of enzyme inhibition and cell penetration. We also solved the crystal structure of one potent inhibitor, bound to FPPS. The results are of interest since they suggest the possibility of a combined chemo/immuno-therapeutic approach to anti-malarial development in which both direct parasite killing as well as γδ T cell activation can be achieved with a single compound.
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Affiliation(s)
- Yonghui Zhang
- PrenylX Research Institute, Zhangjiagang 215600, People’s Republic
of China
| | | | | | - Hong Wang
- Division of Immunology, Department
of Internal Medicine, the Interdisciplinary Graduate Program in Immunology, University of Iowa Carver College of Medicine, Veterans
Affairs Health Care System, Iowa City, Iowa 52242, United States
| | | | | | - Joo Hwan No
- Center for Neglected Diseases Drug
Discovery, Institute Pasteur Korea, Seongnam-si,
Gyeonggi-do 463-400, South Korea
| | - Lawrence Ayong
- Center for Neglected Diseases Drug
Discovery, Institute Pasteur Korea, Seongnam-si,
Gyeonggi-do 463-400, South Korea
| | | | | | - Lucio Freitas-Junior
- Center for Neglected Diseases Drug
Discovery, Institute Pasteur Korea, Seongnam-si,
Gyeonggi-do 463-400, South Korea
| | - Craig T. Morita
- Division of Immunology, Department
of Internal Medicine, the Interdisciplinary Graduate Program in Immunology, University of Iowa Carver College of Medicine, Veterans
Affairs Health Care System, Iowa City, Iowa 52242, United States
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82
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Leung CY, Langille AM, Mancuso J, Tsantrizos YS. Discovery of thienopyrimidine-based inhibitors of the human farnesyl pyrophosphate synthase—Parallel synthesis of analogs via a trimethylsilyl ylidene intermediate. Bioorg Med Chem 2013; 21:2229-2240. [DOI: 10.1016/j.bmc.2013.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/01/2013] [Accepted: 02/11/2013] [Indexed: 01/20/2023]
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83
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Park J, Lin YS, De Schutter JW, Tsantrizos YS, Berghuis AM. Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure. BMC STRUCTURAL BIOLOGY 2012; 12:32. [PMID: 23234314 PMCID: PMC3539973 DOI: 10.1186/1472-6807-12-32] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/07/2012] [Indexed: 02/06/2023]
Abstract
BACKGROUND Human farnesyl pyrophosphate synthase (FPPS) controls intracellular levels of farnesyl pyrophosphate, which is essential for various biological processes. Bisphosphonate inhibitors of human FPPS are valuable therapeutics for the treatment of bone-resorption disorders and have also demonstrated efficacy in multiple tumor types. Inhibition of human FPPS by bisphosphonates in vivo is thought to involve closing of the enzyme's C-terminal tail induced by the binding of the second substrate isopentenyl pyrophosphate (IPP). This conformational change, which occurs through a yet unclear mechanism, seals off the enzyme's active site from the solvent environment and is essential for catalysis. The crystal structure of human FPPS in complex with a novel bisphosphonate YS0470 and in the absence of a second substrate showed partial ordering of the tail in the closed conformation. RESULTS We have determined crystal structures of human FPPS in ternary complex with YS0470 and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi), and IPP. Binding of PPi or IPP to the enzyme-inhibitor complex, but not that of Pi, resulted in full ordering of the C-terminal tail, which is most notably characterized by the anchoring of the R351 side chain to the main frame of the enzyme. Isothermal titration calorimetry experiments demonstrated that PPi binds more tightly to the enzyme-inhibitor complex than IPP, and differential scanning fluorometry experiments confirmed that Pi binding does not induce the tail ordering. Structure analysis identified a cascade of conformational changes required for the C-terminal tail rigidification involving Y349, F238, and Q242. The residues K57 and N59 upon PPi/IPP binding undergo subtler conformational changes, which may initiate this cascade. CONCLUSIONS In human FPPS, Y349 functions as a safety switch that prevents any futile C-terminal closure and is locked in the "off" position in the absence of bound IPP. Q242 plays the role of a gatekeeper and directly controls the anchoring of R351 side chain. The interactions between the residues K57 and N59 and those upstream and downstream of Y349 are likely responsible for the switch activation. The findings of this study can be exploited for structure-guided optimization of existing inhibitors as well as development of new pharmacophores.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
| | - Joris W De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
| | - Youla S Tsantrizos
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Department of Microbiology and Immunology, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada
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84
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Liu PL, Wan JN, Guo YP, Ge S, Rao GY. Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism. BMC Evol Biol 2012; 12:214. [PMID: 23137178 PMCID: PMC3518182 DOI: 10.1186/1471-2148-12-214] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chrysanthemyl diphosphate synthase (CDS) is a key enzyme in biosynthetic pathways producing pyrethrins and irregular monoterpenes. These compounds are confined to plants of the tribe Anthemideae of the Asteraceae, and play an important role in defending the plants against herbivorous insects. It has been proposed that the CDS genes arose from duplication of the farnesyl diphosphate synthase (FDS) gene and have different function from FDSs. However, the duplication time toward the origin of CDS and the evolutionary force behind the functional divergence of the CDS gene are still unknown. RESULTS Two duplication events were detected in the evolutionary history of the FDS gene family in the Asteraceae, and the second duplication led to the origin of CDS. CDS occurred after the divergence of the tribe Mutisieae from other tribes of Asteraceae but before the birth of the Anthemideae tribe. After its origin, CDS accumulated four mutations in sites homologous to the substrate-binding and catalysis sites of FDS. Of these, two sites were involved in the binding of the nucleophilic substrate isopentenyl diphosphate in FDS. Maximum likelihood analyses showed that some sites in CDS were under positive selection and were scattered throughout primary sequences, whereas in the three-dimensional structure model they clustered in the large central cavity. CONCLUSION Positive selection associated with gene duplication played a major role in the evolution of CDS.
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Affiliation(s)
- Ping-Li Liu
- College of Life Sciences, Peking University, Beijing 100871, China
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85
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Keim V, Manzano D, Fernández FJ, Closa M, Andrade P, Caudepón D, Bortolotti C, Vega MC, Arró M, Ferrer A. Characterization of Arabidopsis FPS isozymes and FPS gene expression analysis provide insight into the biosynthesis of isoprenoid precursors in seeds. PLoS One 2012; 7:e49109. [PMID: 23145086 PMCID: PMC3492304 DOI: 10.1371/journal.pone.0049109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 10/07/2012] [Indexed: 11/19/2022] Open
Abstract
Arabidopsis thaliana contains two genes encoding farnesyl diphosphate (FPP) synthase (FPS), the prenyl diphoshate synthase that catalyzes the synthesis of FPP from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In this study, we provide evidence that the two Arabidopsis short FPS isozymes FPS1S and FPS2 localize to the cytosol. Both enzymes were expressed in E. coli, purified and biochemically characterized. Despite FPS1S and FPS2 share more than 90% amino acid sequence identity, FPS2 was found to be more efficient as a catalyst, more sensitive to the inhibitory effect of NaCl, and more resistant to thermal inactivation than FPS1S. Homology modelling for FPS1S and FPS2 and analysis of the amino acid differences between the two enzymes revealed an increase in surface polarity and a greater capacity to form surface salt bridges of FPS2 compared to FPS1S. These factors most likely account for the enhanced thermostability of FPS2. Expression analysis of FPS::GUS genes in seeds showed that FPS1 and FPS2 display complementary patterns of expression particularly at late stages of seed development, which suggests that Arabidopsis seeds have two spatially segregated sources of FPP. Functional complementation studies of the Arabidopsis fps2 knockout mutant seed phenotypes demonstrated that under normal conditions FPS1S and FPS2 are functionally interchangeable. A putative role for FPS2 in maintaining seed germination capacity under adverse environmental conditions is discussed.
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Affiliation(s)
- Verónica Keim
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - David Manzano
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Francisco J. Fernández
- Department of Structural and Quantitative Biology, Centre for Biological Research (CIB-CSIC), Madrid, Spain
| | - Marta Closa
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Paola Andrade
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Daniel Caudepón
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Cristina Bortolotti
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - M. Cristina Vega
- Department of Structural and Quantitative Biology, Centre for Biological Research (CIB-CSIC), Madrid, Spain
| | - Montserrat Arró
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Albert Ferrer
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) (CSIC-IRTA-UAB-UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
- * E-mail:
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86
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Gao Y, Honzatko RB, Peters RJ. Terpenoid synthase structures: a so far incomplete view of complex catalysis. Nat Prod Rep 2012; 29:1153-75. [PMID: 22907771 PMCID: PMC3448952 DOI: 10.1039/c2np20059g] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.
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Affiliation(s)
- Yang Gao
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J. Peters
- Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA 50011, USA
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87
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De Schutter JW, Shaw J, Lin YS, Tsantrizos YS. Design of potent bisphosphonate inhibitors of the human farnesyl pyrophosphate synthase via targeted interactions with the active site ‘capping’ phenyls. Bioorg Med Chem 2012; 20:5583-91. [DOI: 10.1016/j.bmc.2012.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/04/2012] [Accepted: 07/13/2012] [Indexed: 11/28/2022]
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88
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Cirak Y, Varol U, Atmaca H, Kisim A, Sezgin C, Karabulut B, Uzunoglu S, Uslu R, Karaca B. Zoledronic acid in combination with serine/threonine phosphatase inhibitors induces enhanced cytotoxicity and apoptosis in hormone-refractory prostate cancer cell lines by decreasing the activities of PP1 and PP2A. BJU Int 2012; 110:E1147-54. [DOI: 10.1111/j.1464-410x.2012.11392.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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89
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Structures, mechanisms and inhibitors of undecaprenyl diphosphate synthase: A cis-prenyltransferase for bacterial peptidoglycan biosynthesis. Bioorg Chem 2012; 43:51-7. [DOI: 10.1016/j.bioorg.2011.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/13/2011] [Accepted: 09/15/2011] [Indexed: 12/20/2022]
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90
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Aripirala S, Szajnman SH, Jakoncic J, Rodriguez JB, Docampo R, Gabelli SB, Amzel LM. Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase. J Med Chem 2012; 55:6445-54. [PMID: 22715997 DOI: 10.1021/jm300425y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Linear 2-alkylaminoethyl-1,1-bisphosphonates are effective agents against proliferation of Trypanosoma cruzi , the etiologic agent of American trypanosomiasis (Chagas disease), exhibiting IC(50) values in the nanomolar range against the parasites. This activity is associated with inhibition at the low nanomolar level of the T. cruzi farnesyl diphosphate synthase (TcFPPS). X-ray structures and thermodynamic data of the complexes TcFPPS with five compounds of this family show that the inhibitors bind to the allylic site of the enzyme, with their alkyl chain occupying the cavity that binds the isoprenoid chain of the substrate. The compounds bind to TcFPPS with unfavorable enthalpy compensated by a favorable entropy that results from a delicate balance between two opposing effects: the loss of conformational entropy due to freezing of single bond rotations and the favorable burial of the hydrophobic alkyl chains. The data suggest that introduction of strategically placed double bonds and methyl branches should increase affinity substantially.
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Affiliation(s)
- Srinivas Aripirala
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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91
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2-alkylaminoethyl-1,1-bisphosphonic acids are potent inhibitors of the enzymatic activity of Trypanosoma cruzi squalene synthase. Antimicrob Agents Chemother 2012; 56:4483-6. [PMID: 22585217 DOI: 10.1128/aac.00796-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
As part of our efforts aimed at searching for new antiparasitic agents, the effect of representative 2-alkylaminoethyl-1,1-bisphosphonic acids on Trypanosoma cruzi squalene synthase (TcSQS) was investigated. These compounds had proven to be potent inhibitors of T. cruzi. This cellular activity had been associated with an inhibition of the enzymatic activity of T. cruzi farnesyl diphosphate synthase. 2-Alkylaminoethyl-1,1-bisphosphonic acids appear to have a dual action, since they also inhibit TcSQS at the nanomolar range.
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92
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Lin FY, Liu YL, Li K, Cao R, Zhu W, Axelson J, Pang R, Oldfield E. Head-to-head prenyl tranferases: anti-infective drug targets. J Med Chem 2012; 55:4367-72. [PMID: 22486710 DOI: 10.1021/jm300208p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report X-ray crystallographic structures of three inhibitors bound to dehydrosqualene synthase from Staphylococcus aureus: 1 (BPH-651), 2 (WC-9), and 3 (SQ-109). Compound 2 binds to the S2 site with its -SCN group surrounded by four hydrogen bond donors. With 1, we report two structures: in both, the quinuclidine headgroup binds in the allylic (S1) site with the side chain in S2, but in the presence of PPi and Mg(2+), the quinuclidine's cationic center interacts with PPi and three Mg(2+), mimicking a transition state involved in diphosphate ionization. With 3, there are again two structures. In one, the geranyl side chain binds to either S1 or S2 and the adamantane headgroup binds to S1. In the second, the side chain binds to S2 while the headgroup binds to S1. These results provide structural clues for the mechanism and inhibition of the head-to-head prenyl transferases and should aid future drug design.
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Affiliation(s)
- Fu-Yang Lin
- Center for Biophysics and Computational Biology,University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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93
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Thermodynamic dissociation constants of risedronate using spectrophotometric and potentiometric pH-titration. OPEN CHEM 2012. [DOI: 10.2478/s11532-011-0150-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractRisedronate inhibits bone resorption in diseases like osteoporosis, Paget’s disease, tumor bone diseases or the malfunction of phosphocalcium metabolism. The acid-base properties of risedronate in an aqueous solution have been studied in a pH range from 2 to 12 and can be described in terms of four dissociation steps: pK a,2, pK a,4, pK a,5 (related to the dissociation of POH groups) and pK a,3 related to the dissociation of protonated amino group NH3+. The mixed dissociation constants were determined at different ionic strengths I = 0.02 to 0.20 mol dm−3 KCl and of 25°C and 37°C using pH-spectrophotometric and pH-potentiometric titration methods. Determination of group parameters L 0, H T might lead to false estimates of common parameters p K a;therefore, the computational strategy employed is important. A comparison between the two programs ESAB and HYPERQUAD demonstrated that the ESAB program provides a better fit of potentiometric titration curve. The thermodynamic dissociation constants pK aT were estimated by a nonlinear regression of (pK a, I) data and a Debye-Hückel equation at 25°C and 37°C, pK a,2T = 2.37(1) and 2.44(1), pK a,3T = 6.29(3) and 6.26(1), pK a,4T = 7.48(1) and 7.46(2) and pK a,5T = 9.31(7) and 8.70(3) at 25°C and 37°C using pH-spectroscopic data and pK a,2T = 2.48(3) and 2.43(1), pK a,3T= 6.12(2) and 6.10(2), pK a,4T = 7.25(2) and 7.23(1) and pK a,5T = 12.04(5) and 11.81(2) at 25°C and 37°C. The ascertained estimates of three dissociation constants pK a,3, pK a,4, pK a,5 are in agreement with the predicted values obtained using PALLAS
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94
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Lin YS, Park J, De Schutter JW, Huang XF, Berghuis AM, Sebag M, Tsantrizos YS. Design and Synthesis of Active Site Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Apoptosis and Inhibition of ERK Phosphorylation in Multiple Myeloma Cells. J Med Chem 2012; 55:3201-15. [PMID: 22390415 DOI: 10.1021/jm201657x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal,
QC, Canada H3A 0B8
| | - Jaeok Park
- Department
of Biochemistry, McGill University, 3649
Promenade Sir William Osler,
Montreal, QC, Canada H3G 0B1
| | - Joris W. De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal,
QC, Canada H3A 0B8
| | - Xian Fang Huang
- Division of Haematology, McGill University Health Center, Royal Victoria Hospital,
C6.80, 687 Pine Avenue West, Montreal, QC, Canada H3A 1A1
| | - Albert M. Berghuis
- Department
of Biochemistry, McGill University, 3649
Promenade Sir William Osler,
Montreal, QC, Canada H3G 0B1
| | - Michael Sebag
- Division of Haematology, McGill University Health Center, Royal Victoria Hospital,
C6.80, 687 Pine Avenue West, Montreal, QC, Canada H3A 1A1
| | - Youla S. Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal,
QC, Canada H3A 0B8
- Department
of Biochemistry, McGill University, 3649
Promenade Sir William Osler,
Montreal, QC, Canada H3G 0B1
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95
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Li L, Zhang W, Cheng S, Cao D, Parent M. Isoprenoids and related pharmacological interventions: potential application in Alzheimer's disease. Mol Neurobiol 2012; 46:64-77. [PMID: 22418893 DOI: 10.1007/s12035-012-8253-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/28/2012] [Indexed: 12/18/2022]
Abstract
Two major isoprenoids, farnesyl pyrophosphate and geranylgeranyl pyrophosphate, serve as lipid donors for the posttranslational modification (known as prenylation) of proteins that possess a characteristic C-terminal motif. The prenylation reaction is catalyzed by prenyltransferases. The lipid prenyl group facilitates to anchor the proteins in cell membranes and mediates protein-protein interactions. A variety of important intracellular proteins undergo prenylation, including almost all members of small GTPase superfamilies as well as heterotrimeric G protein subunits and nuclear lamins. These prenylated proteins are involved in regulating a wide range of cellular processes and functions, such as cell growth, differentiation, cytoskeletal organization, and vesicle trafficking. Prenylated proteins are also implicated in the pathogenesis of different types of diseases. Consequently, isoprenoids and/or prenyltransferases have emerged as attractive therapeutic targets for combating various disorders. This review attempts to summarize the pharmacological agents currently available or under development that control isoprenoid availability and/or the process of prenylation, mainly focusing on statins, bisphosphonates, and prenyltransferase inhibitors. Whereas statins and bisphosphonates deplete the production of isoprenoids by inhibiting the activity of upstream enzymes, prenyltransferase inhibitors directly block the prenylation of proteins. As the importance of isoprenoids and prenylated proteins in health and disease continues to emerge, the therapeutic potential of these pharmacological agents has expanded across multiple disciplines. This review mainly discusses their potential application in Alzheimer's disease.
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Affiliation(s)
- Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota, 2001 6th St SE, MTRF 4-208, Minneapolis, MN 55455, USA.
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96
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Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity. Proc Natl Acad Sci U S A 2012; 109:4058-63. [PMID: 22392982 DOI: 10.1073/pnas.1118215109] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the results of an in vitro screening assay targeting the intraerythrocytic form of the malaria parasite Plasmodium falciparum using a library of 560 prenyl-synthase inhibitors. Based on "growth-rescue" and enzyme-inhibition experiments, geranylgeranyl diphosphate synthase (GGPPS) is shown to be a major target for the most potent leads, BPH-703 and BPH-811, lipophilic analogs of the bone-resorption drugs zoledronate and risedronate. We determined the crystal structures of these inhibitors bound to a Plasmodium GGPPS finding that their head groups bind to the [Mg(2+)](3) cluster in the active site in a similar manner to that found with their more hydrophilic parents, whereas their hydrophobic tails occupy a long-hydrophobic tunnel spanning both molecules in the dimer. The results of isothermal-titration-calorimetric experiments show that both lipophilic bisphosphonates bind to GGPPS with, on average, a ΔG of -9 kcal mol(-1), only 0.5 kcal mol(-1) worse than the parent bisphosphonates, consistent with the observation that conversion to the lipophilic species has only a minor effect on enzyme activity. However, only the lipophilic species are active in cells. We also tested both compounds in mice, finding major decreases in parasitemia and 100% survival. These results are of broad general interest because they indicate that it may be possible to overcome barriers to cell penetration of existing bisphosphonate drugs in this and other systems by simple covalent modification to form lipophilic analogs that retain their enzyme-inhibition activity and are also effective in vitro and in vivo.
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97
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Szajnman SH, Rosso VS, Malayil L, Smith A, Moreno SNJ, Docampo R, Rodriguez JB. 1-(Fluoroalkylidene)-1,1-bisphosphonic acids are potent and selective inhibitors of the enzymatic activity of Toxoplasma gondii farnesyl pyrophosphate synthase. Org Biomol Chem 2012; 10:1424-33. [PMID: 22215028 PMCID: PMC3458512 DOI: 10.1039/c1ob06602a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Fluorinated-1,1-bisphosphonic acids derived from fatty acids were designed, synthesized and biologically evaluated against Trypanosoma cruzi, the etiologic agent of Chagas disease, and against Toxoplasma gondii, the agent responsible for toxoplasmosis, and also towards the target parasitic enzymes farnesyl pyrophosphate synthase of T. cruzi (TcFPPS) and T. gondii (TgFPPS). Interestingly, 1-fluorononylidene-1,1-bisphosphonic acid (compound 43) proved to be an extremely potent inhibitor of the enzymatic activity of TgFPPS at the low nanomolar range, exhibiting an IC(50) of 30 nM. This compound was two-fold more potent than risedronate (IC(50) = 74 nM) that was taken as a positive control. This enzymatic activity was associated with a strong cell growth inhibition against tachyzoites of T. gondii, with an IC(50) value of 2.7 μM.
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Affiliation(s)
- Sergio H Szajnman
- Departamento de Química Orgánica and UMYMFOR (CONICET-FCEyN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
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98
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Demoro B, Caruso F, Rossi M, Benítez D, González M, Cerecetto H, Galizzi M, Malayil L, Docampo R, Faccio R, Mombrú AW, Gambino D, Otero L. Bisphosphonate metal complexes as selective inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase. Dalton Trans 2012; 41:6468-76. [PMID: 22344249 DOI: 10.1039/c2dt12179d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the search for a pharmacological answer to treat Chagas disease, eight metal complexes with two bioactive bisphosphonates, alendronate (Ale) and pamidronate (Pam), were described. Complexes of the formula [M(2)(II)(Ale)(4)(H(2)O)(2)]·2H(2)O, with M = Cu, Co, Mn, Ni, and ([CuPam]·H(2)O)(n) as well as [M(II)(Pam)(2)(H(2)O)(2)]·3H(2)O, with M = Co, Mn and Ni, were synthesized and fully characterized. Crystal structure of [Cu(2)(II)(Ale)(4)(H(2)O)(2)]·2H(2)O, [Co(II)(Pam)(2)(H(2)O)(2)] and [Ni(II)(Pam)(2)(H(2)O)(2)] were solved by X-ray single crystal diffraction methods and the structures of [M(2)(II)(Ale)(4)(H(2)O)(2)]·2H(2)O complexes M = Co, Mn and Ni were studied by X-ray powder diffraction methods. All obtained complexes were active against the amastigote form of Trypanosoma cruzi (T. cruzi), etiological agent of Chagas disease. Most of them were more active than the corresponding free ligands showing no toxicity for mammalian cells. The main mechanism of the antiparasitic action of bisphosphonates, inhibition of parasitic farnesyl diphosphate synthase (TcFPPS), remains in the obtained metal complexes and an increase in the inhibiting enzyme levels was observed upon coordination. Observed enzymatic inhibition was selective for TcFPPS as the metal complexes showed no or little inhibition of human FPPS. Additionally, metal complexation might improve the bioavailability of the complexes through the hindrance of the phosphonate group's ionization at physiological pH and, eventually, through the ability of plasma proteins to work as complex transporters.
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Affiliation(s)
- Bruno Demoro
- Cátedra de Química Inorgánica, DEC, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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99
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NMR, potentiometric and ESI-MS combined studies on the zinc(II) magnesium(II) and calcium(II) complexation by (morpholin-1-yl)methane-1,1-diphosphonic acid and its thio-analog. Polyhedron 2012. [DOI: 10.1016/j.poly.2011.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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100
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Galezowska J, Gumienna-Kontecka E. Phosphonates, their complexes and bio-applications: A spectrum of surprising diversity. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.07.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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