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Covelli V, Buonocore M, Grimaldi M, Scrima M, Santoro A, Marino C, De Simone V, van Baarle L, Biscu F, Scala MC, Sala M, Matteoli G, D'Ursi AM, Rodriquez M. Peptides as modulators of FPPS enzyme: A multifaceted evaluation from the design to the mechanism of action. Eur J Med Chem 2024; 279:116871. [PMID: 39303514 DOI: 10.1016/j.ejmech.2024.116871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/02/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024]
Abstract
Bone diseases are medical conditions caused by the loss of bone homeostasis consecutive to increased osteoclast activity and diminished osteoblast activity. The mevalonate pathway (MVA) is crucial for maintaining this balance since it drives the post-translational prenylation of small guanosine triphosphatases (GTPases) proteins. Farnesyl pyrophosphate synthase (FPPS) plays a crucial role in the MVA pathway. Consequently, in the treatment of bone-related diseases, FPPS is the target of FDA-approved nitrogen-containing bisphosphonates (N-BPs), which have tropism mainly for bone tissue due to their poor penetration in soft tissues. The development of inhibitors targeting the FPPS enzyme has garnered significant interest in recent decades due to FPPS's role in the biosynthesis of cholesterol and other isoprenoids, which are implicated in cancer, bone diseases, and other conditions. In this study, we describe a multidisciplinary approach to designing novel FPPS inhibitors, combining computational modeling, biochemical assays, and biophysical techniques. A series of peptides and phosphopeptides were designed, synthesized, and evaluated for their ability to inhibit FPPS activity. Molecular docking was employed to predict the binding modes of these compounds to FPPS, while Surface Plasmon Resonance (SPR) and Nuclear Magnetic Resonance (NMR) spectroscopy experiments - based on Saturation Transfer Difference (STD) and an enzymatic NMR assay - were used to measure their binding affinities and kinetics. The biological activity of the most promising compounds was further assessed in cellular assays using murine colorectal cancer (CRC) cells. Additionally, genomics and metabolomics profiling allowed to unravel the possible mechanisms underlying the activity of the peptides, confirming their involvement in the modulation of the MVA pathway. Our findings demonstrate that the designed peptides and phosphopeptides exhibit significant inhibitory activity against FPPS and possess antiproliferative effects on CRC cells, suggesting their potential as therapeutic agents for cancer.
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Affiliation(s)
- Verdiana Covelli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano, 49, 80131, Naples, Italy.
| | - Michela Buonocore
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy; Department of Chemical Sciences and Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Strada Comunale Cintia, 80126, Naples, Italy.
| | - Manuela Grimaldi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Mario Scrima
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Angelo Santoro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy; Department of Pharmacy, Scuola di Specializzazione in Farmacia Ospedaliera, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Carmen Marino
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Veronica De Simone
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA)-Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Herestraat, 49, 3000, Leuven, Belgium.
| | - Lies van Baarle
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA)-Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Herestraat, 49, 3000, Leuven, Belgium.
| | - Francesca Biscu
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA)-Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Herestraat, 49, 3000, Leuven, Belgium.
| | - Maria Carmina Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Gianluca Matteoli
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA)-Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Herestraat, 49, 3000, Leuven, Belgium.
| | - Anna Maria D'Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Manuela Rodriquez
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano, 49, 80131, Naples, Italy.
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2
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Picard MÈ, Cusson M, Sen SE, Shi R. Rational design of Lepidoptera-specific insecticidal inhibitors targeting farnesyl diphosphate synthase, a key enzyme of the juvenile hormone biosynthetic pathway. JOURNAL OF PESTICIDE SCIENCE 2021; 46:7-15. [PMID: 33746541 PMCID: PMC7953025 DOI: 10.1584/jpestics.d20-078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Reducing the use of broad-spectrum insecticides is one of the many challenges currently faced by insect pest management practitioners. For this reason, efforts are being made to develop environmentally benign pest-control products through bio-rational approaches that aim at disrupting physiological processes unique to specific groups of pests. Perturbation of hormonal regulation of insect development and reproduction is one such strategy. It has long been hypothesized that some enzymes in the juvenile hormone biosynthetic pathway of moths, butterflies and caterpillars (order Lepidoptera) display unique structural features that could be targeted for the development of Lepidoptera-specific insecticides, a promising avenue given the numerous agricultural and forest pests belonging to this order. Farnesyl diphosphate synthase, FPPS, is one such enzyme, with recent work suggesting that it has structural characteristics that may enable its selective inhibition. This review synthesizes current knowledge on FPPS and summarizes recent advances in its use as a target for insecticide development.
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Affiliation(s)
- Marie-Ève Picard
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada
- To whom correspondence should be addressed. E-mail:
| | - Michel Cusson
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Station Ste. Foy, Quebec City, QC, G1V 4C7, Canada
| | - Stephanie E. Sen
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ 08628, USA
| | - Rong Shi
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada
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3
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Lu Z, Peng B, Ebert BE, Dumsday G, Vickers CE. Auxin-mediated protein depletion for metabolic engineering in terpene-producing yeast. Nat Commun 2021; 12:1051. [PMID: 33594068 PMCID: PMC7886869 DOI: 10.1038/s41467-021-21313-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
In metabolic engineering, loss-of-function experiments are used to understand and optimise metabolism. A conditional gene inactivation tool is required when gene deletion is lethal or detrimental to growth. Here, we exploit auxin-inducible protein degradation as a metabolic engineering approach in yeast. We demonstrate its effectiveness using terpenoid production. First, we target an essential prenyl-pyrophosphate metabolism protein, farnesyl pyrophosphate synthase (Erg20p). Degradation successfully redirects metabolic flux toward monoterpene (C10) production. Second, depleting hexokinase-2, a key protein in glucose signalling transduction, lifts glucose repression and boosts production of sesquiterpene (C15) nerolidol to 3.5 g L-1 in flask cultivation. Third, depleting acetyl-CoA carboxylase (Acc1p), another essential protein, delivers growth arrest without diminishing production capacity in nerolidol-producing yeast, providing a strategy to decouple growth and production. These studies demonstrate auxin-mediated protein degradation as an advanced tool for metabolic engineering. It also has potential for broader metabolic perturbation studies to better understand metabolism.
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Affiliation(s)
- Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences (SCMB), the University of Queensland, Brisbane, QLD, Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia.
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia.
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia
| | | | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia.
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia.
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Park J, Pandya VR, Ezekiel SJ, Berghuis AM. Phosphonate and Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthases: A Structure-Guided Perspective. Front Chem 2021; 8:612728. [PMID: 33490038 PMCID: PMC7815940 DOI: 10.3389/fchem.2020.612728] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphonates and bisphosphonates have proven their pharmacological utility as inhibitors of enzymes that metabolize phosphate and pyrophosphate substrates. The blockbuster class of drugs nitrogen-containing bisphosphonates represent one of the best-known examples. Widely used to treat bone-resorption disorders, these drugs work by inhibiting the enzyme farnesyl pyrophosphate synthase. Playing a key role in the isoprenoid biosynthetic pathway, this enzyme is also a potential anticancer target. Here, we provide a comprehensive overview of the research efforts to identify new inhibitors of farnesyl pyrophosphate synthase for various therapeutic applications. While the majority of these efforts have been directed against the human enzyme, some have been targeted on its homologs from other organisms, such as protozoan parasites and insects. Our particular focus is on the structures of the target enzymes and how the structural information has guided the drug discovery efforts.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Vishal R Pandya
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sean J Ezekiel
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
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Cai R, Dong X, Yu K, He X, Liu X, Wang Y. Chemical Proteomic Profiling of the Interacting Proteins of Isoprenoid Pyrophosphates. Anal Chem 2020; 92:8031-8036. [PMID: 32420730 DOI: 10.1021/acs.analchem.0c01676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isoprenoid pyrophosphates are involved in protein prenylation and assume regulatory roles in cells; however, little is known about the cellular proteins that can interact with isoprenoid pyrophosphates. Here, we devised a chemical proteomic strategy, capitalizing on the use of a desthiobiotin-geranyl pyrophosphate (GPP) acyl phosphate probe for the enrichment and subsequent identification of GPP-binding proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS). By combining stable isotope labeling by amino acids in cell culture (SILAC) and competitive labeling with low vs high concentrations of GPP probe, with ATP vs GPP acyl phosphate probes, or with the GPP probe in the presence of different concentrations of free GPP, we uncovered a number of candidate GPP-binding proteins. We also discovered, for the first time, histone deacetylase 1 (HDAC1) as a GPP-binding protein. Furthermore, we found that the enzymatic activity of HDAC1 could be modulated by isoprenoid pyrophosphates. Together, we developed a novel chemical proteomic method for the proteome-wide discovery of GPP-binding proteins, which sets the stage for a better understanding about the biological functions of isoprenoids.
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Affiliation(s)
- Rong Cai
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States.,School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Xuejiao Dong
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Kailin Yu
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Xiaomei He
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Xiaochuan Liu
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
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6
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Grimaldi M, Randino R, Ciaglia E, Scrima M, Buonocore M, Stillitano I, Abate M, Covelli V, Tosco A, Gazzerro P, Bifulco M, Rodriquez M, D'Ursi AM. NMR for screening and a biochemical assay: Identification of new FPPS inhibitors exerting anticancer activity. Bioorg Chem 2019; 98:103449. [PMID: 32057422 DOI: 10.1016/j.bioorg.2019.103449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/01/2019] [Accepted: 11/14/2019] [Indexed: 01/14/2023]
Abstract
Farnesyl pyrophosphate synthase (FPPS) is a crucial enzyme for the synthesis of isoprenoids and the key target of nitrogen-containing bisphosphonates (N-BPs). N-BPs are potent and selective FPPS inhibitors that are used in the treatment of bone-related diseases, but have poor pharmacokinetic properties. Given the key role played by FPPS in many cancer-related pathways and the pharmacokinetic limits of N-BPs, hundreds of molecules have been screened to identify new FPPS inhibitors characterized by improved drug-like properties that are useful for broader therapeutic applications in solid, non-skeletal tumours. We have previously shown that N6-isopentenyladenosine (i6A) and its related compound N6-benzyladenosine (2) exert anti-glioma activity by interfering with the mevalonate pathway and inhibiting FPPS. Here, we report the design and synthesis of a panel of N6-benzyladenosine derivatives (compounds 2a-m) incorporating different chemical moieties on the benzyl ring. Compounds 2a-m show in vitro antiproliferative activity in U87MG glioma cells and, analogous to the bisphosphonate FPPS inhibitors, exhibit immunogenic properties in ex vivo γδ T cells from stimulated peripheral blood mononuclear cells (PBMCs). Using saturation transfer difference (STD) and quantitative 1H nuclear magnetic resonance (NMR) experiments, we found that 2f, the N6-benzyladenosine analogue that includes a tertbutyl moiety in the para position of the benzyl ring, is endowed with increased FPPS binding and inhibition compared to the parent compounds i6A and 2. N6-benzyladenosine derivatives, characterized by structural features that are significantly different from those of N-BPs, have been confirmed to be promising chemical scaffolds for the development of non N-BP FPPS inhibitors, exerting combined cytotoxic and immunostimulatory activities.
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Affiliation(s)
- Manuela Grimaldi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, V.le J.F. Kennedy 54 - Pad. 20 Mostra d'Oltremare, 80125 Naples, Italy
| | - Rosario Randino
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via Salvatore Allende, 84081 Baronissi, Salerno, Italy
| | - Mario Scrima
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Michela Buonocore
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Ilaria Stillitano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Mario Abate
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via Salvatore Allende, 84081 Baronissi, Salerno, Italy
| | - Verdiana Covelli
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Via Pansini, 80131 Naples, Italy; Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via Salvatore Allende, 84081 Baronissi, Salerno, Italy
| | - Manuela Rodriquez
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Anna Maria D'Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
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7
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Waller DD, Park J, Tsantrizos YS. Inhibition of farnesyl pyrophosphate (FPP) and/or geranylgeranyl pyrophosphate (GGPP) biosynthesis and its implication in the treatment of cancers. Crit Rev Biochem Mol Biol 2019; 54:41-60. [DOI: 10.1080/10409238.2019.1568964] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Jaeok Park
- Department of Chemistry, McGill University, Montreal, Canada
- Department of Biochemistry, McGill University, Montreal, Canada
| | - Youla S. Tsantrizos
- Department of Chemistry, McGill University, Montreal, Canada
- Department of Biochemistry, McGill University, Montreal, Canada
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8
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Petrova TE, Boyko KM, Nikolaeva AY, Stekhanova TN, Gruzdev EV, Mardanov AV, Stroilov VS, Littlechild JA, Popov VO, Bezsudnova EY. Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans. Extremophiles 2018; 22:877-888. [PMID: 30062607 DOI: 10.1007/s00792-018-1044-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 07/20/2018] [Indexed: 01/23/2023]
Abstract
A novel type 1 geranylgeranyl pyrophosphate synthase GACE1337 has been identified within the genome of a newly identified hyperthermophilic archaeon Geoglobus acetivorans. The enzyme has been cloned and over-expressed in Escherichia coli. The recombinant enzyme has been biochemically and structurally characterized. It is able to catalyze the synthesis of geranylgeranyl pyrophosphate as a major product and of farnesyl pyrophosphate in smaller amounts, as measured by gas chromatography-mass spectrometry at an elevated temperature of 60 °C. Its ability to produce two products is consistent with the fact that GACE1337 is the only short-chain isoprenyl diphosphate synthase in G. acetivorans. Attempts to crystallize the enzyme were successful only at 37 °C. The three-dimensional structure of GACE1337 was determined by X-ray diffraction to 2.5 Å resolution. A comparison of its structure with those of related enzymes revealed that the Geoglobus enzyme has the features of both type I and type III geranylgeranyl pyrophosphate synthases, which allow it to regulate the product length. The active enzyme is a dimer and has three aromatic amino acids, two Phe, and a Tyr, located in the hydrophobic cleft between the two subunits. It is proposed that these bulky residues play a major role in the synthetic reaction by controlling the product elongation.
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Affiliation(s)
- Tatiana E Petrova
- Institute of Mathematical Problems of Biology, RAS, Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, Professor Vitkevich St., Pushchino, 142290, Russian Federation.
| | - Konstantin M Boyko
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation.,NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr, 1, Moscow, 123182, Russian Federation
| | - Alena Yu Nikolaeva
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Tatiana N Stekhanova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Eugeny V Gruzdev
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Andrey V Mardanov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
| | - Viktor S Stroilov
- N. D. Zelinsky Institute of Organic Chemistry (ZIOC RAS), Leninsky Prospekt, 47, Moscow, 119991, Russian Federation
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Vladimir O Popov
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation.,NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr, 1, Moscow, 123182, Russian Federation
| | - Ekaterina Yu Bezsudnova
- Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation
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9
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Picard MÈ, Nisole A, Béliveau C, Sen S, Barbar A, Shi R, Cusson M. Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 92:84-92. [PMID: 29183817 DOI: 10.1016/j.ibmb.2017.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) is an enzyme from the class of short chain (E)-prenyltransferases that catalyzes the condensation of two molecules of isopentenyl diphosphate (IPP, C5) with dimethylallyl diphosphate (DMAPP, C5) to generate the C15 product FPP. In insects, FPPS plays a key role in the biosynthesis of the morphogenetic and gonadotropic "juvenile hormone" (JH). Lepidopteran genomes encode two very distinct FPPS paralogs, one of which ("type-II") is expressed almost exclusively in the JH-producing glands, the corpora allata. This paralog has been hypothesized to display structural features that enable the binding of the bulkier precursors required for the biosynthesis of lepidopteran ethyl-branched JHs. Here, we report on the first crystal structures of an insect FPPS solved to date. Apo, ligand-bound, and inhibitor-bound structures of type-II FPPS (FPPS2) from the spruce budworm, Choristoneura fumiferana (Order: Lepidoptera), were obtained. Comparison of apo and inhibitor-bound enzymes revealed differences in both inhibitor binding and structural plasticity of CfFPPS2 compared to other FPPSs. Our data showed that IPP is not essential to the closure of the C-terminal tail. Ortho-substituted pyridinium bisphosphonates, previously shown to inhibit CfFPPS2, bound to the allylic site, as predicted; however, their alkyl groups were oriented towards the homoallylic binding site, with the bulkier propyl-substituted inhibitor penetrating deeply into the IPP binding pocket. The current study sheds light on the structural basis of substrate specificity of type-II FPPS of the spruce budworm. Through a comparison with other inhibitor-bound FPPSs, we propose several approaches to improve inhibitor selectivity and potency.
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Affiliation(s)
- Marie-Ève Picard
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Audrey Nisole
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Catherine Béliveau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Stephanie Sen
- Department of Chemistry, The College of New Jersey, P.O. Box 7718, Ewing, NJ, 08628, USA.
| | - Aline Barbar
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
| | - Rong Shi
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Michel Cusson
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, PROTEO, Université Laval, Quebec City, QC, G1V 0A6, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., C.P. 10380, Station Sainte-Foy, Quebec City, QC, G1V 4C7, Canada.
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10
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Park J, Rodionov D, De Schutter JW, Lin YS, Tsantrizos YS, Berghuis AM. Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. PLoS One 2017; 12:e0186447. [PMID: 29036218 PMCID: PMC5643135 DOI: 10.1371/journal.pone.0186447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/02/2017] [Indexed: 11/18/2022] Open
Abstract
Human farnesyl pyrophosphate synthase (hFPPS) catalyzes the production of the 15-carbon isoprenoid farnesyl pyrophosphate. The enzyme is a key regulator of the mevalonate pathway and a well-established drug target. Notably, it was elucidated as the molecular target of nitrogen-containing bisphosphonates, a class of drugs that have been widely successful against bone resorption disorders. More recently, research has focused on the anticancer effects of these inhibitors. In order to achieve increased non-skeletal tissue exposure, we created phenylaminopyridine bisphosphonates (PNP-BPs) that have bulky hydrophobic side chains through a structure-based approach. Some of these compounds have proven to be more potent than the current clinical drugs in a number of antiproliferation assays using multiple myeloma cell lines. In the present work, we characterized the binding of our most potent PNP-BPs to the target enzyme, hFPPS. Co-crystal structures demonstrate that the molecular interactions designed to elicit tighter binding are indeed established. We carried out thermodynamic studies as well; the newly introduced protein-ligand interactions are clearly reflected in the enthalpy of binding measured, which is more favorable for the new PNP-BPs than for the lead compound. These studies also indicate that the affinity of the PNP-BPs to hFPPS is comparable to that of the current drug risedronate. Risedronate forms additional polar interactions via its hydroxyl functional group and thus exhibits more favorable binding enthalpy; however, the entropy of binding is more favorable for the PNP-BPs, owing to the greater desolvation effects resulting from their large hydrophobic side chains. These results therefore confirm the overall validity of our drug design strategy. With a distinctly different molecular scaffold, the PNP-BPs described in this report represent an interesting new group of future drug candidates. Further investigation should follow to characterize the tissue distribution profile and assess the potential clinical benefits of these compounds.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Dmitry Rodionov
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | - Yih-Shyan Lin
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Youla S. Tsantrizos
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- * E-mail:
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11
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New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs. J Comput Aided Mol Des 2017. [PMID: 28631130 DOI: 10.1007/s10822-017-0034-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Pamidronate, alendronate, APHBP and neridronate are a group of drugs, known as second-generation bisphosphonates (2G-BPs), commonly used in the treatment of bone-resorption disorders, and recently their use has been related to some collateral side effects. The therapeutic activity of 2G-BPs is related to the inhibition of the human Farnesyl Pyrophosphate Synthase (hFPPS). Available inhibitory activity values show that 2G-BPs act time-dependently, showing big differences in their initial inhibitory activities but similar final IC50 values. However, there is a lack of information explaining this similar final inhibitory potency. Although different residues have been identified in the stabilization of the R2 side chain of 2G-BPs into the active site, similar free binding energies were obtained that highlighted a similar stability of the ternary complexes, which in turns justified the similar IC50 values reported. Free binding energy calculations also demonstrated that the union of 2G-BPs to the active site were 38 to 54 kcal mol-1 energetically more favourable than the union of the natural substrate, which is the basis of the inhibition potency of the hFPPS activity.
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12
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Park J, Zielinski M, Magder A, Tsantrizos YS, Berghuis AM. Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product. Nat Commun 2017; 8:14132. [PMID: 28098152 PMCID: PMC5253651 DOI: 10.1038/ncomms14132] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/02/2016] [Indexed: 12/13/2022] Open
Abstract
Farnesyl pyrophosphate synthase (FPPS) is an enzyme of the mevalonate pathway and a well-established therapeutic target. Recent research has focused around a newly identified druggable pocket near the enzyme's active site. Pharmacological exploitation of this pocket is deemed promising; however, its natural biological function, if any, is yet unknown. Here we report that the product of FPPS, farnesyl pyrophosphate (FPP), can bind to this pocket and lock the enzyme in an inactive state. The Kd for this binding is 5–6 μM, within a catalytically relevant range. These results indicate that FPPS activity is sensitive to the product concentration. Kinetic analysis shows that the enzyme is inhibited through FPP accumulation. Having a specific physiological effector, FPPS is a bona fide allosteric enzyme. This allostery offers an exquisite mechanism for controlling prenyl pyrophosphate levels in vivo and thus contributes an additional layer of regulation to the mevalonate pathway. Farnesyl pyrophosphate (FPP) is a key building block for the synthesis of many lipids. Here the authors determine the crystal structure of farnesyl pyrophosphate synthase (FPPS) with its bound product and use kinetic measurements to show that FPP is an allosteric effector of the enzyme.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
| | - Michal Zielinski
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
| | - Alexandr Magder
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
| | - Youla S Tsantrizos
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1.,Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
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13
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G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA. Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Biochemistry 2016; 55:5180-90. [PMID: 27564465 DOI: 10.1021/acs.biochem.6b00398] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a molecular dynamics investigation of the structure, function, and inhibition of geranylgeranyl diphosphate synthase (GGPPS), a potential drug target, from the malaria parasite Plasmodium vivax. We discovered several GGPPS inhibitors, benzoic acids, and determined their structures crystallographically. We then used molecular dynamics simulations to investigate the dynamics of three such inhibitors and two bisphosphonate inhibitors, zoledronate and a lipophilic analogue of zoledronate, as well as the enzyme's product, GGPP. We were able to identify the main motions that govern substrate binding and product release as well as the molecular features required for GGPPS inhibition by both classes of inhibitor. The results are of broad general interest because they represent the first detailed investigation of the mechanism of action, and inhibition, of an important antimalarial drug target, geranylgeranyl diphosphate synthase, and may help guide the development of other, novel inhibitors as new drug leads.
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Affiliation(s)
- Clarisse G Ricci
- Department of Pharmacology and Department of Chemistry & Biochemistry, University of California at San Diego , La Jolla, California 92093, United States.,Howard Hughes Medical Institute, University of California at San Diego , La Jolla, California 92093, United States.,National Biomedical Computation Resource, University of California at San Diego , La Jolla, California 92093, United States
| | - Yi-Liang Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yonghui Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yang Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wei Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - J Andrew McCammon
- Department of Pharmacology and Department of Chemistry & Biochemistry, University of California at San Diego , La Jolla, California 92093, United States.,Howard Hughes Medical Institute, University of California at San Diego , La Jolla, California 92093, United States.,National Biomedical Computation Resource, University of California at San Diego , La Jolla, California 92093, United States
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14
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Abstract
Background:
Bisphosphonates are drugs commonly used for the medication and prevention of diseases caused by decreased mineral density. Despite such important medicinal use, they display a variety of physiologic activities, which make them promising anti-cancer, anti-protozoal, antibacterial and antiviral agents.
Objective:
To review physiological activity of bisphosphonates with special emphasis on their ongoing and potential applications in medicine and agriculture.
Method:
Critical review of recent literature data.
Results:
Comprehensive review of activities revealed by bisphosphonates.
Conclusion:
although bisphosphonates are mostly recognized by their profound effects on bone physiology their medicinal potential has not been fully evaluated yet. Literature data considering enzyme inhibition suggest possibilities of far more wide application of these compounds. These applications are, however, limited by their low bioavailability and therefore intensive search for new chemical entities overcoming this shortage are carried out.
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15
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Rodriguez JB, Falcone BN, Szajnman SH. Approaches for Designing new Potent Inhibitors of Farnesyl Pyrophosphate Synthase. Expert Opin Drug Discov 2016; 11:307-20. [DOI: 10.1517/17460441.2016.1143814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Sharifirad A, Mohammadian S, Yakhchali B, Mehrpooyan S, Fatemi SSA. Characterization of a farnesyl diphosphate synthase gene from Penicillium brevicompactum MUCL 19011. Biotechnol Lett 2015; 38:71-9. [PMID: 26334936 DOI: 10.1007/s10529-015-1943-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/18/2015] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Farnesyl diphosphate synthase is a critical enzyme in the isoprenoids biosynthesis pathway responsible for ergosterol and secondary metabolites biosynthesis in fungi. RESULTS Characterization of fds from Penicillium brevicompactum (Pbfds) was performed using TAIL-PCR and RT-PCR followed by complementation tests in Saccharomyces cerevisiae and determination of its expression profile by semi-quantitative RT-PCR. Promoter analysis suggests some binding sites for transcription factors some of which are involved in fungal growth and response to environmental stress. The Pbfds ORF encodes a cytosolic 39.7 kDa protein with a high conservation among Eurotiomycetes and the highest identity (96 %) with Pen. chrysogenum. Homology-based structural modeling suggests that the PbFDS is formed by the arrangement of 15 core helices around a large central cavity where the catalytic reaction takes place. Superimposition of the predicted 3D structure of the enzyme on its ortholog in human reveals the same folding pattern in the counterparts. CONCLUSION The Pbfds expression may be stimulated in response to the environmental stresses and fungal growth and encodes the PBFDS--a cytosolic enzyme which with a key role in ergosterol and secondary metabolites biosynthesis.
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Affiliation(s)
- Atefeh Sharifirad
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Somayeh Mohammadian
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Bagher Yakhchali
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Sina Mehrpooyan
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Seyed Safa-ali Fatemi
- Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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17
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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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18
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Gelat F, Lacomme C, Berger O, Gavara L, Montchamp JL. Synthesis of (phosphonomethyl)phosphinate pyrophosphate analogues via the phospha-Claisen condensation. Org Biomol Chem 2015; 13:825-33. [DOI: 10.1039/c4ob02007c] [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
Pyrophosphate analogues are of great importance especially for the design of biologically active molecules.
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Affiliation(s)
- Fabien Gelat
- Department of Chemistry
- Box 298860
- Texas Christian University
- Texas 76133
- USA
| | - Claire Lacomme
- Department of Chemistry
- Box 298860
- Texas Christian University
- Texas 76133
- USA
| | - Olivier Berger
- Department of Chemistry
- Box 298860
- Texas Christian University
- Texas 76133
- USA
| | - Laurent Gavara
- Department of Chemistry
- Box 298860
- Texas Christian University
- Texas 76133
- USA
| | - J.-L. Montchamp
- Department of Chemistry
- Box 298860
- Texas Christian University
- Texas 76133
- USA
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19
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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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20
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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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21
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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: 40] [Impact Index Per Article: 3.6] [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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22
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Simeonov A. Recent developments in the use of differential scanning fluorometry in protein and small molecule discovery and characterization. Expert Opin Drug Discov 2013; 8:1071-82. [PMID: 23738712 DOI: 10.1517/17460441.2013.806479] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Despite tremendous advances in the application of biophysical methods in drug discovery, the preponderance of instruments and techniques still require sophisticated analyses by dedicated personnel and/or large amounts of frequently hard-to-produce proteins. A technique which carries the promise of simplicity and relatively low protein consumption is the differential scanning fluorometry (DSF). This technique monitors protein through the use of environmentally sensitive fluorescent dye, in a temperature-ramp regime by observing the gradual exposure to the solvent of otherwise buried hydrophobic faces of protein domains. AREAS COVERED This review describes recent developments in the field of DSF. This article pays a particular emphasis on the advances published during the 2010 - 2013 period. EXPERT OPINION There has been a significant diversification of DSF applications beyond initial small molecule discovery into areas such as protein therapeutic development, formulation studies and various mechanistic investigations. This serves as a further indication of the broad penetration of the technique. In the small molecule arena, DSF has expanded toward sophisticated co-dependency MOA tests, demonstrating the wealth of information which the technique can provide. Importantly, the first public deposition of a large screening dataset may enable the use of thermal stabilization data in refining in silico models for small molecule binding.
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Affiliation(s)
- Anton Simeonov
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Discovery Innovation, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
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