1
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Li FR, Wang Q, Pan X, Xu HM, Dong LB. Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase. Angew Chem Int Ed Engl 2024; 63:e202401669. [PMID: 38651244 DOI: 10.1002/anie.202401669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.
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Affiliation(s)
- Fang-Ru Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Qingling Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui-Min Xu
- The Public Laboratory Platform, China Pharmaceutical University, Nanjing, 211198, China
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
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2
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Gaona-López C, Méndez-Álvarez D, Moreno-Rodríguez A, Bautista-Martínez JL, De Fuentes-Vicente JA, Nogueda-Torres B, García-Torres I, López-Velázquez G, Rivera G. TATA-Binding Protein-Based Virtual Screening of FDA Drugs Identified New Anti-Giardiasis Agents. Int J Mol Sci 2024; 25:6238. [PMID: 38892424 PMCID: PMC11172525 DOI: 10.3390/ijms25116238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Parasitic diseases, predominantly prevalent in developing countries, are increasingly spreading to high-income nations due to shifting migration patterns. The World Health Organization (WHO) estimates approximately 300 million annual cases of giardiasis. The emergence of drug resistance and associated side effects necessitates urgent research to address this growing health concern. In this study, we evaluated over eleven thousand pharmacological compounds sourced from the FDA database to assess their impact on the TATA-binding protein (TBP) of the early diverging protist Giardia lamblia, which holds medical significance. We identified a selection of potential pharmacological compounds for combating this parasitic disease through in silico analysis, employing molecular modeling techniques such as homology modeling, molecular docking, and molecular dynamics simulations. Notably, our findings highlight compounds DB07352 and DB08399 as promising candidates for inhibiting the TBP of Giardia lamblia. Also, these compounds and DB15584 demonstrated high efficacy against trophozoites in vitro. In summary, this study identifies compounds with the potential to combat giardiasis, offering the prospect of specific therapies and providing a robust foundation for future research.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico;
| | - Domingo Méndez-Álvarez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico;
| | - Adriana Moreno-Rodríguez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (A.M.-R.); (J.L.B.-M.)
| | - Juan Luis Bautista-Martínez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma “Benito Juárez” de Oaxaca, Oaxaca 68120, Mexico; (A.M.-R.); (J.L.B.-M.)
| | | | - Benjamín Nogueda-Torres
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Itzhel García-Torres
- Laboratorio de Biomoléculas y Salud Infantil, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (I.G.-T.); (G.L.-V.)
| | - Gabriel López-Velázquez
- Laboratorio de Biomoléculas y Salud Infantil, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (I.G.-T.); (G.L.-V.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico;
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3
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Juteršek M, Gerasymenko IM, Petek M, Haumann E, Vacas S, Kallam K, Gianoglio S, Navarro-Llopis V, Heethoff M, Fuertes IN, Patron N, Orzáez D, Gruden K, Warzecha H, Baebler Š. Transcriptome-informed identification and characterization of Planococcus citri cis- and trans-isoprenyl diphosphate synthase genes. iScience 2024; 27:109441. [PMID: 38523795 PMCID: PMC10960109 DOI: 10.1016/j.isci.2024.109441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/13/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS coding sequences of the pest mealybug Planococcus citri. We queried the available genomic and newly generated short- and long-read P. citri transcriptomic data and identified 18 putative IDS genes, whose phylogenetic analysis indicates several gene family expansion events. In vitro testing confirmed regular short-chain coupling activity with five gene products. With the candidate with highest IDS activity, we also detected low amounts of irregular coupling products, and determined amino acid residues important for chain-length preference and irregular coupling activity. This work therefore provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, including the sex pheromone biosynthesis in P. citri.
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Affiliation(s)
- Mojca Juteršek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Iryna M. Gerasymenko
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Marko Petek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Elisabeth Haumann
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Sandra Vacas
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Vicente Navarro-Llopis
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Michael Heethoff
- Animal Evolutionary Ecology, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | | | - Nicola Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Diego Orzáez
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Špela Baebler
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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4
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Katsavou E, Sarafoglou C, Balabanidou V, Skoufa E, Nauen R, Linka M, Geibel S, Denecke S, Vontas J. Characterisation of lepidopteran geranylgeranyl diphosphate synthase as a putative pesticide target. INSECT MOLECULAR BIOLOGY 2024; 33:147-156. [PMID: 37962063 DOI: 10.1111/imb.12885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023]
Abstract
Geranylgeranyl pyrophosphate (diphosphate) synthase (GGPPS) plays an important role in various physiological processes in insects, such as isoprenoid biosynthesis and protein prenylation. Here, we functionally characterised the GGPPS from the major agricultural lepidopteran pests Spodoptera frugiperda and Helicoverpa armigera. Partial disruption of GGPPS by CRISPR in S. frugiperda decreased embryo hatching rate and larval survival, suggesting that this gene is essential. Functional expression in vitro of Helicoverpa armigera GGPPS in Escherichia coli revealed a catalytically active enzyme. Next, we developed and optimised an enzyme assay to screen for potential inhibitors, such as the zoledronate and the minodronate, which showed a dose-dependent inhibition. Phylogenetic analysis of GGPPS across insects showed that GGPPS is highly conserved but also revealed several residues likely to be involved in substrate binding, which were substantially different in bee pollinator and human GGPPS. Considering the essentiality of GGPPS and its putative binding residue variability qualifies a GGPPS as a novel pesticide target. The developed assay may contribute to the identification of novel insecticide leads.
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Affiliation(s)
- Evangelia Katsavou
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Chara Sarafoglou
- Department of Biology, University of Crete, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Vasileia Balabanidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Evangelia Skoufa
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Ralf Nauen
- R&D Pest Control, Crop Science Division, Bayer AG, Monheim am Rhein, Germany
| | - Marc Linka
- R&D Pest Control, Crop Science Division, Bayer AG, Monheim am Rhein, Germany
| | - Sven Geibel
- R&D Pest Control, Crop Science Division, Bayer AG, Monheim am Rhein, Germany
| | - Shane Denecke
- Department of Biology, University of Crete, Crete, Greece
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John Vontas
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, Greece
- Department of Biology, University of Crete, Crete, Greece
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5
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Pham AC, Holstein SA, Borgstahl GE. Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy. Mol Cancer Ther 2024; 23:14-23. [PMID: 37756579 PMCID: PMC10762340 DOI: 10.1158/1535-7163.mct-23-0358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Geranylgeranyl diphosphate synthase (GGDPS), the source of the isoprenoid donor in protein geranylgeranylation reactions, has become an attractive target for anticancer therapy due to the reliance of cancers on geranylgeranylated proteins. Current GGDPS inhibitor development focuses on optimizing the drug-target enzyme interactions of nitrogen-containing bisphosphonate-based drugs. To advance GGDPS inhibitor development, understanding the enzyme structure, active site, and ligand/product interactions is essential. Here we provide a comprehensive structure-focused review of GGDPS. We reviewed available yeast and human GGDPS structures and then used AlphaFold modeling to complete unsolved structural aspects of these models. We delineate the elements of higher-order structure formation, product-substrate binding, the electrostatic surface, and small-molecule inhibitor binding. With the rise of structure-based drug design, the information provided here will serve as a valuable tool for rationally optimizing inhibitor selectivity and effectiveness.
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Affiliation(s)
- Andrew C. Pham
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sarah A. Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gloria E.O. Borgstahl
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
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6
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Wafa SSAE, El-Ashmawy AA, Kassem HAH, Eissa IH, Abu-Elghait M, Younis NA, Younis IY. Optimization of oil yield of Pelargonium graveolens L'Hér using Box-Behnken design in relation to its antimicrobial activity and in silico study. Sci Rep 2023; 13:19887. [PMID: 37963988 PMCID: PMC10645939 DOI: 10.1038/s41598-023-47170-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Pelargonium graveolens L'Hér is an important species of genus Pelargonium with an economic value. The unique rose scent of its oil is used in perfume and cosmetic industry. The oil is characterized by the presence of citronellol, geraniol and rose oxide. Fresh aerial parts of P. graveolens at GC-MS analysis of four seasons revealed that autumn constituted the highest yield of the oil. For the first time, optimization of the yield of extracted oil of P. graveolens was performed employing 3-level Box-Behnken design using 3-factors. The GC-MS analysis of the essential oil was performed for the 17-runs. The optimized extraction of the oil was performed employing numerical optimization and studied for antimicrobial, Minimum Inhibitory Concentration (MIC) and biofilm inhibitory activities. The 3 factors followed rank (plant material amount > water volume > NaCl percent in water), in their magnitude of effect on increasing yield of the oil. Increasing the plant material amount increased the yield of the oil by 6-folds compared to NaCl percent in water. The optimized yield of oil (4 ml) was obtained from extraction criteria (150 g of plant, 750 ml of water and 3.585% (26.85 g) of NaCl). Computational docking was performed to overcome the multi-drug resistant Gram-negative bacilli targeting undecaprenyl pyrophosphate synthase (UPPS). The optimized oil exhibited a promising inhibitory activity against Gram-negative bacteria (K. pneumonia and P. aeruginosa) with significant antibiofilm action (P < 0.05). Moreover, it exerted a synergistic effect when combined with various antibiotics (Cefoxitin, Cloxacillin, Oxacillin and Vancomycin) against MRSA clinical strains.
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Affiliation(s)
| | - Ahmed A El-Ashmawy
- Medicinal and Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, 12622, Egypt
| | - Hanaa A H Kassem
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Mohammed Abu-Elghait
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Nermin A Younis
- Pharmacognosy Department, Faculty of Pharmacy, Ahram Canadian University, Giza, 12451, Egypt
| | - Inas Y Younis
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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7
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Gulia K, Hassan AHE, Lenhard JR, Farahat AA. Escaping ESKAPE resistance: in vitro and in silico studies of multifunctional carbamimidoyl-tethered indoles against antibiotic-resistant bacteria. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230020. [PMID: 37090961 PMCID: PMC10113819 DOI: 10.1098/rsos.230020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Combining the hybridization and repurposing strategies, six compounds from our in-house library and having a designed hybrid structure of MBX-1162, pentamidine and MMV688271 were repurposed as potential antibacterial agents. Among, compounds 1a and 1d elicited potential sub-µg ml-1 activity against the high-priority antibiotic-resistant Gram-positive members of ESKAPE bacteria as well as antibiotic-susceptible Gram-positive bacteria. Furthermore, they showed potential low µg ml-1 activity against the explored critical-priority antibiotic-resistant Gram-negative members of ESKAPE bacteria. In time-kill assay, compound 1a has effective 0.5 and 0.25 µg ml-1 antibacterial lethal concentrations against MRSA in exponential growth phase. In silico investigations predicted compounds 1a and 1d as inhibitors of the open conformation of undecaprenyl diphosphate synthase involved in bacterial isoprenoid synthesis. In addition, compounds 1a and 1d were predicted as inhibitors of NADPH-free but not NADPH-bound form of ketol-acid reductoisomerase and may also serve as potential B-DNA minor groove binders with possible differences in the molecular sequence recognition. Overall, compounds 1a and 1d are presented as multifunctional potential antibacterial agents for further development against high- and critical-priority Gram-positive and Gram-negative antibiotic-resistant ESKAPE bacterial pathogens as well as antibiotic-susceptible Gram-positive bacterial pathogens.
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Affiliation(s)
- Kanika Gulia
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- College of Medicine, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Ahmed H. E. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Justin R. Lenhard
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Abdelbasset A. Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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8
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Muehlebach ME, Holstein SA. Geranylgeranyl diphosphate synthase: Role in human health, disease and potential therapeutic target. Clin Transl Med 2023; 13:e1167. [PMID: 36650113 PMCID: PMC9845123 DOI: 10.1002/ctm2.1167] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
Geranylgeranyl diphosphate synthase (GGDPS), an enzyme in the isoprenoid biosynthesis pathway, is responsible for the production of geranylgeranyl pyrophosphate (GGPP). GGPP serves as a substrate for the post-translational modification (geranylgeranylation) of proteins, including those belonging to the Ras superfamily of small GTPases. These proteins play key roles in signalling pathways, cytoskeletal regulation and intracellular transport, and in the absence of the prenylation modification, cannot properly localise and function. Aberrant expression of GGDPS has been implicated in various human pathologies, including liver disease, type 2 diabetes, pulmonary disease and malignancy. Thus, this enzyme is of particular interest from a therapeutic perspective. Here, we review the physiological function of GGDPS as well as its role in pathophysiological processes. We discuss the current GGDPS inhibitors under development and the therapeutic implications of targeting this enzyme.
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Affiliation(s)
- Molly E. Muehlebach
- Cancer Research Doctoral ProgramUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Sarah A. Holstein
- Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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9
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Lanzi M, Rogge T, Truong TS, Houk KN, Wencel-Delord J. Cyclic Diaryl λ 3-Chloranes: Reagents and Their C-C and C-O Couplings with Phenols via Aryne Intermediates. J Am Chem Soc 2022; 145:345-358. [PMID: 36535642 PMCID: PMC9837845 DOI: 10.1021/jacs.2c10090] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hypervalent chloranes are a class of rare and poorly explored reagents. Their unique electronic properties confer reactivity that is complementary to that of the common iodanes and emerging bromanes. Highly chemo- and regioselective, metal-free, and mild C-C and C-O couplings are reported here. Experimental and computational mechanistic studies elucidate the unprecedented reactivities and selectivities of these systems and the intermediacy of aryne intermediates. The synthetic potential of these transformations is further demonstrated via the post-functionalization of C-C and C-O coupling products obtained from reactions of chloranes with phenols under different conditions.
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Affiliation(s)
- Matteo Lanzi
- Laboratoire
d’Innovation Moléculaire et Applications (UMR CNRS 7042),
Université de Strasbourg/Université de Haute Alsace,
ECPM, 67087Strasbourg, France
| | - Torben Rogge
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States
| | - Tan Sang Truong
- Laboratoire
d’Innovation Moléculaire et Applications (UMR CNRS 7042),
Université de Strasbourg/Université de Haute Alsace,
ECPM, 67087Strasbourg, France
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California90095, United States,
| | - Joanna Wencel-Delord
- Laboratoire
d’Innovation Moléculaire et Applications (UMR CNRS 7042),
Université de Strasbourg/Université de Haute Alsace,
ECPM, 67087Strasbourg, France,
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10
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Li M, Chen Y, Wang L, Lu C, Chen P, Jin Y, Li J, Gao F, Shang Z, Lin W. Investigations into the antibacterial effects and potential mechanism of gambogic acid and neogambogic acid. Front Microbiol 2022; 13:1045291. [PMID: 36578570 PMCID: PMC9791066 DOI: 10.3389/fmicb.2022.1045291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
The growing threat of antibiotic-resistant bacterial infections to public health necessitates the development of novel antibacterial agents. Inhibiting bacterial cell wall synthesis has remained a key focus for antibiotic development. Our search for inhibitors of undecaprenyl diphosphate synthase (UPPS), an essential enzyme required for bacterial cell wall formation, revealed that two primary components of gamboge, gambogic acid (GA) and neogambogic acid (NGA), significantly inhibited the activity of Enterococcus faecalis UPPS (EfaUPPS) with the half maximal inhibitory concentrations (IC50) of 3.08 μM and 3.07 μM, respectively. In the in vitro antibacterial assay, both GA and NGA also exhibited inhibitory activities against E. faecalis with the minimal inhibitory concentrations (MICs) of 2 μg/mL. Using microscale thermophoresis, molecular docking, and enzymatic assays, we further confirmed that GA and NGA occupy the substrate binding pocket of EfaUPPS with micro-molar binding affinity, preventing the natural substrates farnesyl diphosphate (FPP) from entering. Mutagenesis analysis revealed that L91 and L146 are two key residues in the binding between GA/NGA and UPPS. Furthermore, we also demonstrated that GA and NGA can improve E. faecalis-induced undesirable inflammation in a mouse infection model. Taken together, our findings provide a basis for structural optimization of GA/NGA to develop improved antibiotic leads and enhance treatment success rates in clinical practice.
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Affiliation(s)
- Mingzhu Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China,Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China,*Correspondence: Yuan Chen,
| | - Lijuan Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chujie Lu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China,School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peiying Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanling Jin
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiacong Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fei Gao
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- School of Pharmaeutical Sciences, Shandong University, Jinan, China,Zhuo Shang,
| | - Wei Lin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China,Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Nanjing, China,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Nanjing, China,Wei Lin,
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11
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Arnesen JA, Borodina I. Engineering of Yarrowia lipolytica for terpenoid production. Metab Eng Commun 2022; 15:e00213. [PMID: 36387772 PMCID: PMC9663531 DOI: 10.1016/j.mec.2022.e00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/31/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Terpenoids are a group of chemicals of great importance for human health and prosperity. Terpenoids can be used for human and animal nutrition, treating diseases, enhancing agricultural output, biofuels, fragrances, cosmetics, and flavouring. However, due to the rapid depletion of global natural resources and manufacturing practices relying on unsustainable petrochemical synthesis, there is a need for economic alternatives to supply the world's demand for these essential chemicals. Microbial biosynthesis offers the means to develop scalable and sustainable bioprocesses for terpenoid production. In particular, the non-conventional yeast Yarrowia lipolytica demonstrates excellent potential as a chassis for terpenoid production due to its amenability to industrial production scale-up, genetic engineering, and high accumulation of terpenoid precursors. This review aims to illustrate the scientific progress in developing Y. lipolytica terpenoid cell factories, focusing on metabolic engineering approaches for strain improvement and cultivation optimization.
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Affiliation(s)
- Jonathan Asmund Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
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12
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Satta A, Esquirol L, Ebert BE, Newman J, Peat TS, Plan M, Schenk G, Vickers CE. Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase. FEBS J 2022; 289:6672-6693. [PMID: 35704353 PMCID: PMC9796789 DOI: 10.1111/febs.16556] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/03/2022] [Accepted: 06/14/2022] [Indexed: 01/07/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes with strong potential to be used for industrial terpenoid production. However, the key enzymes forming the principal terpenoid building blocks, called short-chain prenyltransferases (SPTs), are insufficiently characterized. Here, we examined SPTs in the model cyanobacteria Synechococcus elongatus sp. PCC 7942 and Synechocystis sp. PCC 6803. Each species has a single putative SPT (SeCrtE and SyCrtE, respectively). Sequence analysis identified these as type-II geranylgeranyl pyrophosphate synthases (GGPPSs) with high homology to GGPPSs found in the plastids of green plants and other photosynthetic organisms. In vitro analysis demonstrated that SyCrtE is multifunctional, producing geranylgeranyl pyrophosphate (GGPP; C20 ) primarily but also significant amounts of farnesyl pyrophosphate (FPP, C15 ) and geranyl pyrophosphate (GPP, C10 ); whereas SeCrtE appears to produce only GGPP. The crystal structures were solved to 2.02 and 1.37 Å, respectively, and the superposition of the structures against the GGPPS of Synechococcus elongatus sp. PCC 7002 yield a root mean square deviation of 0.8 Å (SeCrtE) and 1.1 Å (SyCrtE). We also discovered that SeCrtE is co-encoded in an operon with a functional GGPP phosphatase, suggesting metabolic pairing of these two activities and a putative function in tocopherol biosynthesis. This work sheds light on the activity of SPTs and terpenoid synthesis in cyanobacteria. Understanding native prenyl phosphate metabolism is an important step in developing approaches to engineering the production of different chain-length terpenoids in cyanobacteria.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Janet Newman
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Thomas S. Peat
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Manuel Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaAustralia,Sustainable Minerals InstituteThe University of QueenslandSt. LuciaAustralia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia,Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia,ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneAustralia
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13
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Rosconi F, Rudmann E, Li J, Surujon D, Anthony J, Frank M, Jones DS, Rock C, Rosch JW, Johnston CD, van Opijnen T. A bacterial pan-genome makes gene essentiality strain-dependent and evolvable. Nat Microbiol 2022; 7:1580-1592. [PMID: 36097170 PMCID: PMC9519441 DOI: 10.1038/s41564-022-01208-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Transposon insertion sequencing (Tn-seq), whole-genome sequencing and RNA-seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species' pan-genome, we identify a species-wide 'essentialome' that can be subdivided into universal, core strain-specific and accessory essential genes. By employing 'forced-evolution experiments', we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms, we show that gene essentiality can be highly influenced by and/or be dependent on: (1) the composition of the accessory genome, (2) the accumulation of toxic intermediates, (3) functional redundancy, (4) efficient recycling of critical metabolites and (5) pathway rewiring. While this functional characterization underscores the evolvability potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.
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Affiliation(s)
| | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jien Li
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Matthew Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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14
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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15
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Houston DR, Hanna JG, Lathe JC, Hillier SG, Lathe R. Evidence that nuclear receptors are related to terpene synthases. J Mol Endocrinol 2022; 68:153-166. [PMID: 35112668 PMCID: PMC8942334 DOI: 10.1530/jme-21-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/08/2022]
Abstract
Ligand-activated nuclear receptors (NRs) orchestrate development, growth, and reproduction across all animal lifeforms - the Metazoa - but how NRs evolved remains mysterious. Given the NR ligands including steroids and retinoids are predominantly terpenoids, we asked whether NRs might have evolved from enzymes that catalyze terpene synthesis and metabolism. We provide evidence suggesting that NRs may be related to the terpene synthase (TS) enzyme superfamily. Based on over 10,000 3D structural comparisons, we report that the NR ligand-binding domain and TS enzymes share a conserved core of seven α-helical segments. In addition, the 3D locations of the major ligand-contacting residues are also conserved between the two protein classes. Primary sequence comparisons reveal suggestive similarities specifically between NRs and the subfamily of cis-isoprene transferases, notably with dehydrodolichyl pyrophosphate synthase and its obligate partner, NUS1/NOGOB receptor. Pharmacological overlaps between NRs and TS enzymes add weight to the contention that they share a distant evolutionary origin, and the combined data raise the possibility that a ligand-gated receptor may have arisen from an enzyme antecedent. However, our findings do not formally exclude other interpretations such as convergent evolution, and further analysis will be necessary to confirm the inferred relationship between the two protein classes.
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Affiliation(s)
- Douglas R Houston
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jane G Hanna
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Stephen G Hillier
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
- Correspondence should be addressed to S G Hillier or R Lathe: or
| | - Richard Lathe
- Division of Infection Medicine, University of Edinburgh, Edinburgh, UK
- Correspondence should be addressed to S G Hillier or R Lathe: or
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16
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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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17
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Lee HF, Lacbay CM, Boutin R, Matralis AN, Park J, Waller DD, Guan TL, Sebag M, Tsantrizos YS. Synthesis and Evaluation of Structurally Diverse C-2-Substituted Thienopyrimidine-Based Inhibitors of the Human Geranylgeranyl Pyrophosphate Synthase. J Med Chem 2022; 65:2471-2496. [PMID: 35077178 DOI: 10.1021/acs.jmedchem.1c01913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Novel analogues of C-2-substituted thienopyrimidine-based bisphosphonates (C2-ThP-BPs) are described that are potent inhibitors of the human geranylgeranyl pyrophosphate synthase (hGGPPS). Members of this class of compounds induce target-selective apoptosis of multiple myeloma (MM) cells and exhibit antimyeloma activity in vivo. A key structural element of these inhibitors is a linker moiety that connects their (((2-phenylthieno[2,3-d]pyrimidin-4-yl)amino)methylene)bisphosphonic acid core to various side chains. The structural diversity of this linker moiety, as well as the side chains attached to it, was investigated and found to significantly impact the toxicity of these compounds in MM cells. The most potent inhibitor identified was evaluated in mouse and rat for liver toxicity and systemic exposure, respectively, providing further optimism for the potential value of such compounds as human therapeutics.
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Affiliation(s)
- Hiu-Fung Lee
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Cyrus M Lacbay
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Rebecca Boutin
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Alexios N Matralis
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jaeok Park
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Daniel D Waller
- Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Division of Hematology, McGill University Health Center, Montreal, Quebec H4A 3J1, Canada
| | - Tian Lai Guan
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Michael Sebag
- Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Division of Hematology, McGill University Health Center, Montreal, Quebec H4A 3J1, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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18
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Ronnebaum TA, Eaton SA, Brackhahn EAE, Christianson DW. Engineering the Prenyltransferase Domain of a Bifunctional Assembly-Line Terpene Synthase. Biochemistry 2021; 60:3162-3172. [PMID: 34609847 DOI: 10.1021/acs.biochem.1c00600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Copalyl diphosphate (CPP) synthase from Penicillium verruculosum (PvCPS) is a bifunctional diterpene synthase with both prenyltransferase and class II cyclase activities. The prenyltransferase α domain catalyzes the condensation of C5 dimethylallyl diphosphate with three successively added C5 isopentenyl diphosphates (IPPs) to form C20 geranylgeranyl diphosphate (GGPP), which then undergoes a class II cyclization reaction at the βγ domain interface to generate CPP. The prenyltransferase α domain mediates oligomerization to form a 648-kD (αβγ)6 hexamer. In the current study, we explore prenyltransferase structure-function relationships in this oligomeric assembly-line platform with the goal of generating alternative linear isoprenoid products. Specifically, we report steady-state enzyme kinetics, product analysis, and crystal structures of various site-specific variants of the prenyltransferase α domain. Crystal structures of the H786A, F760A, S723Y, S723F, and S723T variants have been determined at resolutions of 2.80, 3.10, 3.15, 2.65, and 2.00 Å, respectively. The substitution of S723 with bulky aromatic amino acids in the S723Y and S723F variants constricts the active site, thereby directing the formation of the shorter C15 isoprenoid, farnesyl diphosphate. While the S723T substitution only subtly alters enzyme kinetics and does not compromise GGPP biosynthesis, the crystal structure of this variant reveals a nonproductive binding mode for IPP that likely accounts for substrate inhibition at high concentrations. Finally, mutagenesis of the catalytic general acid in the class II cyclase domain, D313A, significantly compromises prenyltransferase activity. This result suggests molecular communication between the prenyltransferase and cyclase domains despite their distant connection by a flexible polypeptide linker.
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Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Samuel A Eaton
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emily A E Brackhahn
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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19
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Workman SD, Day J, Farha MA, El Zahed SS, Bon C, Brown ED, Organ MG, Strynadka NCJ. Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria. J Med Chem 2021; 64:13540-13550. [PMID: 34473495 DOI: 10.1021/acs.jmedchem.1c00941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyprenyl lipid undecaprenyl phosphate (C55P) is the universal carrier lipid for the biosynthesis of bacterial cell wall polymers. C55P is synthesized in its pyrophosphate form by undecaprenyl pyrophosphate synthase (UppS), an essential cis-prenyltransferase that is an attractive target for antibiotic development. We previously identified a compound (MAC-0547630) that showed promise as a novel class of inhibitor and an ability to potentiate β-lactam antibiotics. Here, we provide a structural model for MAC-0547630's inhibition of UppS and a structural rationale for its enhanced effect on UppS from Bacillus subtilis versus Staphylococcus aureus. We also describe the synthesis of a MAC-0547630 derivative (JPD447), show that it too can potentiate β-lactam antibiotics, and provide a structural rationale for its improved potentiation. Finally, we present an improved structural model of clomiphene's inhibition of UppS. Taken together, our data provide a foundation for structure-guided drug design of more potent UppS inhibitors in the future.
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Affiliation(s)
- Sean D Workman
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jonathan Day
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Maya A Farha
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Sara S El Zahed
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Chris Bon
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Michael G Organ
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.,Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie Private, Ottawa, Ontario K1N 6N5, Canada.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur Private, Ottawa, Ontario K1N 6N5, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.,Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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20
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Ugartondo N, Martínez-Gil N, Esteve M, Garcia-Giralt N, Roca-Ayats N, Ovejero D, Nogués X, Díez-Pérez A, Rabionet R, Grinberg D, Balcells S. Functional Analyses of Four CYP1A1 Missense Mutations Present in Patients with Atypical Femoral Fractures. Int J Mol Sci 2021; 22:ijms22147395. [PMID: 34299011 PMCID: PMC8303772 DOI: 10.3390/ijms22147395] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Osteoporosis is the most common metabolic bone disorder and nitrogen-containing bisphosphonates (BP) are a first line treatment for it. Yet, atypical femoral fractures (AFF), a rare adverse effect, may appear after prolonged BP administration. Given the low incidence of AFF, an underlying genetic cause that increases the susceptibility to these fractures is suspected. Previous studies uncovered rare CYP1A1 mutations in osteoporosis patients who suffered AFF after long-term BP treatment. CYP1A1 is involved in drug metabolism and steroid catabolism, making it an interesting candidate. However, a functional validation for the AFF-associated CYP1A1 mutations was lacking. Here we tested the enzymatic activity of four such CYP1A1 variants, by transfecting them into Saos-2 cells. We also tested the effect of commonly used BPs on the enzymatic activity of the CYP1A1 forms. We demonstrated that the p.Arg98Trp and p.Arg136His CYP1A1 variants have a significant negative effect on enzymatic activity. Moreover, all the BP treatments decreased CYP1A1 activity, although no specific interaction with CYP1A1 variants was found. Our results provide functional support to the hypothesis that an additive effect between CYP1A1 heterozygous mutations p.Arg98Trp and p.Arg136His, other rare mutations and long-term BP exposure might generate susceptibility to AFF.
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Affiliation(s)
- Nerea Ugartondo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
| | - Núria Martínez-Gil
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
| | - Mònica Esteve
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
| | - Natàlia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, 08003 Barcelona, Spain; (N.G.-G.); (D.O.); (X.N.); (A.D.-P.)
| | - Neus Roca-Ayats
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
| | - Diana Ovejero
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, 08003 Barcelona, Spain; (N.G.-G.); (D.O.); (X.N.); (A.D.-P.)
| | - Xavier Nogués
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, 08003 Barcelona, Spain; (N.G.-G.); (D.O.); (X.N.); (A.D.-P.)
| | - Adolfo Díez-Pérez
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, 08003 Barcelona, Spain; (N.G.-G.); (D.O.); (X.N.); (A.D.-P.)
| | - Raquel Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
- Correspondence: (D.G.); (S.B.); Tel.: +34-934035418 (S.B.)
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, 08028 Barcelona, Spain; (N.U.); (N.M.-G.); (M.E.); (N.R.-A.); (R.R.)
- Correspondence: (D.G.); (S.B.); Tel.: +34-934035418 (S.B.)
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21
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Fernández-Del-Río L, Rodríguez-López S, Gutiérrez-Casado E, González-Reyes JA, Clarke CF, Burón MI, Villalba JM. Regulation of hepatic coenzyme Q biosynthesis by dietary omega-3 polyunsaturated fatty acids. Redox Biol 2021; 46:102061. [PMID: 34246922 PMCID: PMC8274332 DOI: 10.1016/j.redox.2021.102061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/29/2021] [Indexed: 11/24/2022] Open
Abstract
Dietary fats are important for human health, yet it is not fully understood how different fats affect various health problems. Although polyunsaturated fatty acids (PUFAs) are generally considered as highly oxidizable, those of the n-3 series can ameliorate the risk of many age-related disorders. Coenzyme Q (CoQ) is both an essential component of the mitochondrial electron transport chain and the only lipid-soluble antioxidant that animal cells can synthesize. Previous work has documented the protective antioxidant properties of CoQ against the autoxidation products of PUFAs. Here, we have explored in vitro and in vivo models to better understand the regulation of CoQ biosynthesis by dietary fats. In mouse liver, PUFAs increased CoQ content, and PUFAs of the n-3 series increased preferentially CoQ10. This response was recapitulated in hepatic cells cultured in the presence of lipid emulsions, where we additionally demonstrated a role for n-3 PUFAs as regulators of CoQ biosynthesis via the upregulation of several COQ proteins and farnesyl pyrophosphate levels. In both models, n-3 PUFAs altered the mitochondrial network without changing the overall mitochondrial mass. Furthermore, in cellular systems, n-3 PUFAs favored the synthesis of CoQ10 over CoQ9, thus altering the ratio between CoQ isoforms through a mechanism that involved downregulation of farnesyl diphosphate synthase activity. This effect was recapitulated by both siRNA silencing and by pharmacological inhibition of farnesyl diphosphate synthase with zoledronic acid. We highlight here the ability of n-3 PUFAs to regulate CoQ biosynthesis, CoQ content, and the ratio between its isoforms, which might be relevant to better understand the health benefits associated with this type of fat. Additionally, we identify for the first time zoledronic acid as a drug that inhibits CoQ biosynthesis, which must be also considered with respect to its biological effects on patients.
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Affiliation(s)
- Lucía Fernández-Del-Río
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Córdoba, Spain; Department of Chemistry & Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Sandra Rodríguez-López
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Córdoba, Spain
| | - Elena Gutiérrez-Casado
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Córdoba, Spain
| | - José Antonio González-Reyes
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Córdoba, Spain
| | - Catherine F Clarke
- Department of Chemistry & Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - María Isabel Burón
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Córdoba, Spain
| | - José Manuel Villalba
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Córdoba, Spain.
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22
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Gralow JR, Barlow WE, Paterson AHG, M'iao JL, Lew DL, Stopeck AT, Hayes DF, Hershman DL, Schubert MM, Clemons M, Van Poznak CH, Dees EC, Ingle JN, Falkson CI, Elias AD, Messino MJ, Margolis JH, Dakhil SR, Chew HK, Dammann KZ, Abrams JS, Livingston RB, Hortobagyi GN. Phase III Randomized Trial of Bisphosphonates as Adjuvant Therapy in Breast Cancer: S0307. J Natl Cancer Inst 2021; 112:698-707. [PMID: 31693129 DOI: 10.1093/jnci/djz215] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/19/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Adjuvant bisphosphonates, when given in a low-estrogen environment, can decrease breast cancer recurrence and death. Treatment guidelines include recommendations for adjuvant bisphosphonates in postmenopausal patients. SWOG/Alliance/Canadian Cancer Trials Group/ECOG-ACRIN/NRG Oncology study S0307 compared the efficacy of three bisphosphonates in early-stage breast cancer. METHODS Patients with stage I-III breast cancer were randomly assigned to 3 years of intravenous zoledronic acid, oral clodronate, or oral ibandronate. The primary endpoint was disease-free survival (DFS) with overall survival as a secondary outcome. All statistical tests were two-sided. RESULTS A total of 6097 patients enrolled. Median age was 52.7 years. Prior to being randomly assigned, 73.2% patients indicated preference for oral vs intravenous formulation. DFS did not differ across arms in a log-rank test (P = .49); 5-year DFS was 88.3% (zoledronic acid: 95% confidence interval [CI] = 86.9% to 89.6%), 87.6% (clodronate: 95% CI = 86.1% to 88.9%), and 87.4% (ibandronate: 95% CI = 85.6% to 88.9%). Additionally, 5-year overall survival did not differ between arms (log rank P = .50) and was 92.6% (zoledronic acid: 95% CI = 91.4% to 93.6%), 92.4% (clodronate: 95% CI = 91.2% to 93.5%), and 92.9% (ibandronate: 95% CI = 91.5% to 94.1%). Bone as first site of recurrence did not differ between arms (P = .93). Analyses based on age and tumor subtypes showed no treatment differences. Grade 3/4 toxicity was 8.8% (zoledronic acid), 8.3% (clodronate), and 10.5% (ibandronate). Osteonecrosis of the jaw was highest for zoledronic acid (1.26%) compared with clodronate (0.36%) and ibandronate (0.77%). CONCLUSIONS We found no evidence of differences in efficacy by type of bisphosphonate, either in overall analysis or subgroups. Despite an increased rate of osteonecrosis of the jaw with zoledronic acid, overall toxicity grade differed little across arms. Given that patients expressed preference for oral formulation, efforts to make oral agents available in the United States should be considered.
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Affiliation(s)
| | | | | | | | | | - Alison T Stopeck
- Stony Brook Cancer Center, Stony Brook University Cancer Center, Stony Brook, NY
| | - Daniel F Hayes
- University of Michigan, Ann Arbor, MI (DFH, CHVP); Columbia University, New York, NY
| | | | | | - Mark Clemons
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | | | | | | | | | - Helen K Chew
- University of California at Davis, Sacramento, CA
| | | | - Jeffrey S Abrams
- Cancer Therapy and Evaluation Program, National Cancer Institute, Bethesda, MD
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23
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Kameda Y, Aizawa M, Sato T, Honda M. Zoledronic Acid-Loaded β-TCP Inhibits Tumor Proliferation and Osteoclast Activation: Development of a Functional Bone Substitute for an Efficient Osteosarcoma Treatment. Int J Mol Sci 2021; 22:1889. [PMID: 33672879 PMCID: PMC7918630 DOI: 10.3390/ijms22041889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/31/2022] Open
Abstract
Osteosarcoma has a poor survival rate due to relapse and metastasis. Zoledronic acid (ZOL), an anti-resorptive and anti-tumor agent, is used for treating osteosarcoma. Delivery of ZOL to the target region is difficult due to its high binding affinity to bone minerals. This study developed a novel treatment for osteosarcoma by delivering ZOL to the target region locally and sustainably. In this study, we fabricated a novel bone substitute by loading ZOL on β-tricalcium phosphate (β-TCP). The ZOL-loaded β-TCP (ZOL/β-TCP) would be expected to express the inhibitory effects via both bound-ZOL (bound to β-TCP) and free-ZOL (release from ZOL/β-TCP). To explore the ability to release ZOL from the ZOL/β-TCP, the amount of released ZOL was measured. The released profile indicates that a small amount of ZOL was released, and most of it remained on the β-TCP. Our data showed that ZOL/β-TCP could successfully express the effects of ZOL via both bound-ZOL and free-ZOL. In addition, we examined the biological effects of bound/free-ZOL using osteosarcoma and osteoclasts (target cells). The results showed that two states of ZOL (bound/free) inhibit target cell activities. As a result, ZOL/β-TCP is a promising candidate for application as a novel bone substitute.
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Affiliation(s)
- Yuka Kameda
- Department of Applied Chemistry, School of Science and Technology, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan; (Y.K.); (M.A.)
| | - Mamoru Aizawa
- Department of Applied Chemistry, School of Science and Technology, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan; (Y.K.); (M.A.)
| | - Taira Sato
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan;
| | - Michiyo Honda
- Department of Applied Chemistry, School of Science and Technology, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan; (Y.K.); (M.A.)
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24
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Barbosa JS, Almeida Paz FA, Braga SS. Bisphosphonates, Old Friends of Bones and New Trends in Clinics. J Med Chem 2021; 64:1260-1282. [PMID: 33522236 DOI: 10.1021/acs.jmedchem.0c01292] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bisphosphonates, used for a long time in osteoporosis management, are currently the target of intensive research, from pre-formulation studies to more advanced stages of clinical practice. This review presents an overview of the contributions of this family of compounds to human health, starting with the chemistry and clinical uses of bisphosphonates. Following this, their pharmacology is described, highlighting administration-borne handicaps and undesirable effects. The last three sections of the review describe the research efforts that seek to curb delivery-related issues and expand bisphosphonate use. Innovative routes and strategies of administration, such as nano-encapsulation for oral intake or injectable cements for local or in-bone delivery are presented, as well as the latest results of case studies or preclinical studies proposing new therapeutic indications for the clinically approved bisphosphonates. Finally, a selection of anti-infectious bisphosphonate new drug candidates is shown, with focus on the molecules reported in the last two decades.
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Affiliation(s)
- Jéssica S Barbosa
- CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal.,LAQV-Requimte, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Filipe A Almeida Paz
- CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Susana Santos Braga
- LAQV-Requimte, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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25
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Chang HY, Cheng TH, Wang AHJ. Structure, catalysis, and inhibition mechanism of prenyltransferase. IUBMB Life 2020; 73:40-63. [PMID: 33246356 PMCID: PMC7839719 DOI: 10.1002/iub.2418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/02/2020] [Accepted: 11/14/2020] [Indexed: 12/31/2022]
Abstract
Isoprenoids, also known as terpenes or terpenoids, represent a large family of natural products composed of five‐carbon isopentenyl diphosphate or its isomer dimethylallyl diphosphate as the building blocks. Isoprenoids are structurally and functionally diverse and include dolichols, steroid hormones, carotenoids, retinoids, aromatic metabolites, the isoprenoid side‐chain of ubiquinone, and isoprenoid attached signaling proteins. Productions of isoprenoids are catalyzed by a group of enzymes known as prenyltransferases, such as farnesyltransferases, geranylgeranyltransferases, terpenoid cyclase, squalene synthase, aromatic prenyltransferase, and cis‐ and trans‐prenyltransferases. Because these enzymes are key in cellular processes and metabolic pathways, they are expected to be potential targets in new drug discovery. In this review, six distinct subsets of characterized prenyltransferases are structurally and mechanistically classified, including (1) head‐to‐tail prenyl synthase, (2) head‐to‐head prenyl synthase, (3) head‐to‐middle prenyl synthase, (4) terpenoid cyclase, (5) aromatic prenyltransferase, and (6) protein prenylation. Inhibitors of those enzymes for potential therapies against several diseases are discussed. Lastly, recent results on the structures of integral membrane enzyme, undecaprenyl pyrophosphate phosphatase, are also discussed.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Tien-Hsing Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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26
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Song J, Malwal SR, Baig N, Schurig-Briccio LA, Gao Z, Vaidya GS, Yang K, Abutaleb NS, Seleem MN, Gennis RB, Pogorelov TV, Oldfield E, Feng X. Discovery of Prenyltransferase Inhibitors with In Vitro and In Vivo Antibacterial Activity. ACS Infect Dis 2020; 6:2979-2993. [PMID: 33085463 DOI: 10.1021/acsinfecdis.0c00472] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cis-prenyltransferases such as undecaprenyl diphosphate synthase (UPPS) and decaprenyl diphosphate synthase (DPPS) are essential enzymes in bacteria and are involved in cell wall biosynthesis. UPPS and DPPS are absent in the human genome, so they are of interest as targets for antibiotic development. Here, we screened a library of 750 compounds from National Cancer Institute Diversity Set V for the inhibition of Mycobacterium tuberculosis DPPS and found 17 hits, and then IC50s were determined using dose-response curves. Compounds were tested for growth inhibition against a panel of bacteria, for in vivo activity in a Staphylococcus aureus/Caenorhabditis elegans model, and for mammalian cell toxicity. The most active DPPS inhibitor was the dicarboxylic acid redoxal (compound 10), which also inhibited undecaprenyl diphosphate synthase (UPPS) as well as farnesyl diphosphate synthase. 10 was active against S. aureus, Clostridiodes difficile, Bacillus anthracis Sterne, and Bacillus subtilis, and there was a 3.4-fold increase in IC50 on addition of a rescue agent, undecaprenyl monophosphate. We found that 10 was also a weak protonophore uncoupler, leading to the idea that it targets both isoprenoid biosynthesis and the proton motive force. In an S. aureus/C. elegans in vivo model, 10 reduced the S. aureus burden 3 times more effectively than did ampicillin.
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Affiliation(s)
- Junfeng Song
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | | | | | | | | | | | - Kailing Yang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | - Nader S. Abutaleb
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mohamed N. Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | | | | | | | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
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27
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Risk factors for bisphosphonate-associated osteonecrosis of the jaw in the prospective randomized trial of adjuvant bisphosphonates for early-stage breast cancer (SWOG 0307). Support Care Cancer 2020; 29:2509-2517. [PMID: 32929540 DOI: 10.1007/s00520-020-05748-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Bisphosphonates reduce bone metastases in postmenopausal women with early-stage breast cancer but carry the risk of bisphosphonate-related osteonecrosis of the jaw (BRONJ). We describe risk factors for BRONJ and compare BRONJ provoked by infection or trauma with spontaneous lesions, which carry a better prognosis. METHODS SWOG 0307 randomized women with stage I-III breast cancer to receive zoledronic acid (ZA), clodronate (CL), or ibandronate (IB) for 3 years, implemented BRONJ prevention guidelines, and collected information about dental health and development of BRONJ. All statistical tests were two-sided. RESULTS Of 6018 women, 48 developed BRONJ. Infection was present in 21 (43.8%). Median time to BRONJ was 2.1 years for ZA, 2.0 years for IB, and 3.4 years for clodronate (p = 0.04). BRONJ was associated with bisphosphonate type (28/2231 (1.26%) for ZA, 8/2235 (0.36%) for CL, 12/1552 (0.77%) for IB), dental calculus (OR 2.03), gingivitis (OR 2.11), moderate/severe periodontal disease (OR 2.87), and periodontitis > 4 mm (OR 2.20) (p < 0.05). Of 57 lesions, BRONJ occurred spontaneously in 20 (35.1%) and was provoked by dental extraction in 20 (35.1%), periodontal disease in 14 (24.6%), denture trauma in 6 (10.5%), and dental surgery in 2 (3.5%). Spontaneous BRONJ occurred more frequently at the mylohyoid ridge. There were no differences in dental disease, infection, or bisphosphonate type between spontaneous and provoked BRONJ. CONCLUSION ZA and worse dental health were associated with increased incidence of BRONJ, with a trend toward additive risk when combined. BRONJ incidence was lower than in similar studies, with prevention strategies likely linked to this. CLINICAL TRIAL NUMBER NCT00127205 REGISTRATION DATE: July 2005.
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28
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Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A 2020; 117:20794-20802. [PMID: 32817466 PMCID: PMC7456142 DOI: 10.1073/pnas.2008381117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
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Affiliation(s)
- Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Eon Joo Park
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin Siciliano
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Ya Ha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520;
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
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29
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Feng Y, Morgan RML, Fraser PD, Hellgardt K, Nixon PJ. Crystal Structure of Geranylgeranyl Pyrophosphate Synthase (CrtE) Involved in Cyanobacterial Terpenoid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:589. [PMID: 32523588 PMCID: PMC7261888 DOI: 10.3389/fpls.2020.00589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes that perform oxygenic photosynthesis. Due to their ability to use the photon energy of sunlight to fix carbon dioxide into biomass, cyanobacteria are promising hosts for the sustainable production of terpenoids, also known as isoprenoids, a diverse class of natural products with potential as advanced biofuels and high-value chemicals. However, the cyanobacterial enzymes involved in the biosynthesis of the terpene precursors needed to make more complicated terpenoids are poorly characterized. Here we show that the predicted type II prenyltransferase CrtE encoded by the model cyanobacterium Synechococcus sp. PCC 7002 is homodimeric and able to synthesize C20-geranylgeranyl pyrophosphate (GGPP) from C5-isopentenyl pyrophosphate (IPP) and C5-dimethylallyl pyrophosphate (DMAPP). The crystal structure of CrtE solved to a resolution of 2.7 Å revealed a strong structural similarity to the large subunit of the heterodimeric geranylgeranyl pyrophosphate synthase 1 from Arabidopsis thaliana with each subunit containing 14 helices. Using mutagenesis, we confirmed that the fourth and fifth amino acids (Met-87 and Ser-88) before the first conserved aspartate-rich motif (FARM) play important roles in controlling chain elongation. While the WT enzyme specifically produced GGPP, variants M87F and S88Y could only generate C15-farnesyl pyrophosphate (FPP), indicating that residues with large side chains obstruct product elongation. In contrast, replacement of M87 with the smaller Ala residue allowed the formation of the longer C25-geranylfarnesyl pyrophosphate (GFPP) product. Overall, our results provide new structural and functional information on the cyanobacterial CrtE enzyme that could lead to the development of improved cyanobacterial platforms for terpenoid production.
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Affiliation(s)
- Yuchi Feng
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - R. Marc L. Morgan
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paul D. Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, United Kingdom
| | - Klaus Hellgardt
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Peter J. Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
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30
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Workman SD, Strynadka NCJ. A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid. J Mol Biol 2020; 432:4964-4982. [PMID: 32234311 DOI: 10.1016/j.jmb.2020.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/20/2023]
Abstract
The biosynthesis of bacterial cell envelope polysaccharides such as peptidoglycan relies on the use of a dedicated carrier lipid both for the assembly of precursors at the cytoplasmic face of the plasma membrane and for the translocation of lipid linked oligosaccharides across the plasma membrane into the periplasmic space. This dedicated carrier lipid, undecaprenyl phosphate, results from the dephosphorylation of undecaprenyl pyrophosphate, which is generated de novo in the cytoplasm by undecaprenyl pyrophosphate synthase and released as a by-product when newly synthesized glycans are incorporated into the existing cell envelope. The de novo synthesis of undecaprenyl pyrophosphate has been thoroughly characterized from a structural and mechanistic standpoint; however, its dephosphorylation to the active carrier lipid form, both in the course of de novo synthesis and recycling, has only been begun to be studied in depth in recent years. This review provides an overview of bacterial carrier lipid synthesis and presents the current state of knowledge regarding bacterial carrier lipid recycling.
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Affiliation(s)
- Sean D Workman
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.
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Chen CC, Zhang L, Yu X, Ma L, Ko TP, Guo RT. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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Serra-Vinardell J, Roca-Ayats N, De-Ugarte L, Vilageliu L, Balcells S, Grinberg D. Bone development and remodeling in metabolic disorders. J Inherit Metab Dis 2020; 43:133-144. [PMID: 30942483 DOI: 10.1002/jimd.12097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/29/2019] [Indexed: 02/01/2023]
Abstract
There are many metabolic disorders that present with bone phenotypes. In some cases, the pathological bone symptoms are the main features of the disease whereas in others they are a secondary characteristic. In general, the generation of the bone problems in these disorders is not well understood and the therapeutic options for them are scarce. Bone development occurs in the early stages of embryonic development where the bone formation, or osteogenesis, takes place. This osteogenesis can be produced through the direct transformation of the pre-existing mesenchymal cells into bone tissue (intramembranous ossification) or by the replacement of the cartilage by bone (endochondral ossification). In contrast, bone remodeling takes place during the bone's growth, after the bone development, and continues throughout the whole life. The remodeling involves the removal of mineralized bone by osteoclasts followed by the formation of bone matrix by the osteoblasts, which subsequently becomes mineralized. In some metabolic diseases, bone pathological features are associated with bone development problems but in others they are associated with bone remodeling. Here, we describe three examples of impaired bone development or remodeling in metabolic diseases, including work by others and the results from our research. In particular, we will focus on hereditary multiple exostosis (or osteochondromatosis), Gaucher disease, and the susceptibility to atypical femoral fracture in patients treated with bisphosphonates for several years.
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Affiliation(s)
- Jenny Serra-Vinardell
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Neus Roca-Ayats
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Laura De-Ugarte
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Anatomy and Cell Biology, Indiana Center for Musculoskeletal Health, Indianapolis, Indiana
| | - Lluïsa Vilageliu
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
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Manaswiyoungkul P, de Araujo ED, Gunning PT. Targeting prenylation inhibition through the mevalonate pathway. RSC Med Chem 2020; 11:51-71. [PMID: 33479604 PMCID: PMC7485146 DOI: 10.1039/c9md00442d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/10/2019] [Indexed: 12/13/2022] Open
Abstract
Protein prenylation is a critical mediator in several diseases including cancer and acquired immunodeficiency syndrome (AIDS). Therapeutic intervention has focused primarily on directly targeting the prenyltransferase enzymes, FTase and GGTase I and II. To date, several drugs have advanced to clinical trials and while promising, they have yet to gain approval in a medical setting due to off-target effects and compensatory mechanisms activated by the body which results in drug resistance. While the development of dual inhibitors has mitigated undesirable side effects, potency remains sub-optimal for clinical development. An alternative approach involves antagonizing the upstream mevalonate pathway enzymes, FPPS and GGPPS, which mediate prenylation as well as cholesterol synthesis. The development of these inhibitors presents novel opportunities for dual inhibition of cancer-driven prenylation as well as cholesterol accumulation. Herein, we highlight progress towards the development of inhibitors against the prenylation machinery.
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Affiliation(s)
- Pimyupa Manaswiyoungkul
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Elvin D de Araujo
- Department of Chemical and Physical Sciences , University of Toronto Mississauga , 3359 Mississauga Rd N. , Mississauga , Ontario L5L 1C6 , Canada .
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences , University of Toronto Mississauga , 3359 Mississauga Rd N. , Mississauga , Ontario L5L 1C6 , Canada .
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
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Han J, Huang C, Jiang J, Jiang D. Activation of autophagy during farnesyl pyrophosphate synthase inhibition is mediated through PI3K/AKT/mTOR signaling. J Int Med Res 2019; 48:300060519875371. [PMID: 31884848 PMCID: PMC7607048 DOI: 10.1177/0300060519875371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objectives Autophagy is divided into three phases: autophagosome engulfment of intracellular organelles and proteins, autophagosome fusion with lysosomes, and autolysosome degradation. The farnesyl pyrophosphate synthase inhibitor ibandronate (IBAN) has in vivo cardioprotective properties, potentially via anti-oxidant effects. Whether autophagy is involved in the cardioprotective effect of IBAN remains unexplored. Methods Human umbilical vein endothelial cells (HUVECs) were treated in vitro with IBAN to assess autophagy induction. Lysosomal activation and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling were assessed using a LysoTracker assay, acridine orange staining and western blotting. An MTS assay was used to assess cellular proliferation. Autophagy was inhibited using chloroquine or RNA silencing of autophagy-related 7 (Atg7) expression. Results IBAN induced autophagy in HUVECs. Moreover, IBAN activated lysosomal function, which is pivotal to autophagy induction. PI3K/AKT/mTOR activity was inhibited in IBAN-treated HUVECs, indicating the involvement of this pathway in IBAN-induced autophagy. Inhibition of autophagy using either chloroquine or Atg7 siRNA potentiated inhibition of HUVEC growth by IBAN, suggesting the involvement of non-autophagy pathways in the antiproliferative effects of IBAN. Conclusions These findings provide insights into the role of autophagy in the cardioprotective effects of IBAN and the molecular mechanisms underlying autophagy induction by IBAN.
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Affiliation(s)
- Jie Han
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chaoyang Huang
- Department of Cardiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiukun Jiang
- Department of Emergency, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dongmei Jiang
- Department of Cardiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Park YE, Bava U, Lin JM, Cornish J, Naot D, Reid IR. Bone-Bound Bisphosphonates Inhibit Proliferation of Breast Cancer Cells. Calcif Tissue Int 2019; 105:497-505. [PMID: 31324954 DOI: 10.1007/s00223-019-00590-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/12/2019] [Indexed: 12/31/2022]
Abstract
Bisphosphonates are used in treating patients with breast cancer. In vitro studies have shown that bisphosphonates act directly on tumour cells, inhibiting cell proliferation and inducing apoptosis. In most such studies, drugs were added to culture media exposing cells to high bisphosphonate concentrations in solution. However, since bisphosphonates bind to bone hydroxyapatite with high affinity and remain bound for very long periods of time, these experimental systems are not an optimal model for the action of the drugs in vivo. The aim of this study was to determine whether bone-bound zoledronate has direct effects on adjacent breast cancer cells. Bone slices were pre-incubated with bisphosphonate solutions, washed, and seeded with cells of the breast cancer cell lines, MCF7 or MDA-MB-231. Proliferation was assessed by cell counts and thymidine incorporation for up to 72 h. Inhibition of the mevalonate pathway was tested by measuring the levels of unprenylated Rap1A, and apoptosis was examined by the presence of cleaved caspase-8 on western blots. The proliferation rate of breast cancer cells on zoledronate-treated bone was significantly lower compared to cells on control bone. Other bisphosphonates showed a similar inhibitory effect, with an order of potency similar to their clinical potencies. Unprenylated Rap1A accumulated in MCF7 cells on zoledronate-treated bone, suggesting zoledronate acted through the inhibition of the mevalonate pathway. Accumulation of cleaved caspase-8 in MDA-MB-231 cells on bisphosphonate-treated bone indicated increased apoptosis in the cells. In conclusion, bone-bound zoledronate inhibits breast cancer cell proliferation, an activity that may contribute to its clinical anti-tumour effects.
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Affiliation(s)
- Young-Eun Park
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Usha Bava
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jian-Ming Lin
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jillian Cornish
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Dorit Naot
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Ian R Reid
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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Kim S, Kim EJ, Park JB, Kim SW, Kim KJ. Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6. Biochem Biophys Res Commun 2019; 518:479-485. [PMID: 31427080 DOI: 10.1016/j.bbrc.2019.08.071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 10/26/2022]
Abstract
Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain lengths. We hereby present the crystal structure of geranylgeranyl pyrophosphate synthase from the marine flavobacterium Nonlabens dokdonensis DSW-6 (NdGGPPS). NdGGPPS forms a hexamer composed of homodimeric trimer, and the monomeric structure is composed of 15 α-helices (α1-α15). In this structure, we observed the binding of one pyrophosphate molecule and two glycerol molecules that mimicked substrate binding to the enzyme. The substrate binding site of NdGGPPS contains large hydrophobic residues such as Phe, His and Tyr, and structural and amino acids sequence analyses thereof suggest that the protein belongs to the short-chain prenyltransferase family.
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Affiliation(s)
- Sangwoo Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea
| | - Eun-Jung Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea
| | - Ji-Bin Park
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea.
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Helal AM, Sayed AM, Omara M, Elsebaei MM, Mayhoub AS. Peptidoglycan pathways: there are still more! RSC Adv 2019; 9:28171-28185. [PMID: 35530449 PMCID: PMC9071014 DOI: 10.1039/c9ra04518j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
The discovery of 3rd and 4th generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
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Affiliation(s)
- Ahmed M Helal
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Ahmed M Sayed
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaei
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
- University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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Lisnyansky M, Yariv E, Segal O, Marom M, Loewenstein A, Ben-Tal N, Giladi M, Haitin Y. Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase–Bisphosphonate Interactions: A Crystallographic and Computational Analysis. Mol Pharmacol 2019; 96:580-588. [DOI: 10.1124/mol.119.117499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022] Open
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Ma J, Ko TP, Yu X, Zhang L, Ma L, Zhai C, Guo RT, Liu W, Li H, Chen CC. Structural insights to heterodimeric cis-prenyltransferases through yeast dehydrodolichyl diphosphate synthase subunit Nus1. Biochem Biophys Res Commun 2019; 515:621-626. [DOI: 10.1016/j.bbrc.2019.05.135] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022]
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40
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Buranrat B, Bootha S. Antiproliferative and antimigratory activities of bisphosphonates in human breast cancer cell line MCF-7. Oncol Lett 2019; 18:1246-1258. [PMID: 31423185 PMCID: PMC6607035 DOI: 10.3892/ol.2019.10438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/05/2019] [Indexed: 12/16/2022] Open
Abstract
Bisphosphonates (BPs) are antiresorptive drugs that act as effective inhibitors of cancer cell proliferation. However, not all bisphosphonates are equally effective against breast cancer cells in vitro. The present study investigated the extent to which three BPs decrease the viability of MCF-7 human breast cancer cells, stimulate cell apoptosis and inhibit cell migration by modulating proteins in the mevalonate pathway. The three BPs exerted direct anticancer effects against MCF-7 cells in a dose- and time-dependent manner, with pamidronate demonstrating the highest efficacy. In addition, the BPs inhibited colony formation ability. The activity of BPs against MCF-7 cells was inhibited by the mevalonate product geranylgeranyl pyrophosphate, which was potentiated by doxorubicin. It was also identified that BPs modulated Ras-related C3 botulinum toxin substrate 1, Ras homolog gene family member A and cell division control protein 42 homolog gene expression. Consistent with the observed growth inhibitory effects, BPs also inhibited the cell cycle by promoting G1 phase arrest and the downregulation of cyclin D1 and upregulation of p21. Additionally, BPs were revealed to induce reactive oxygen species expression, caspase-3 activity and increase the mitochondrial transmembrane potential, which was associated with apoptosis. BP-induced cancer cell apoptosis was detected by acridine orange/ethidium bromide staining and flow cytometry analysis, and was identified to be associated with the induction of caspase-3 and cytochrome c protein expression. Furthermore, BPs significantly decreased cancer cell migration in a dose-dependent manner and reduced matrix metallopeptidase-9 protein expression. In summary, the current study demonstrated that BPs exhibited a direct anticancer effect and an antimigratory effect on MCF-7 cells. These findings suggest that BPs may be developed as a therapeutic option for breast cancer and may serve as sensitizing chemotherapeutic agents.
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Affiliation(s)
- Benjaporn Buranrat
- Faculty of Medicine, Mahasarakham University, Maha Sarakham 44000, Thailand
| | - Supavadee Bootha
- School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand
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Vella M, Coniglio D, Abrate A, Scalici Gesolfo C, Lo Presti E, Meraviglia S, Serretta V, Simonato A. Characterization of human infiltrating and circulating gamma-delta T cells in prostate cancer. Investig Clin Urol 2019; 60:91-98. [PMID: 30838341 PMCID: PMC6397928 DOI: 10.4111/icu.2019.60.2.91] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/03/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose The aim of our study was to prospectively evaluate the distribution of gamma-delta (γδ)1 and γδ2 T cells and their phenotypes in peripheral blood and prostate samples of patients diagnosed with or without prostate cancer (PCa) at prostate biopsy. Materials and Methods A consecutive series of 43 outpatients underwent trans-rectal echo-guided prostate biopsy for suspected PCa. Flow cytometry analysis was used to identify and characterize the γδ T cells populations in peripheral blood and tissue samples. Patients were stratified according to the presence or not of PCa, and its International Society of Urological Pathology (ISUP) grade (1 vs. ≥2). Results The distribution of γδ T cells in peripheral blood and prostate tissue showed wide variability and non-significant differences. A slightly higher percentage of δ2 T cells and a slightly lower percentage of δ1 T cells were found in peripheral blood of cancer patients. A non-significantly higher percentage of both Vδ1 and Vδ2 was expressed in cancer tissues, but a trend for lower distribution of δ1 and δ2 T cells was observed in ISUP grade ≥2. The "central memory" and "effector memory" were the most expressed T cells phenotype in peripheral blood and tissue samples. However no substantial differences in T cells subtypes distribution between cancer and healthy tissue were observed. Conclusions No substantially different percentages of γδ T cells were found in peripheral blood and biopsy samples of healthy and PCa patients. However a non-significant trend for lower infiltrate in higher ISUP grade cancer tissue was observed, suggesting a possible role for the immunosurveillance of PCa.
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Affiliation(s)
- Marco Vella
- Department of Surgical Oncological and Oral Sciences, Section of Urology, University of Palermo, Palermo, Italy
| | - Daniela Coniglio
- Department of Biopathology and Clinical and Forensic Biotechnology, University of Palermo, Palermo, Italy
| | - Alberto Abrate
- Department of Surgical Oncological and Oral Sciences, Section of Urology, University of Palermo, Palermo, Italy
| | - Cristina Scalici Gesolfo
- Department of Surgical Oncological and Oral Sciences, Section of Urology, University of Palermo, Palermo, Italy
| | - Elena Lo Presti
- Department of Biopathology and Clinical and Forensic Biotechnology, University of Palermo, Palermo, Italy
| | - Serena Meraviglia
- Department of Biopathology and Clinical and Forensic Biotechnology, University of Palermo, Palermo, Italy
| | - Vincenzo Serretta
- Department of Surgical Oncological and Oral Sciences, Section of Urology, University of Palermo, Palermo, Italy
| | - Alchiede Simonato
- Department of Surgical Oncological and Oral Sciences, Section of Urology, University of Palermo, Palermo, Italy
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42
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Malwal SR, Chen L, Hicks H, Qu F, Liu W, Shillo A, Law WX, Zhang J, Chandnani N, Han X, Zheng Y, Chen CC, Guo RT, AbdelKhalek A, Seleem MN, Oldfield E. Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis. J Med Chem 2019; 62:2564-2581. [PMID: 30730737 DOI: 10.1021/acs.jmedchem.8b01878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report that alkyl-substituted bisphosphonates have activity against Bacillus anthracis Sterne (0.40 μg/mL), Mycobacterium smegmatis (1.4 μg/mL), Bacillus subtilis (1.0 μg/mL), and Staphylococcus aureus (13 μg/mL). In many cases, there is no effect of serum binding, as well as low activity against a human embryonic kidney cell line. Targeting of isoprenoid biosynthesis is involved with 74 having IC50 values of ∼100 nM against heptaprenyl diphosphate synthase and 200 nM against farnesyl diphosphate synthase. B. subtilis growth inhibition was rescued by addition of farnesyl diphosphate, menaquinone-4 (MK-4), or undecaprenyl phosphate (UP), and the combination of MK-4 and UP resulted in a 25× increase in ED50, indicating targeting of both quinone and cell wall biosynthesis. Clostridioides difficile was inhibited by 74, and since this organism does not synthesize quinones, cell wall biosynthesis is the likely target. We also solved three X-ray structures of inhibitors bound to octaprenyl diphosphate and/or undecaprenyl diphosphate synthases.
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Affiliation(s)
| | | | | | | | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | | | | | | | | | - Xu Han
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory , Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 200208 , China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Engineering Research Center for Bio-enzyme Catalysis, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Ahmed AbdelKhalek
- Department of Comparative Pathobiology, College of Veterinary Medicine , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine , Purdue University , West Lafayette , Indiana 47907 , United States.,Purdue Institute of Inflammation, Immunology, and Infectious Disease , West Lafayette , Indiana 47907 , United States
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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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44
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Beattie JR, Sophocleous A, Caraher MC, O'Driscoll O, Cummins NM, Bell SEJ, Towler M, Rahimnejad Yazdi A, Ralston SH, Idris AI. Raman spectroscopy as a predictive tool for monitoring osteoporosis therapy in a rat model of postmenopausal osteoporosis. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2019; 30:25. [PMID: 30747334 DOI: 10.1007/s10856-019-6226-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
Pharmacological therapy of osteoporosis reduces bone loss and risk of fracture in patients. Modulation of bone mineral density cannot explain all effects. Other aspects of bone quality affecting fragility and ways to monitor them need to be better understood. Keratinous tissue acts as surrogate marker for bone protein deterioration caused by oestrogen deficiency in rats. Ovariectomised rats were treated with alendronate (ALN), parathyroid hormone (PTH) or estrogen (E2). MicroCT assessed macro structural changes. Raman spectroscopy assessed biochemical changes. Micro CT confirmed that all treatments prevented ovariectomy-induced macro structural bone loss in rats. PTH induced macro structural changes unrelated to ovariectomy. Raman analysis revealed ALN and PTH partially protect against molecular level changes to bone collagen (80% protection) and mineral (50% protection) phases. E2 failed to prevent biochemical change. The treatments induced alterations unassociated with the ovariectomy; increased beta sheet with E2, globular alpha helices with PTH and fibrous alpha helices with both ALN and PTH. ALN is closest to maintaining physiological status of the animals, while PTH (comparable protective effect) induces side effects. E2 is unable to prevent molecular level changes associated with ovariectomy. Raman spectroscopy can act as predictive tool for monitoring pharmacological therapy of osteoporosis in rodents. Keratinous tissue is a useful surrogate marker for the protein related impact of these therapies.The results demonstrate utility of surrogates where a clear systemic causation connects the surrogate to the target tissue. It demonstrates the need to assess broader biomolecular impact of interventions to examine side effects.
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Affiliation(s)
- J Renwick Beattie
- J Renwick Beattie Consulting, Causeway Enterprise Agency, Ballycastle, UK
| | | | - M Clare Caraher
- ICON plc, South County Business Park, Leopardstown, Dublin, Ireland
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast, UK
| | - Olive O'Driscoll
- AventaMed, Rubicon Centre, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Niamh M Cummins
- Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | - Steven E J Bell
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast, UK
| | - Mark Towler
- Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, Canada.
| | | | - Stuart H Ralston
- Rheumatology and Bone Diseases Unit, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Aymen I Idris
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Beech Hill Road, Sheffield, UK
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45
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Jukič M, Rožman K, Sova M, Barreteau H, Gobec S. Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis. Front Microbiol 2019; 9:3322. [PMID: 30692977 PMCID: PMC6339874 DOI: 10.3389/fmicb.2018.03322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report the successful implementation of virtual screening in the discovery of new inhibitors of undecaprenyl pyrophosphate synthase (UppS) from Escherichia coli. UppS is an essential enzyme in the biosynthesis of bacterial cell wall. It catalyzes the condensation of farnesyl pyrophosphate (FPP) with eight consecutive isopentenyl pyrophosphate units (IPP), in which new cis-double bonds are formed, to generate undecaprenyl pyrophosphate. The latter serves as a lipid carrier for peptidoglycan synthesis, thus representing an important target in the antibacterial drug design. A pharmacophore model was designed on a known bisphosphonate BPH-629 and used to prepare an enriched compound library that was further docked into UppS conformational ensemble generated by molecular dynamics experiment. The docking resulted in three anthranilic acid derivatives with promising inhibitory activity against UppS. Compound 2 displayed high inhibitory potency (IC50 = 25 μM) and good antibacterial activity against E. coli BW25113 ΔtolC strain (MIC = 0.5 μg/mL).
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Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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46
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Roca-Ayats N, Ng PY, Garcia-Giralt N, Falcó-Mascaró M, Cozar M, Abril JF, Quesada Gómez JM, Prieto-Alhambra D, Nogués X, Dunford JE, Russell RG, Baron R, Grinberg D, Balcells S, Díez-Pérez A. Functional Characterization of a GGPPS Variant Identified in Atypical Femoral Fracture Patients and Delineation of the Role of GGPPS in Bone-Relevant Cell Types. J Bone Miner Res 2018; 33:2091-2098. [PMID: 30184270 DOI: 10.1002/jbmr.3580] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 08/06/2018] [Accepted: 08/26/2018] [Indexed: 12/25/2022]
Abstract
Atypical femoral fractures (AFFs) are a rare but potentially devastating event, often but not always linked to bisphosphonate (BP) therapy. The pathogenic mechanisms underlying AFFs remain obscure, and there are no tests available that might assist in identifying those at high risk of AFF. We previously used exome sequencing to explore the genetic background of three sisters with AFFs and three additional unrelated AFF cases, all previously treated with BPs. We detected 37 rare mutations (in 34 genes) shared by the three sisters. Notably, we found a p.Asp188Tyr mutation in the enzyme geranylgeranyl pyrophosphate synthase, a component of the mevalonate pathway, which is critical to osteoclast function and is inhibited by N-BPs. In addition, the CYP1A1 gene, responsible for the hydroxylation of 17β-estradiol, estrone, and vitamin D, was also mutated in all three sisters and one unrelated patient. Here we present a detailed list of the variants found and report functional analyses of the GGPS1 p.Asp188Tyr mutation, which showed a severe reduction in enzyme activity together with oligomerization defects. Unlike BP treatment, this genetic mutation will affect all cells in the carriers. RNAi knockdown of GGPS1 in osteoblasts produced a strong mineralization reduction and a reduced expression of osteocalcin, osterix, and RANKL, whereas in osteoclasts, it led to a lower resorption activity. Taken together, the impact of the mutated GGPPS and the relevance of the downstream effects in bone cells make it a strong candidate for AFF susceptibility. We speculate that other genes such as CYP1A1 might be involved in AFF pathogenesis, which remains to be functionally proved. The identification of the genetic background for AFFs provides new insights for future development of novel risk assessment tools. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Neus Roca-Ayats
- Department of Genetics, Microbiology, and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Spain
| | - Pei Ying Ng
- Division of Bone and Mineral Research, Department of Oral Medicine, Harvard School of Dental Medicine, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Natàlia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Maite Falcó-Mascaró
- Department of Genetics, Microbiology, and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Spain
| | - Mónica Cozar
- Department of Genetics, Microbiology, and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Spain
| | - Josep Francesc Abril
- Department of Genetics, Microbiology, and Statistics, Facultat de Biologia, Universitat de Barcelona, IBUB, Barcelona, Spain
| | - José Manuel Quesada Gómez
- Mineral Metabolism Unit, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, CIBERFES, ISCII, Córdoba, Spain
| | - Daniel Prieto-Alhambra
- GREMPAL (Grup de Recerca en Malalties Prevalents de l'Aparell Locomotor), Idiap Jordi Gol Primary Care Research Institute, CIBERFES, Autonomous University of Barcelona, Barcelona, Spain.,NIHR Musculoskeletal BRU and Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Xavier Nogués
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - James E Dunford
- NIHR Musculoskeletal BRU and Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - R Graham Russell
- NIHR Musculoskeletal BRU and Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK.,The Mellanby Centre for Bone Research, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Roland Baron
- Division of Bone and Mineral Research, Department of Oral Medicine, Harvard School of Dental Medicine, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel Grinberg
- Department of Genetics, Microbiology, and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Spain
| | - Susana Balcells
- Department of Genetics, Microbiology, and Statistics, Facultat de Biologia, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, IBUB, IRSJD, Barcelona, Spain
| | - Adolfo Díez-Pérez
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
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47
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Ko TP, Huang CH, Lai SJ, Chen Y. Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2018; 74:765-769. [PMID: 30511669 PMCID: PMC6277960 DOI: 10.1107/s2053230x18012931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/13/2018] [Indexed: 04/06/2024] Open
Abstract
Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side chains of the catalytic aspartate and serine. These observations may provide a structural basis for inhibitor design against AbUPPS.
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Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Hung Huang
- Department of Biotechnology, HungKuang University, Taichung, Taiwan
| | - Shu-Jung Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yeh Chen
- Department of Biotechnology, HungKuang University, Taichung, Taiwan
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48
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Burda-Grabowska M, Macegoniuk K, Flick R, Nocek BP, Joachimiak A, Yakunin AF, Mucha A, Berlicki Ł. Bisphosphonic acids and related compounds as inhibitors of nucleotide- and polyphosphate-processing enzymes: A PPK1 and PPK2 case study. Chem Biol Drug Des 2018; 93:1197-1206. [PMID: 30484959 DOI: 10.1111/cbdd.13439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/18/2018] [Accepted: 10/28/2018] [Indexed: 12/26/2022]
Abstract
Bisphosphonic acids, which are structural analogs of pyrophosphate, constitute a class of compounds with very high potential for the construction of effective inhibitors of enzymes operating on oligo- and polyphosphates. The bisphosphonate-based methodology was applied for the discovery of inhibitors of two families of polyphosphate kinases (PPK1 and PPK2). Screening of thirty-two structurally diverse bisphosphonic acids and related compounds revealed several micromolar inhibitors of both enzymes. Importantly, selectivity of bisphosphonates could be achieved by application of the appropriate side chain.
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Affiliation(s)
- Małgorzata Burda-Grabowska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Katarzyna Macegoniuk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Boguslaw P Nocek
- Department of Biosciences, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois
| | - Andrzej Joachimiak
- Department of Biosciences, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Artur Mucha
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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49
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Yeh YS, Jheng HF, Iwase M, Kim M, Mohri S, Kwon J, Kawarasaki S, Li Y, Takahashi H, Ara T, Nomura W, Kawada T, Goto T. The Mevalonate Pathway Is Indispensable for Adipocyte Survival. iScience 2018; 9:175-191. [PMID: 30396151 DOI: 10.1016/j.isci.2018.10.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/26/2018] [Accepted: 10/16/2018] [Indexed: 01/20/2023] Open
Abstract
The mevalonate pathway is essential for the synthesis of isoprenoids and cholesterol. Adipose tissue is known as a major site for cholesterol storage; however, the role of the local mevalonate pathway and its synthesized isoprenoids remains unclear. In this study, adipose-specific mevalonate pathway-disrupted (aKO) mice were generated through knockout of 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase (HMGCR). aKO mice showed serious lipodystrophy accompanied with glucose and lipid metabolic disorders and hepatomegaly. These metabolic variations in aKO mice were dramatically reversed after fat transplantation. In addition, HMGCR-disrupted adipocytes exhibited loss of lipid accumulation and an increase of cell death, which were ameliorated by the supplementation of mevalonate and geranylgeranyl pyrophosphate but not farnesyl pyrophosphate and squalene. Finally, we found that apoptosis may be involved in adipocyte death induced by HMGCR down-regulation. Our findings indicate that the mevalonate pathway is essential for adipocytes and further suggest that this pathway is an important regulator of adipocyte turnover.
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Affiliation(s)
- Yu-Sheng Yeh
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Huei-Fen Jheng
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Mari Iwase
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Minji Kim
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Shinsuke Mohri
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Jungin Kwon
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Satoko Kawarasaki
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Yongjia Li
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Haruya Takahashi
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Takeshi Ara
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Wataru Nomura
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan; Research Unit for Physiological Chemistry, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Teruo Kawada
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan; Research Unit for Physiological Chemistry, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Goto
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan; Research Unit for Physiological Chemistry, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan.
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50
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Lisnyansky M, Kapelushnik N, Ben-Bassat A, Marom M, Loewenstein A, Khananshvili D, Giladi M, Haitin Y. Reduced Activity of Geranylgeranyl Diphosphate Synthase Mutant Is Involved in Bisphosphonate-Induced Atypical Fractures. Mol Pharmacol 2018; 94:1391-1400. [PMID: 30275041 DOI: 10.1124/mol.118.113670] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/26/2018] [Indexed: 11/22/2022] Open
Abstract
Bisphosphonates are widely used for treating osteoporosis, a common disorder in which bone strength is reduced, increasing the risk for fractures. Rarely, bisphosphonates can paradoxically lead to atypical fractures occurring spontaneously or with trivial trauma. Recently, a novel missense mutation (D188Y) in the GGPS1 gene, encoding for geranylgeranyl diphosphate synthase (GGPPS), was associated with bisphosphonate-induced atypical fractures. However, the molecular basis for GGPPS involvement in this devastating condition remains elusive. Here, we show that while maintaining an overall unperturbed global enzyme structure, the D188Y mutation leads to ∼4-fold catalytic activity decrease. Furthermore, GGPPS-D188Y is unable to support cross-species complementation, highlighting the functional significance of the reduced catalytic activity observed in vitro. We next determined the crystal structure of apo-GGPPS-D188Y, revealing that while Y188 does not alter the protein fold, its bulky side chain sterically interferes with substrate binding. In agreement, we show that GGPPS-D188Y exhibits ∼3-fold reduction in the binding affinity of zoledronate, a commonly used bisphosphonate. However, inhibition of the mutated enzyme by zoledronate, in pharmacologically relevant concentrations, is maintained. Finally, we determined the crystal structure of zoledronate-bound GGPPS-D188Y, revealing large ligand-induced binding pocket rearrangements, revising the previous model for GGPPS-bisphosphonate interactions. In conclusion, we propose that among heterozygotes residual GGPPS activity is sufficient to support physiologic cellular function, concealing any pathologic phenotype. However, under bisphosphonate treatment, GGPPS activity is reduced below a crucial threshold for osteoclast function, leading to impaired bone remodeling and increased susceptibility to atypical fractures.
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Affiliation(s)
- Michal Lisnyansky
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Noa Kapelushnik
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Ariel Ben-Bassat
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Milit Marom
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Anat Loewenstein
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Moshe Giladi
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology (M.L., A.B.-B., M.M., D.K., M.G., Y.H.), Sackler Faculty of Medicine (N.K., A.L.), Tel Aviv University, Tel Aviv, Israel; and Division of Ophthalmology (A.L.), Tel Aviv Sourasky Medical Center (M.G.), Tel Aviv, Israel
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