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Boutin R, Lee HF, Guan TL, Nguyen TT, Huang XF, Waller DD, Lu J, Christine Chio II, Michel RP, Sebag M, Tsantrizos YS. Discovery and Evaluation of C6-Substituted Pyrazolopyrimidine-Based Bisphosphonate Inhibitors of the Human Geranylgeranyl Pyrophosphate Synthase and Evaluation of Their Antitumor Efficacy in Multiple Myeloma, Pancreatic Ductal Adenocarcinoma, and Colorectal Cancer. J Med Chem 2023; 66:15776-15800. [PMID: 37982711 PMCID: PMC10832233 DOI: 10.1021/acs.jmedchem.3c01271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Novel C6-substituted pyrazolo[3,4-d]pyrimidine- and C2-substituted purine-based bisphosphonate (C6-PyraP-BP and C2-Pur-BP, respectively) inhibitors of the human geranylgeranyl pyrophosphate synthase (hGGPPS) were designed and evaluated for their ability to block the proliferation of multiple myeloma (MM), pancreatic ductal adenocarcinoma (PDAC), and colorectal cancer (CRC) cells. Pyrazolo[3,4-d]pyrimidine analogs were identified that induce selective intracellular target engagement leading to apoptosis and downregulate the prenylation of Rap-1A in MM, PDAC, and CRC cells. The C6-PyraP-BP inhibitor RB-07-16 was found to exhibit antitumor efficacy in xenograft mouse models of MM and PDAC, significantly reducing tumor growth without substantially increasing liver enzymes or causing significant histopathologic damage, usually associated with hepatotoxicity. RB-07-16 is a metabolically stable compound in cross-species liver microsomes, does not inhibit key CYP 450 enzymes, and exhibits good systemic circulation in rat. Collectively, the current studies provide encouraging support for further optimization of the pyrazolo[3,4-d]pyrimidine-based GGPPS inhibitors as potential human therapeutics for various cancers.
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Affiliation(s)
- Rebecca Boutin
- Department of Chemistry, McGill University, Montreal, Québec H3A 0B8, Canada
| | - Hiu-Fung Lee
- Department of Chemistry, McGill University, Montreal, Québec H3A 0B8, Canada
| | - Tian Lai Guan
- Department of Chemistry, McGill University, Montreal, Québec H3A 0B8, Canada
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Tan Trieu Nguyen
- Department of Medicine, McGill University, Montreal, Québec H3A 1A1, Canada
| | - Xian Fang Huang
- Department of Medicine, McGill University, Montreal, Québec H3A 1A1, Canada
| | - Daniel D Waller
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, British Columbia V5Z 1L3, Canada
| | - Jordan Lu
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Iok In Christine Chio
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, United States
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - René P Michel
- Department of Pathology, McGill University, Montréal, Québec H3A 1A1, Canada
| | - Michael Sebag
- Department of Medicine, McGill University, Montreal, Québec H3A 1A1, Canada
- Division of Hematology, McGill University Health Center, Montreal, Québec H4A 3J1, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, Montreal, Québec H3A 0B8, Canada
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
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Khedr MA, Al-Wabli RI, Almutairi MS, Zaghary WA. Design, Synthesis, Molecular Docking, Dynamics and in vitro Evaluation of Novel 2-substituted-1-hydroxyethane-1, 1-bis(phosphonic acid) Derivatives as Human Farnesyl Pyrophosphate Synthase Inhibitors with Expected Anticancer Activity. Curr Pharm Des 2023; 29:48-59. [PMID: 36476435 DOI: 10.2174/1381612829666221202114947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/31/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Nitrogenous bisphosphonates (NBPs) are the major class of drugs that are used to treat osteoporosis. Recently, bisphosphonates (BPs) were reported to have an anticancer effect. These agents feature a high affinity that enables them to bind strongly to the human farnesyl pyrophosphate synthase enzyme. The correlation between this affinity and their anticancer effect was confirmed. OBJECTIVE To date, the use of an oxygen atom as an isosteric replacement for the electronegative nitrogen atom in NBPs has not been reported, and its ability to retain the linker length and bisphosphonate pharmacophore remains unknown. The main aim of this work was to design some isosteric bisphosphonate analogs with oxygen atoms and evaluation of their binding affinity and anticancer activity. METHODS The binding mode and stability of the designed compounds were achieved using human farnesyl pyrophosphate synthase (HFPPS) by docking and dynamic simulations. The compounds were synthesized, characterized, and screened for their anticancer activity against the breast cancer MCF-7 cell line and lung cancer A-549 cell line. The inhibitory activity of the tested compounds against HFPPS was evaluated. RESULTS The compounds under investigation showed potential anticancer activity against the lung cell line with IC50 values of 41.7, 47.4, and 34.8 μg/ml in comparison to that of Risedronic acid (115 μg/ml). However, they do not exhibit potential activity against the breast cancer cell line. CONCLUSION Compounds VII and VIII showed in vitro inhibition of human farnesyl pyrophosphate synthase with IC50 values of 82.2 and 98.8 μg/ml, respectively. Further optimization may be required in the future.
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Affiliation(s)
- Mohammed A Khedr
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, Safat, 13110, Kuwait
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ein Helwan, Cairo, 11790, Egypt
| | - Reem I Al-Wabli
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Maha S Almutairi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Wafaa A Zaghary
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Ein Helwan, Cairo, 11790, Egypt
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One-Pot and Catalyst-Free Transformation of N-Protected 1-Amino-1-Ethoxyalkylphosphonates into Bisphosphonic Analogs of Protein and Non-Protein α-Amino Acids. Molecules 2022; 27:molecules27113571. [PMID: 35684508 PMCID: PMC9182278 DOI: 10.3390/molecules27113571] [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: 05/19/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Herein, we describe the development of one-pot transformation of α-ethoxy derivatives of phosphorus analogs of protein and non-protein α-amino acids into biologically important N-protected 1-aminobisphosphonates. The proposed strategy, based on the three-component reaction of 1-(N-acylamino)-1-ethoxyphosphonates with triphenylphosphonium tetrafluoroborate and triethyl phosphite, facilitates good to excellent yields under mild reaction conditions. The course of the reaction was monitored by 31P NMR spectroscopy, allowing the identification of probable intermediate species, thus making it possible to propose a reaction mechanism. In most cases, there is no need to use a catalyst to provide transformation efficiency, which increases its attractiveness both in economic and ecological terms. Furthermore, we demonstrate that the one-pot procedure can be successfully applied for the synthesis of structurally diverse N-protected bisphosphonic analogs of α-amino acids. As shown, the indirect formation of the corresponding phosphonium salt as a reactive intermediate during the conversion of 1-(N-acylamino)-1-ethoxyphosphonate into a 1-aminobisphosphonate derivative is a crucial component of the developed methodology.
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Ershov P, Kaluzhskiy L, Mezentsev Y, Yablokov E, Gnedenko O, Ivanov A. Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. Biomedicines 2021; 9:biomedicines9080895. [PMID: 34440098 PMCID: PMC8389681 DOI: 10.3390/biomedicines9080895] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
A global protein interactome ensures the maintenance of regulatory, signaling and structural processes in cells, but at the same time, aberrations in the repertoire of protein-protein interactions usually cause a disease onset. Many metabolic enzymes catalyze multistage transformation of cholesterol precursors in the cholesterol biosynthesis pathway. Cancer-associated deregulation of these enzymes through various molecular mechanisms results in pathological cholesterol accumulation (its precursors) which can be disease risk factors. This work is aimed at systematization and bioinformatic analysis of the available interactomics data on seventeen enzymes in the cholesterol pathway, encoded by HMGCR, MVK, PMVK, MVD, FDPS, FDFT1, SQLE, LSS, DHCR24, CYP51A1, TM7SF2, MSMO1, NSDHL, HSD17B7, EBP, SC5D, DHCR7 genes. The spectrum of 165 unique and 21 common protein partners that physically interact with target enzymes was selected from several interatomic resources. Among them there were 47 modifying proteins from different protein kinases/phosphatases and ubiquitin-protein ligases/deubiquitinases families. A literature search, enrichment and gene co-expression analysis showed that about a quarter of the identified protein partners was associated with cancer hallmarks and over-represented in cancer pathways. Our results allow to update the current fundamental view on protein-protein interactions and regulatory aspects of the cholesterol synthesis enzymes and annotate of their sub-interactomes in term of possible involvement in cancers that will contribute to prioritization of protein targets for future drug development.
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Madan B, Virshup DM, Nes WD, Leaver DJ. Unearthing the Janus-face cholesterogenesis pathways in cancer. Biochem Pharmacol 2021; 196:114611. [PMID: 34010597 DOI: 10.1016/j.bcp.2021.114611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022]
Abstract
Cholesterol biosynthesis, primarily associated with eukaryotes, occurs as an essential component of human metabolism with biosynthetic deregulation a factor in cancer viability. The segment that partitions between squalene and the C27-end cholesterol yields the main cholesterogenesis branch subdivided into the Bloch and Kandutsch-Russell pathways. Their importance in cell viability, in normal growth and development originates primarily from the amphipathic property and shape of the cholesterol molecule which makes it suitable as a membrane insert. Cholesterol can also convert to variant oxygenated product metabolites of distinct function producing a complex interplay between cholesterol synthesis and overall steroidogenesis. In this review, we disassociate the two sides of cholesterogenesisis affecting the type and amounts of systemic sterols-one which is beneficial to human welfare while the other dysfunctional leading to misery and disease that could result in premature death. Our focus here is first to examine the cholesterol biosynthetic genes, enzymes, and order of biosynthetic intermediates in human cholesterogenesis pathways, then compare the effect of proximal and distal inhibitors of cholesterol biosynthesis against normal and cancer cell growth and metabolism. Collectively, the inhibitor studies of druggable enzymes and specific biosynthetic steps, suggest a potential role of disrupted cholesterol biosynthesis, in coordination with imported cholesterol, as a factor in cancer development and as discussed some of these inhibitors have chemotherapeutic implications.
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Affiliation(s)
- Babita Madan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore; Department of Pediatrics, Duke University, Durham, NC, USA
| | - W David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
| | - David J Leaver
- Department of Biology, Geology, and Physical Sciences, Sul Ross State University, Alpine, TX, USA.
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Park J, Pandya VR, Ezekiel SJ, Berghuis AM. Phosphonate and Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthases: A Structure-Guided Perspective. Front Chem 2021; 8:612728. [PMID: 33490038 PMCID: PMC7815940 DOI: 10.3389/fchem.2020.612728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphonates and bisphosphonates have proven their pharmacological utility as inhibitors of enzymes that metabolize phosphate and pyrophosphate substrates. The blockbuster class of drugs nitrogen-containing bisphosphonates represent one of the best-known examples. Widely used to treat bone-resorption disorders, these drugs work by inhibiting the enzyme farnesyl pyrophosphate synthase. Playing a key role in the isoprenoid biosynthetic pathway, this enzyme is also a potential anticancer target. Here, we provide a comprehensive overview of the research efforts to identify new inhibitors of farnesyl pyrophosphate synthase for various therapeutic applications. While the majority of these efforts have been directed against the human enzyme, some have been targeted on its homologs from other organisms, such as protozoan parasites and insects. Our particular focus is on the structures of the target enzymes and how the structural information has guided the drug discovery efforts.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Vishal R Pandya
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sean J Ezekiel
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
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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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Ghanakota P, DasGupta D, Carlson HA. Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. J Chem Inf Model 2019; 59:2035-2045. [PMID: 31017411 DOI: 10.1021/acs.jcim.8b00925] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In our recent efforts to map protein surfaces using mixed-solvent molecular dynamics (MixMD) (Ghanakota, P.; Carlson, H. A. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. J. Phys. Chem. B 2016, 120, 8685-8695), we were able to successfully capture active sites and allosteric sites within the top-four most occupied hotspots. In this study, we describe our approach for estimating the thermodynamic profile of the binding sites identified by MixMD. First, we establish a framework for calculating free energies from MixMD simulations, and we compare our approach to alternative methods. Second, we present a means to obtain a relative ranking of the binding sites by their configurational entropy. The theoretical maximum and minimum free energy and entropy values achievable under such a framework along with the limitations of the techniques are discussed. Using this approach, the free energy and relative entropy ranking of the top-four MixMD binding sites were computed and analyzed across our allosteric protein targets: Abl Kinase, Androgen Receptor, Pdk1 Kinase, Farnesyl Pyrophosphate Synthase, Chk1 Kinase, Glucokinase, and Protein Tyrosine Phosphatase 1B.
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Affiliation(s)
- Phani Ghanakota
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Debarati DasGupta
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
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9
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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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10
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Zhang Z, Zhu Z, Luo C, Zhu C, Zhang C, Guo Z, Wang X. A Potential Bone-Targeting Hypotoxic Platinum(II) Complex with an Unusual Cytostatic Mechanism toward Osteosarcoma Cells. Inorg Chem 2018. [PMID: 29513007 DOI: 10.1021/acs.inorgchem.7b03261] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Osteosarcoma (OS) is the most common primary pediatric bone tumor lethal to children and adolescents. Chemotherapeutic agents such as cisplatin are not effective for OS because of their poor accessibility to this cancer and severe systemic toxicity. In this study, a lipophilic platinum(II) complex bearing a bisphosphonate bone-targeting moiety, cis-[PtL(NH3)2Cl]NO3 {BPP; L = tetraethyl [2-(pyridin-2-yl)ethane-1,1-diyl]bisphosphonate}, was prepared and characterized by NMR, electrospray ionization mass spectrometry, and single-crystal X-ray crystallography. The cytotoxicity of BPP toward OS cell lines U2OS and MG-63 was tested by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. BPP exhibits moderate inhibition against U2OS cells through a mechanism involving both DNA binding and a mevalonate pathway. The acute toxicity of BPP to mice is 7-fold lower than that of cisplatin. The relative low systemic toxicity may result from the steric hindrance of the ligand, which blocks BPP approaching the bases of DNA. The results suggest that incorporating bisphosphonates into a platinum complex not only enhances its bone-targeting property but also minimizes its reactivity toward DNA and thereby lowers the systematic toxicity of the complex. The diminished cytotoxicity of BPP could be compensated for by increasing the therapeutic dose with marginal harm. This strategy provides a new possibility for overcoming the ineffectiveness and systemic toxicity of platinum drugs in the treatment of OS.
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Affiliation(s)
- Zhenqin Zhang
- School of Pharmacy , Nanjing Medical University , Nanjing 211166 , People's Republic of China
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11
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Chao MN, Storey M, Li C, Rodríguez MG, Di Salvo F, Szajnman SH, Moreno SN, Docampo R, Rodriguez JB. Selenium-containing analogues of WC-9 are extremely potent inhibitors of Trypanosoma cruzi proliferation. Bioorg Med Chem 2017; 25:6435-6449. [DOI: 10.1016/j.bmc.2017.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/06/2017] [Accepted: 10/15/2017] [Indexed: 12/21/2022]
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12
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Liu QZ, Wang SS, Li X, Zhao XY, Li K, Lv GC, Qiu L, Lin JG. 3D-QSAR, molecular docking, and ONIOM studies on the structure-activity relationships and action mechanism of nitrogen-containing bisphosphonates. Chem Biol Drug Des 2017; 91:735-746. [DOI: 10.1111/cbdd.13134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/15/2017] [Accepted: 10/14/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Qing-Zhu Liu
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
| | - Shan-Shan Wang
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
- School of Chemical and Material Engineering; Jiangnan University; Wuxi China
| | - Xi Li
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
- School of Chemical and Material Engineering; Jiangnan University; Wuxi China
| | - Xue-Yu Zhao
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
- School of Chemical and Material Engineering; Jiangnan University; Wuxi China
| | - Ke Li
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
| | - Gao-Chao Lv
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
| | - Ling Qiu
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
| | - Jian-Guo Lin
- Key Laboratory of Nuclear Medicine; Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi China
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13
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Park J, Rodionov D, De Schutter JW, Lin YS, Tsantrizos YS, Berghuis AM. Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. PLoS One 2017; 12:e0186447. [PMID: 29036218 PMCID: PMC5643135 DOI: 10.1371/journal.pone.0186447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/02/2017] [Indexed: 11/18/2022] Open
Abstract
Human farnesyl pyrophosphate synthase (hFPPS) catalyzes the production of the 15-carbon isoprenoid farnesyl pyrophosphate. The enzyme is a key regulator of the mevalonate pathway and a well-established drug target. Notably, it was elucidated as the molecular target of nitrogen-containing bisphosphonates, a class of drugs that have been widely successful against bone resorption disorders. More recently, research has focused on the anticancer effects of these inhibitors. In order to achieve increased non-skeletal tissue exposure, we created phenylaminopyridine bisphosphonates (PNP-BPs) that have bulky hydrophobic side chains through a structure-based approach. Some of these compounds have proven to be more potent than the current clinical drugs in a number of antiproliferation assays using multiple myeloma cell lines. In the present work, we characterized the binding of our most potent PNP-BPs to the target enzyme, hFPPS. Co-crystal structures demonstrate that the molecular interactions designed to elicit tighter binding are indeed established. We carried out thermodynamic studies as well; the newly introduced protein-ligand interactions are clearly reflected in the enthalpy of binding measured, which is more favorable for the new PNP-BPs than for the lead compound. These studies also indicate that the affinity of the PNP-BPs to hFPPS is comparable to that of the current drug risedronate. Risedronate forms additional polar interactions via its hydroxyl functional group and thus exhibits more favorable binding enthalpy; however, the entropy of binding is more favorable for the PNP-BPs, owing to the greater desolvation effects resulting from their large hydrophobic side chains. These results therefore confirm the overall validity of our drug design strategy. With a distinctly different molecular scaffold, the PNP-BPs described in this report represent an interesting new group of future drug candidates. Further investigation should follow to characterize the tissue distribution profile and assess the potential clinical benefits of these compounds.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Dmitry Rodionov
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | - Yih-Shyan Lin
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Youla S. Tsantrizos
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- * E-mail:
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14
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Kaźmierczak A, Kusy D, Niinivehmas SP, Gmach J, Joachimiak Ł, Pentikäinen OT, Gendaszewska-Darmach E, Błażewska KM. Identification of the Privileged Position in the Imidazo[1,2-a]pyridine Ring of Phosphonocarboxylates for Development of Rab Geranylgeranyl Transferase (RGGT) Inhibitors. J Med Chem 2017; 60:8781-8800. [PMID: 28953373 DOI: 10.1021/acs.jmedchem.7b00811] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Members of the Rab GTPase family are master regulators of vesicle trafficking. When disregulated, they are associated with a number of pathological states. The inhibition of RGGT, an enzyme responsible for post-translational geranylgeranylation of Rab GTPases represents one way to control the activity of these proteins. Because the number of molecules modulating RGGT is limited, we combined molecular modeling with biological assays to ascertain how modifications of phosphonocarboxylates, the first reported RGGT inhibitors, rationally improve understanding of their structure-activity relationship. We have identified the privileged position in the core scaffold of the imidazo[1,2-a]pyridine ring, which can be modified without compromising compounds' potency. Thus modified compounds are micromolar inhibitors of Rab11A prenylation, simultaneously being inactive against Rap1A/Rap1B modification, with the ability to inhibit proliferation of the HeLa cancer cell line. These findings were rationalized by molecular docking, which recognized interaction of phosphonic and carboxylic groups as decisive in phosphonocarboxylate localization in the RGGT binding site.
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Affiliation(s)
- Aleksandra Kaźmierczak
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology , Stefanowskiego Street 4/10, 90-924 Łódź, Poland
| | - Damian Kusy
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology , Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Sanna P Niinivehmas
- Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä , P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Joanna Gmach
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology , Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology , Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Olli T Pentikäinen
- Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä , P.O. Box 35, FI-40014 University of Jyväskylä, Finland.,Institute of Biomedicine, University of Turku , FI-20520 Turku, Finland
| | - Edyta Gendaszewska-Darmach
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology , Stefanowskiego Street 4/10, 90-924 Łódź, Poland
| | - Katarzyna M Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology , Żeromskiego Street 116, 90-924 Łódź, Poland
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15
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Three-Component Reaction of Benzylamines, Diethyl Phosphite and Triethyl Orthoformate: Dependence of the Reaction Course on the Structural Features of the Substrates and Reaction Conditions. Molecules 2017; 22:molecules22030450. [PMID: 28287472 PMCID: PMC6155184 DOI: 10.3390/molecules22030450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 11/17/2022] Open
Abstract
The reaction between benzyl amines, triethyl orthoformate, and diethyl phosphite affords either bisphosphonic (compound 1) or N-benzylaminobenzylphosphonic (compound 2) acid depending on the reaction conditions. The final output of the reaction can be manipulated by the choice of reaction conditions, particularly the molar ratio of substrates.
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16
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Park J, Leung CY, Matralis AN, Lacbay CM, Tsakos M, Fernandez De Troconiz G, Berghuis AM, Tsantrizos YS. Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase. J Med Chem 2017; 60:2119-2134. [PMID: 28208018 DOI: 10.1021/acs.jmedchem.6b01888] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The human farnesyl pyrophosphate synthase (hFPPS), a key regulatory enzyme in the mevalonate pathway, catalyzes the biosynthesis of the C-15 isoprenoid farnesyl pyrophosphate (FPP). FPP plays a crucial role in the post-translational prenylation of small GTPases that perform a plethora of cellular functions. Although hFPPS is a well-established therapeutic target for lytic bone diseases, the currently available bisphosphonate drugs exhibit poor cellular uptake and distribution into nonskeletal tissues. Recent drug discovery efforts have focused primarily on allosteric inhibition of hFPPS and the discovery of non-bisphosphonate drugs for potentially treating nonskeletal diseases. Hit-to-lead optimization of a new series of thienopyrimidine-based monosphosphonates (ThP-MPs) led to the identification of analogs with nanomolar potency in inhibiting hFPPS. Their interactions with the allosteric pocket of the enzyme were characterized by crystallography, and the results provide further insight into the pharmacophore requirements for allosteric inhibition.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University , 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Chun Yuen Leung
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Alexios N Matralis
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Cyrus M Lacbay
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Michail Tsakos
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | | | - Albert M Berghuis
- Department of Biochemistry, McGill University , 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada.,Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.,Department of Biochemistry, McGill University , 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada.,Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
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17
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Ghanakota P, Carlson HA. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. J Phys Chem B 2016; 120:8685-95. [PMID: 27258368 DOI: 10.1021/acs.jpcb.6b03515] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mixed-solvent molecular dynamics (MixMD) is a hotspot-mapping technique that relies on molecular dynamics simulations of proteins in binary solvent mixtures. Previous work on MixMD has established the technique's effectiveness in capturing binding sites of small organic compounds. In this work, we show that MixMD can identify both competitive and allosteric sites on proteins. The MixMD approach embraces full protein flexibility and allows competition between solvent probes and water. Sites preferentially mapped by probe molecules are more likely to be binding hotspots. There are two important requirements for the identification of ligand-binding hotspots: (1) hotspots must be mapped at very high signal-to-noise ratio and (2) the hotspots must be mapped by multiple probe types. We have developed our mapping protocol around acetonitrile, isopropanol, and pyrimidine as probe solvents because they allowed us to capture hydrophilic, hydrophobic, hydrogen-bonding, and aromatic interactions. Charged probes were needed for mapping one target, and we introduce them in this work. In order to demonstrate the robust nature and wide applicability of the technique, a combined total of 5 μs of MixMD was applied across several protein targets known to exhibit allosteric modulation. Most notably, all the protein crystal structures used to initiate our simulations had no allosteric ligands bound, so there was no preorganization of the sites to predispose the simulations to find the allosteric hotspots. The protein test cases were ABL Kinase, Androgen Receptor, CHK1 Kinase, Glucokinase, PDK1 Kinase, Farnesyl Pyrophosphate Synthase, and Protein-Tyrosine Phosphatase 1B. The success of the technique is demonstrated by the fact that the top-four sites solely map the competitive and allosteric sites. Lower-ranked sites consistently map other biologically relevant sites, multimerization interfaces, or crystal-packing interfaces. Lastly, we highlight the importance of including protein flexibility by demonstrating that MixMD can map allosteric sites that are not detected in half the systems using FTMap applied to the same crystal structures.
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Affiliation(s)
- Phani Ghanakota
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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18
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Rodriguez JB, Falcone BN, Szajnman SH. Approaches for Designing new Potent Inhibitors of Farnesyl Pyrophosphate Synthase. Expert Opin Drug Discov 2016; 11:307-20. [DOI: 10.1517/17460441.2016.1143814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Marzinzik AL, Amstutz R, Bold G, Bourgier E, Cotesta S, Glickman JF, Götte M, Henry C, Lehmann S, Hartwieg JCD, Ofner S, Pellé X, Roddy TP, Rondeau JM, Stauffer F, Stout SJ, Widmer A, Zimmermann J, Zoller T, Jahnke W. Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding. ChemMedChem 2015; 10:1884-91. [PMID: 26381451 DOI: 10.1002/cmdc.201500338] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 12/27/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS) is an established target for the treatment of bone diseases, but also shows promise as an anticancer and anti-infective drug target. Currently available anti-FPPS drugs are active-site-directed bisphosphonate inhibitors, the peculiar pharmacological profile of which is inadequate for therapeutic indications beyond bone diseases. The recent discovery of an allosteric binding site has paved the way toward the development of novel non-bisphosphonate FPPS inhibitors with broader therapeutic potential, notably as immunomodulators in oncology. Herein we report the discovery, by an integrated lead finding approach, of two new chemical classes of allosteric FPPS inhibitors that belong to the salicylic acid and quinoline chemotypes. We present their synthesis, biochemical and cellular activities, structure-activity relationships, and provide X-ray structures of several representative FPPS complexes. These novel allosteric FPPS inhibitors are devoid of any affinity for bone mineral and could serve as leads to evaluate their potential in none-bone diseases.
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Affiliation(s)
| | - René Amstutz
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Conim AG, Oberwiler Kirchweg 4c, 6300, Zug, Switzerland
| | - Guido Bold
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | | | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - J Fraser Glickman
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,High Throughput and Spectroscopy Resource Center, Rockefeller University, New York, NY, 10065, USA
| | - Marjo Götte
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Christelle Henry
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | | | - Silvio Ofner
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Thomas P Roddy
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Agios, Cambridge, MA, 02139-4169, USA
| | | | - Frédéric Stauffer
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Steven J Stout
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Armin Widmer
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Johann Zimmermann
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Polyphor, Hegenheimermattweg 125, 4123, Allschwil, Switzerland
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.
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20
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Kuźnik A, Mazurkiewicz R, Grymel M, Zielińska K, Adamek J, Chmielewska E, Bochno M, Kubica S. A new method for the synthesis of α-aminoalkylidenebisphosphonates and their asymmetric phosphonyl-phosphinyl and phosphonyl-phosphinoyl analogues. Beilstein J Org Chem 2015; 11:1418-24. [PMID: 26425197 PMCID: PMC4578414 DOI: 10.3762/bjoc.11.153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/24/2015] [Indexed: 11/23/2022] Open
Abstract
A convenient approach has been developed to α-aminoalkylidenebisphosphonates and their asymmetric phosphonyl-phosphinyl and phosphonyl-phosphinoyl analogues by α-phosphonylation, α-phosphinylation or α-phosphinoylation of 1-(N-acylamino)alkylphosphonates, that, in turn, are easily accessible from N-acyl-α-amino acids. Effective electrophilic activation of the α-position of 1-(N-acetylamino)alkylphosphonates was achieved by electrochemical α-methoxylation of these compounds in methanol, mediated with NaCl, followed by displacement of the methoxy group with triphenylphosphonium tetrafluoroborate to give hitherto unknown 1-(N-acetylamino)-1-triphenylphosphoniumalkylphosphonate tetrafluoroborates. The latter compounds react smoothly with trialkyl phosphites, dialkyl phosphonites or alkyl phosphinites in the presence of Hünig's base and methyltriphenylphosphonium iodide in a Michaelis-Arbuzov-like reaction to give the expected alkylidenebisphosphonates, 1-phosphinylalkylphosphonates or 1-phosphinoylalkylphosphonates, respectively, in good yields.
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Affiliation(s)
- Anna Kuźnik
- Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Roman Mazurkiewicz
- Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Mirosława Grymel
- Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Katarzyna Zielińska
- Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Jakub Adamek
- Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
| | - Ewa Chmielewska
- Department of Bioorganic Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Marta Bochno
- Department of Bioorganic Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Sonia Kubica
- Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland
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21
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Construction of 1H-pyrrol-2-ylphosphonates via [3+2] cycloaddition of phosphate azomethine ylides with ynones. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.091] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Reddy M, Kalla RMN, Dong LS, Jeong YT. Di-n-butyl ammonium chlorosulfonate as a highly efficient and recyclable ionic liquid for the synthesis of N-containing bisphosphonates. CATAL COMMUN 2015. [DOI: 10.1016/j.catcom.2014.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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23
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Mukherjee P, Li H, Sevrioukova I, Chreifi G, Martásek P, Roman LJ, Poulos TL, Silverman RB. Novel 2,4-disubstituted pyrimidines as potent, selective, and cell-permeable inhibitors of neuronal nitric oxide synthase. J Med Chem 2014; 58:1067-88. [PMID: 25489882 PMCID: PMC4329833 DOI: 10.1021/jm501719e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Selective inhibition of neuronal nitric oxide synthase (nNOS) is an important therapeutic approach to target neurodegenerative disorders. However, the majority of the nNOS inhibitors developed are arginine mimetics and, therefore, suffer from poor bioavailability. We designed a novel strategy to combine a more pharmacokinetically favorable 2-imidazolylpyrimidine head with promising structural components from previous inhibitors. In conjunction with extensive structure-activity studies, several highly potent and selective inhibitors of nNOS were discovered. X-ray crystallographic analysis reveals that these type II inhibitors utilize the same hydrophobic pocket to gain strong inhibitory potency (13), as well as high isoform selectivity. Interestingly, select compounds from this series (9) showed good permeability and low efflux in a Caco-2 assay, suggesting potential oral bioavailability, and exhibited minimal off-target binding to 50 central nervous system receptors. Furthermore, even with heme-coordinating groups in the molecule, modifying other pharmacophoric fragments minimized undesirable inhibition of cytochrome P450s from human liver microsomes.
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Affiliation(s)
- Paramita Mukherjee
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208-3113, United States
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24
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Lacbay CM, Mancuso J, Lin YS, Bennett N, Götte M, Tsantrizos YS. Modular Assembly of Purine-like Bisphosphonates as Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 2014; 57:7435-49. [DOI: 10.1021/jm501010f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Cyrus M. Lacbay
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - John Mancuso
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Yih-Shyan Lin
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Nicholas Bennett
- Department
of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
- Department
of Medicine, Division of Experimental Medicine, McGill University, 1110
Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Youla S. Tsantrizos
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
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25
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Park J, Matralis AN, Berghuis AM, Tsantrizos YS. Human isoprenoid synthase enzymes as therapeutic targets. Front Chem 2014; 2:50. [PMID: 25101260 PMCID: PMC4106277 DOI: 10.3389/fchem.2014.00050] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 06/25/2014] [Indexed: 12/14/2022] Open
Abstract
In the human body, the complex biochemical network known as the mevalonate pathway is responsible for the biosynthesis of all isoprenoids, which consists of a vast array of metabolites that are vital for proper cellular functions. Two key isoprenoids, farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) are responsible for the post-translational prenylation of small GTP-binding proteins, and serve as the biosynthetic precursors to numerous other biomolecules. The down-stream metabolite of FPP and GGPP is squalene, the precursor to steroids, bile acids, lipoproteins, and vitamin D. In the past, interest in prenyl synthase inhibitors focused mainly on the role of the FPP in lytic bone diseases. More recently pre-clinical and clinical studies have strongly implicated high levels of protein prenylation in a plethora of human diseases, including non-skeletal cancers, the progression of neurodegenerative diseases and cardiovascular diseases. In this review, we focus mainly on the potential therapeutic value of down-regulating the biosynthesis of FPP, GGPP, and squalene. We summarize the most recent drug discovery efforts and the structural data available that support the current on-going studies.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University Montreal, QC, Canada
| | | | - Albert M Berghuis
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology, McGill University Montreal, QC, Canada
| | - Youla S Tsantrizos
- Department of Biochemistry, McGill University Montreal, QC, Canada ; Department of Chemistry, McGill University Montreal, QC, Canada
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26
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Coxon FP, Joachimiak L, Najumudeen AK, Breen G, Gmach J, Oetken-Lindholm C, Way R, Dunford JE, Abankwa D, Błażewska KM. Synthesis and characterization of novel phosphonocarboxylate inhibitors of RGGT. Eur J Med Chem 2014; 84:77-89. [PMID: 25016230 DOI: 10.1016/j.ejmech.2014.06.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/14/2014] [Accepted: 06/27/2014] [Indexed: 12/31/2022]
Abstract
Phosphonocarboxylate (PC) analogs of the anti-osteoporotic drugs, bisphosphonates, represent the first class of selective inhibitors of Rab geranylgeranyl transferase (RabGGTase, RGGT), an enzyme implicated in several diseases including ovarian, breast and skin cancer. Here we present the synthesis and biological characterization of an extended set of this class of compounds, including lipophilic derivatives of the known RGGT inhibitors. From this new panel of PCs, we have identified an inhibitor of RGGT that is of similar potency as the most active published phosphonocarboxylate, but of higher selectivity towards this enzyme compared to prenyl pyrophosphate synthases. New insights into structural requirements are also presented, showing that only PC analogs of the most potent 3rd generation bisphosphonates inhibit RGGT. In addition, the first phosphonocarboxylate-derived GGPPS inhibitor is reported.
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Affiliation(s)
- Fraser P Coxon
- Musculoskeletal Programme, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
| | - Lukasz Joachimiak
- Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Arafath Kaja Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - George Breen
- Musculoskeletal Programme, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
| | - Joanna Gmach
- Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | | | - Rebecca Way
- Musculoskeletal Programme, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
| | - James E Dunford
- University of Oxford, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, The Botnar Research Center, UK
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Katarzyna M Błażewska
- Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland.
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27
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De Schutter JW, Park J, Leung CY, Gormley P, Lin YS, Hu Z, Berghuis AM, Poirier J, Tsantrizos YS. Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases. J Med Chem 2014; 57:5764-76. [DOI: 10.1021/jm500629e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Joris W. De Schutter
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Jaeok Park
- Department
of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Chun Yuen Leung
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Patrick Gormley
- Douglas Mental Health University Institute, 6825 Lasalle, Verdun, Quebec, H4H 1R3, Canada
| | - Yih-Shyan Lin
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Zheping Hu
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Albert M. Berghuis
- Department
of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
- Department
of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
- Groupe
de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada
| | - Judes Poirier
- Douglas Mental Health University Institute, 6825 Lasalle, Verdun, Quebec, H4H 1R3, Canada
| | - Youla S. Tsantrizos
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Department
of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
- Groupe
de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada
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28
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Park J, Lin YS, Tsantrizos YS, Berghuis AM. Structure of human farnesyl pyrophosphate synthase in complex with an aminopyridine bisphosphonate and two molecules of inorganic phosphate. Acta Crystallogr F Struct Biol Commun 2014; 70:299-304. [PMID: 24598914 PMCID: PMC3944689 DOI: 10.1107/s2053230x14002106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/29/2014] [Indexed: 12/12/2022] Open
Abstract
Human farnesyl pyrophosphate synthase (hFPPS) produces farnesyl pyrophosphate, an isoprenoid essential for a variety of cellular processes. The enzyme has been well established as the molecular target of the nitrogen-containing bisphosphonates (N-BPs), which are best known for their antiresorptive effects in bone but are also known for their anticancer properties. Crystal structures of hFPPS in ternary complexes with a novel bisphosphonate, YS0470, and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi) and isopentenyl pyrophosphate (IPP) have recently been reported. Only the co-binding of the bisphosphonate with either PPi or IPP resulted in the full closure of the C-terminal tail of the enzyme, a conformational change that is required for catalysis and that is also responsible for the potent in vivo efficacy of N-BPs. In the present communication, a co-crystal structure of hFPPS in complex with YS0470 and two molecules of Pi is reported. The unusually close proximity between these ligands, which was confirmed by anomalous diffraction data, suggests that they interact with one another, with their anionic charges neutralized in their bound state. The structure also showed the tail of the enzyme to be fully disordered, indicating that simultaneous binding of two Pi molecules with a bisphosphonate cannot induce the tail-closing conformational change in hFPPS. Examination of homologous FPPSs suggested that this ligand-dependent tail closure is only conserved in the mammalian proteins. The prevalence of Pi-bound hFPPS structures in the PDB raises a question regarding the in vivo relevance of Pi binding to the function of the enzyme.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Ouest, Montreal, QC H3A 0B8, Canada
| | - Youla S. Tsantrizos
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Department of Chemistry, McGill University, 801 Rue Sherbrooke Ouest, Montreal, QC H3A 0B8, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
- Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
- Department of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, QC H3A 2B4, Canada
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Li J, Li C, Han J, Zhang C, Shang D, Yao Q, Zhang Y, Xu Y, Liu W, Zhou M, Yang H, Su F, Li X. The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. J Biomed Inform 2014; 49:187-97. [PMID: 24561483 DOI: 10.1016/j.jbi.2014.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/17/2013] [Accepted: 02/03/2014] [Indexed: 11/26/2022]
Abstract
The use of genome-wide, sample-matched miRNA (miRNAs)-mRNA expression data provides a powerful tool for the investigation of miRNAs and genes involved in diseases. The identification of miRNA-regulated pathways has been crucial for analysis of the role of miRNAs. However, the classical identification method fails to consider the structural information of pathways and the regulation of miRNAs simultaneously. We proposed a method that simultaneously integrated the change in gene expression and structural information in order to identify pathways. Our method used fold changes in miRNAs and gene products, along with the quantification of the regulatory effect on target genes, to measure the change in gene expression. Topological characteristics were investigated to measure the influence of gene products on entire pathways. Through the analysis of multiple myeloma and prostate cancer expression data, our method was proven to be effective and reliable in identifying disease risk pathways that are regulated by miRNAs. Further analysis showed that the structure of a pathway plays a crucial role in the recognition of the pathway as a factor in disease risk.
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Affiliation(s)
- Jing Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China; Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, PR China
| | - Chunquan Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Junwei Han
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Desi Shang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Qianlan Yao
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Wei Liu
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Meng Zhou
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Fei Su
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Xia Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China.
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30
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Xiang H, Qi J, He Q, Jiang M, Yang C, Deng L. Synthesis of 2-C-substituted benzothiazoles via a copper-promoted domino condensation/S-arylation/heterocyclization process. Org Biomol Chem 2014; 12:4633-6. [DOI: 10.1039/c4ob00564c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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31
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Leung CY, Park J, De Schutter JW, Sebag M, Berghuis AM, Tsantrizos YS. Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition. J Med Chem 2013; 56:7939-50. [PMID: 23998921 DOI: 10.1021/jm400946f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Chun Yuen Leung
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Jaeok Park
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
| | - Joris W. De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Michael Sebag
- Division
of Haematology, McGill University Health Center, Royal Victoria Hospital, C6.80,
687 Pine Avenue West, Montreal, Quebec, Canada H3A 1A1
| | - Albert M. Berghuis
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
- Department of Microbiology and Immunology, McGill University, 801 Sherbrooke Street
West, Montreal, Quebec, Canada H3A 0B8
| | - Youla S. Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
- Department of Biochemistry, McGill University, 3649
Promenade Sir William Osler, Montreal, Quebec, Canada H3G 0B1
- Groupe de Recherche
Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir
William Osler, Montreal, Quebec, Canada H3G 0B1
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Tauro M, Laghezza A, Loiodice F, Agamennone M, Campestre C, Tortorella P. Arylamino methylene bisphosphonate derivatives as bone seeking matrix metalloproteinase inhibitors. Bioorg Med Chem 2013; 21:6456-65. [PMID: 24071448 DOI: 10.1016/j.bmc.2013.08.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/29/2013] [Accepted: 08/23/2013] [Indexed: 11/24/2022]
Abstract
The complexity of matrix metalloproteinase inhibitors (MMPIs) design derives from the difficulty in carefully addressing their inhibitory activity towards the MMP isoforms involved in many pathological conditions. In particular, specific metalloproteinases, such as MMP-2 and MMP-9, are key regulators of the 'vicious cycle' occurring between tumor metastases growth and bone remodeling. In an attempt to devise new approaches to selective inhibitor derivatives, we describe novel bisphosphonate bone seeking MMP inhibitors (BP-MMPIs), capable to be selectively targeted and to overcome undesired side effects of broad spectrum MMPIs. In vitro activity (IC50 values) for each inhibitor was determined against MMP-2, -8, -9 and -14, because of their relevant role in skeletal development and renewal. The results show that BP-MMPIs reached IC50 values of enzymatic inhibition in the low micromolar range. Computational studies, used to rationalize some trends in the observed inhibitory profiles, suggest a possible differential binding mode in MMP-2 that explains the selective inhibition of this isoform. In addition, survival assay was conducted on J774 cell line, a well known model system used to evaluate the structure-activity relationship of BPs for inhibiting bone resorption. The resulting data, confirming the specific activity of BP-MMPIs, and their additional proved propensity to bind hydroxyapatite powder in vitro, suggest a potential use of BP-MMPIs in skeletal malignancies.
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Affiliation(s)
- Marilena Tauro
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi 'Aldo Moro' di Bari, Via Orabona 4, 70126 Bari, Italy
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Fernández D, Ortega-Castro J, Frau J. Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates: a 3D-QSAR study. J Comput Aided Mol Des 2013; 27:739-54. [PMID: 23979193 DOI: 10.1007/s10822-013-9674-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 08/08/2013] [Indexed: 01/06/2023]
Abstract
We report the results of a comparative molecular field analysis and comparative molecular similarity index analysis of the human farnesyl pyrophosphate synthase (FPPS) inhibition by nitrogen bisphosphonates (NBPs) taking into account their time-dependent inhibition efficacies. The 3D-QSAR models obtained provide steric, electrostatic and hydrophobic contour maps consistent with the interactions into the active site of human FPPS observed in available crystallographic structures. Furthermore, the 3D-QSAR models obtained provide accurately IC50 values of the NBPs of the training set. The predictive ability of these 3D-QSAR models was found to rely on the choice of biologically active conformations of the target molecules and on a careful examination of the protonation status of the NBPs in the training set. The best models obtained can be useful to predict biological values of a high number of NBPs that have been used for the treatment of different diseases as potential inhibitors of the activity of the FPPS enzyme.
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Affiliation(s)
- David Fernández
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, Palma de Mallorca, 07122, Spain
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Tuerdi G, Ichinomiya S, Sato H, Siddig S, Suwa E, Iwata H, Yano T, Ueno K. Synergistic effect of combined treatment with gamma-tocotrienol and statin on human malignant mesothelioma cells. Cancer Lett 2013; 339:116-27. [PMID: 23879968 DOI: 10.1016/j.canlet.2013.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/24/2013] [Accepted: 07/15/2013] [Indexed: 02/04/2023]
Abstract
The present study is the first to demonstrate the synergetic effect of statins (atorvastatin and simvastatin) and gamma-tocotrienol (γ-T3) on human malignant mesothelioma (MM). Statin + γ-T3 combinations induced greater cell growth inhibition more than each single treatment via inhibition of mevalonate pathway, a well-known target of both γ-T3 and statins. γ-T3 was necessary for endoplasmic reticulum stress markers CHOP and GRP78, whereas an intrinsic apoptotic marker, caspase 3 activation was induced only in the presence of statins. Overall, the combination of γ-T3 and statins could be useful for MM therapy and functions in a complementary style.
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Affiliation(s)
- Guligena Tuerdi
- Department of Geriatric Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8675, Japan
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35
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Bortezomid enhances the efficacy of lidamycin against human multiple myeloma cells. Anticancer Drugs 2013; 24:609-16. [DOI: 10.1097/cad.0b013e3283615006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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36
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Gao J, Liu J, Qiu Y, Chu X, Qiao Y, Li D. Multi-target-directed design, syntheses, and characterization of fluorescent bisphosphonate derivatives as multifunctional enzyme inhibitors in mevalonate pathway. Biochim Biophys Acta Gen Subj 2013; 1830:3635-42. [DOI: 10.1016/j.bbagen.2013.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/30/2013] [Accepted: 02/12/2013] [Indexed: 11/28/2022]
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Leung CY, Langille AM, Mancuso J, Tsantrizos YS. Discovery of thienopyrimidine-based inhibitors of the human farnesyl pyrophosphate synthase—Parallel synthesis of analogs via a trimethylsilyl ylidene intermediate. Bioorg Med Chem 2013; 21:2229-2240. [DOI: 10.1016/j.bmc.2013.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/01/2013] [Accepted: 02/11/2013] [Indexed: 01/20/2023]
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38
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Park J, Lin YS, De Schutter JW, Tsantrizos YS, Berghuis AM. Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure. BMC STRUCTURAL BIOLOGY 2012; 12:32. [PMID: 23234314 PMCID: PMC3539973 DOI: 10.1186/1472-6807-12-32] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/07/2012] [Indexed: 02/06/2023]
Abstract
BACKGROUND Human farnesyl pyrophosphate synthase (FPPS) controls intracellular levels of farnesyl pyrophosphate, which is essential for various biological processes. Bisphosphonate inhibitors of human FPPS are valuable therapeutics for the treatment of bone-resorption disorders and have also demonstrated efficacy in multiple tumor types. Inhibition of human FPPS by bisphosphonates in vivo is thought to involve closing of the enzyme's C-terminal tail induced by the binding of the second substrate isopentenyl pyrophosphate (IPP). This conformational change, which occurs through a yet unclear mechanism, seals off the enzyme's active site from the solvent environment and is essential for catalysis. The crystal structure of human FPPS in complex with a novel bisphosphonate YS0470 and in the absence of a second substrate showed partial ordering of the tail in the closed conformation. RESULTS We have determined crystal structures of human FPPS in ternary complex with YS0470 and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi), and IPP. Binding of PPi or IPP to the enzyme-inhibitor complex, but not that of Pi, resulted in full ordering of the C-terminal tail, which is most notably characterized by the anchoring of the R351 side chain to the main frame of the enzyme. Isothermal titration calorimetry experiments demonstrated that PPi binds more tightly to the enzyme-inhibitor complex than IPP, and differential scanning fluorometry experiments confirmed that Pi binding does not induce the tail ordering. Structure analysis identified a cascade of conformational changes required for the C-terminal tail rigidification involving Y349, F238, and Q242. The residues K57 and N59 upon PPi/IPP binding undergo subtler conformational changes, which may initiate this cascade. CONCLUSIONS In human FPPS, Y349 functions as a safety switch that prevents any futile C-terminal closure and is locked in the "off" position in the absence of bound IPP. Q242 plays the role of a gatekeeper and directly controls the anchoring of R351 side chain. The interactions between the residues K57 and N59 and those upstream and downstream of Y349 are likely responsible for the switch activation. The findings of this study can be exploited for structure-guided optimization of existing inhibitors as well as development of new pharmacophores.
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Affiliation(s)
- Jaeok Park
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
| | - Joris W De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
| | - Youla S Tsantrizos
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Department of Microbiology and Immunology, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada,Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada
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Vishwakarma RK, Patel KA, Sonawane P, Singh S, Ruby, Kumari U, Agrawal DC, Khan BM. Molecular characterization of farnesyl pyrophosphate synthase from Bacopa monniera by comparative modeling and docking studies. Bioinformation 2012; 8:1075-81. [PMID: 23251041 PMCID: PMC3523221 DOI: 10.6026/97320630081075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 10/26/2012] [Indexed: 11/29/2022] Open
Abstract
UNLABELLED Farnesyl pyrophosphate synthase (FPS; EC 2.5.1.10) is a key enzyme in isoprenoid biosynthetic pathway and provides precursors for the biosynthesis of various pharmaceutically important metabolites. It catalyzes head to tail condensation of two isopentenyl pyrophosphate molecules with dimethylallyl pyrophosphate to form C15 compound farnesyl pyrophosphate. Recent studies have confirmed FPS as a molecular target of bisphosphonates for drug development against bone diseases as well as pathogens. Although large numbers of FPSs from different sources are known, very few protein structures have been reported till date. In the present study, FPS gene from medicinal plant Bacopa monniera (BmFPS) was characterized by comparative modeling and docking. Multiple sequence alignment showed two highly conserved aspartate rich motifs FARM and SARM (DDXXD). The 3-D model of BmFPS was generated based on structurally resolved FPS crystal information of Gallus gallus. The generated models were validated by various bioinformatics tools and the final model contained only α-helices and coils. Further, docking studies of modeled BmFPS with substrates and inhibitors were performed to understand the protein ligand interactions. The two Asp residues from FARM (Asp100 and Asp104) as well as Asp171, Lys197 and Lys262 were found to be important for catalytic activity. Interaction of nitrogen containing bisphosphonates (risedronate, alendronate, zoledronate and pamidronate) with modeled BmFPS showed competitive inhibition; where, apart from Asp (100, 104 and 171), Thr175 played an important role. The results presented here could be useful for designing of mutants for isoprenoid biosynthetic pathway engineering well as more effective drugs against osteoporosis and human pathogens. ABBREVIATIONS IPP - Isopentenyl Pyrophosphate, DMAPP - Dimethylallyl Pyrophosphate, GPP - Geranyl Pyrophosphate, FPP - FPPFarnesyl Pyrophosphate, DOPE - Discrete Optimized Protein Energy, BmFPS - Bacopa monniera Farnesyl Pyrophosphate Synthase, RMSD - Root Mean square Deviation, OPLS-AA - Optimized Potentials for Liquid Simulations- All Atom, FARM - First Aspartate Rich Motif, SARM - Second Aspartate Rich Motif.
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Affiliation(s)
| | | | - Prashant Sonawane
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Somesh Singh
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Ruby
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Uma Kumari
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
| | - Dinesh Chandra Agrawal
- Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
- Authors equally contributed
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Thaler R, Spitzer S, Karlic H, Berger C, Klaushofer K, Varga F. Ibandronate increases the expression of the pro-apoptotic gene FAS by epigenetic mechanisms in tumor cells. Biochem Pharmacol 2012; 85:173-85. [PMID: 23103563 PMCID: PMC3557391 DOI: 10.1016/j.bcp.2012.10.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/16/2012] [Accepted: 10/16/2012] [Indexed: 12/13/2022]
Abstract
There is growing evidence that aminobisphosphonates like ibandronate show anticancer activity by an unknown mechanism. Biochemically, they prevent posttranslational isoprenylation of small GTPases, thus inhibiting their activity. In tumor cells, activated RAS-GTPase, the founding member of the gene family, down-regulates the expression of the pro-apoptotic gene FAS via epigenetic DNA-methylation by DNMT1. We compared ibandronate treatment in neoplastic human U-2 osteosarcoma and in mouse CCL-51 breast cancer cells as well as in the immortalized non-neoplastic MC3T3-E1 osteoblastic cells. Ibandronate attenuated cell proliferation in all cell lines tested. In the neoplastic cells we found up-regulation of caspases suggesting apoptosis. Further we found stimulation of FAS-expression as a result of epigenetic DNA demethylation that was due to down-regulation of DNMT1, which was rescued by re-isoprenylation by both geranylgeranyl-pyrophosphate and farnesylpyrophosphate. In contrast, ibandronate did not affect FAS and DNMT1 expression in MC3T3-E1 non-neoplastic cells. Data suggest that bisphosphonates via modulation of the activity of small-GTPases induce apoptosis in neoplastic cells by DNA-CpG-demethylation and stimulation of FAS-expression. In conclusion the shown epigenetic mechanism underlying the anti-neoplastic activity of farnesyl-transferase-inhibition, also explains the clinical success of other drugs, which target this pathway.
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Affiliation(s)
- R. Thaler
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling, 1st Medical Department, Hanusch Hospital, Vienna, Austria
| | - S. Spitzer
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling, 1st Medical Department, Hanusch Hospital, Vienna, Austria
| | - H. Karlic
- Ludwig Boltzmann Cluster Oncology and Institute for Leukemia Research and Hematology, Hanusch Hospital, Vienna, Austria
| | - C. Berger
- Department of Orthopedics, SMZ-OST, Danube Hospital, Vienna, Austria
| | - K. Klaushofer
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling, 1st Medical Department, Hanusch Hospital, Vienna, Austria
| | - F. Varga
- Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Center Meidling, 1st Medical Department, Hanusch Hospital, Vienna, Austria
- Corresponding author at: Ludwig Boltzmann Institute of Osteology, 1st Medical Department, Hanusch Hospital, Heinrich Collin-Str. 30, A-1140 Vienna, Austria. Tel.: +43 1 91021 86933; fax: +43 1 91021 86929.
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De Schutter JW, Shaw J, Lin YS, Tsantrizos YS. Design of potent bisphosphonate inhibitors of the human farnesyl pyrophosphate synthase via targeted interactions with the active site ‘capping’ phenyls. Bioorg Med Chem 2012; 20:5583-91. [DOI: 10.1016/j.bmc.2012.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/04/2012] [Accepted: 07/13/2012] [Indexed: 11/28/2022]
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The preparation of N-substituted aminomethylidenebisphosphonates and their tetraalkyl esters via reaction of isonitriles with trialkyl phosphites and hydrogen chloride. Part 1. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.07.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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43
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Xiang H, Qi X, Xie Y, Xu G, Yang C. One-pot syntheses of novel pyrazole-containing bisphosphonate esters at room temperature. Org Biomol Chem 2012; 10:7730-8. [DOI: 10.1039/c2ob25889g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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