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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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De Schutter JW, Morrison JP, Morrison MJ, Ciulli A, Imperiali B. Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni. J Med Chem 2017; 60:2099-2118. [PMID: 28182413 DOI: 10.1021/acs.jmedchem.6b01869] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The glycoproteins of selected microbial pathogens often include highly modified carbohydrates such as 2,4-diacetamidobacillosamine (diNAcBac). These glycoconjugates are involved in host-cell interactions and may be associated with the virulence of medically significant Gram-negative bacteria. In light of genetic studies demonstrating the attenuated virulence of bacterial strains in which modified carbohydrate biosynthesis enzymes have been knocked out, we are developing small molecule inhibitors of selected enzymes as tools to evaluate whether such compounds modulate virulence. We performed fragment-based and high-throughput screens against an amino-sugar acetyltransferase enzyme, PglD, involved in biosynthesis of UDP-diNAcBac in Campylobacter jejuni. Herein we report optimization of the hits into potent small molecule inhibitors (IC50 < 300 nM). Biophysical characterization shows that the best inhibitors are competitive with acetyl coenzyme A and an X-ray cocrystal structure reveals that binding is biased toward occupation of the adenine subpocket of the AcCoA binding site by an aromatic ring.
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Affiliation(s)
- Joris W De Schutter
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - James P Morrison
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael J Morrison
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , DD1 5EH Dundee, Scotland
| | - Barbara Imperiali
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Department of Biology, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Gritzalis D, Park J, Chiu W, Cho H, Lin YS, De Schutter JW, Lacbay CM, Zielinski M, Berghuis AM, Tsantrizos YS. Probing the molecular and structural elements of ligands binding to the active site versus an allosteric pocket of the human farnesyl pyrophosphate synthase. Bioorg Med Chem Lett 2015; 25:1117-23. [PMID: 25630225 DOI: 10.1016/j.bmcl.2014.12.089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/26/2014] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
In order to explore the interactions of bisphosphonate ligands with the active site and an allosteric pocket of the human farnesyl pyrophosphate synthase (hFPPS), substituted indole and azabenzimidazole bisphosphonates were designed as chameleon ligands. NMR and crystallographic studies revealed that these compounds can occupy both sub-pockets of the active site cavity, as well as the allosteric pocket of hFPPS in the presence of the enzyme's Mg(2+) ion cofactor. These results are consistent with the previously proposed hypothesis that the allosteric pocket of hFPPS, located near the active site, plays a feed-back regulatory role for this enzyme.
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Affiliation(s)
- Dimitrios Gritzalis
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Wei Chiu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Hyungjun Cho
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Joris W De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Cyrus M Lacbay
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Michal Zielinski
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Department of Microbiology and Immunology, McGill University, 3775 Rue University, Montreal, QC H3A 2B4, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada; Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montréal, QC H3G 0B1, Canada.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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 Struct Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [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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Lin YS, Park J, De Schutter JW, Huang XF, Berghuis AM, Sebag M, Tsantrizos YS. Design and Synthesis of Active Site Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Apoptosis and Inhibition of ERK Phosphorylation in Multiple Myeloma Cells. J Med Chem 2012; 55:3201-15. [PMID: 22390415 DOI: 10.1021/jm201657x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yih-Shyan Lin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal,
QC, Canada H3A 0B8
| | - Jaeok Park
- Department
of Biochemistry, McGill University, 3649
Promenade Sir William Osler,
Montreal, QC, Canada H3G 0B1
| | - Joris W. De Schutter
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal,
QC, Canada H3A 0B8
| | - Xian Fang Huang
- Division of Haematology, McGill University Health Center, Royal Victoria Hospital,
C6.80, 687 Pine Avenue West, Montreal, QC, Canada H3A 1A1
| | - Albert M. Berghuis
- Department
of Biochemistry, McGill University, 3649
Promenade Sir William Osler,
Montreal, QC, Canada H3G 0B1
| | - Michael Sebag
- Division of Haematology, McGill University Health Center, Royal Victoria Hospital,
C6.80, 687 Pine Avenue West, Montreal, QC, Canada H3A 1A1
| | - Youla S. Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal,
QC, Canada H3A 0B8
- Department
of Biochemistry, McGill University, 3649
Promenade Sir William Osler,
Montreal, QC, Canada H3G 0B1
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Weill N, Corbeil CR, De Schutter JW, Moitessier N. Toward a computational tool predicting the stereochemical outcome of asymmetric reactions: Development of the molecular mechanics‐based program ACE and application to asymmetric epoxidation reactions. J Comput Chem 2011; 32:2878-89. [DOI: 10.1002/jcc.21869] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/05/2011] [Accepted: 05/21/2011] [Indexed: 01/22/2023]
Affiliation(s)
- Nathanael Weill
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 2K6
| | | | | | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 2K6
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De Schutter JW, Zaretsky S, Welbourn S, Pause A, Tsantrizos YS. Novel bisphosphonate inhibitors of the human farnesyl pyrophosphate synthase. Bioorg Med Chem Lett 2010; 20:5781-6. [DOI: 10.1016/j.bmcl.2010.07.133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 07/30/2010] [Indexed: 11/15/2022]
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Rauws TR, Biancalani C, De Schutter JW, Maes BU. Synthesis of new tetracyclic azaheteroaromatic cores via auto-tandem Pd-catalyzed and one-pot Pd- and Cu-catalyzed double C–N bond formation. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.06.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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