1
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Sultana R, Abid OUR, Sultana N, Fakhar-e-Alam M, Siddique MH, Atif M, Nawaz M, Wadood A, Rehman AU, Farooq W, Shafeeq S, Afzal M. Potential Enzyme Inhibitor Triazoles from Aliphatic esters: Synthesis, enzyme inhibition and docking studies. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2022.101565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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2
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Pederick JL, Horsfall AJ, Jovcevski B, Klose J, Abell AD, Pukala TL, Bruning JB. Discovery of an ʟ-amino acid ligase implicated in Staphylococcal sulfur amino acid metabolism. J Biol Chem 2022; 298:102392. [PMID: 35988643 PMCID: PMC9486568 DOI: 10.1016/j.jbc.2022.102392] [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: 05/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
Enzymes involved in Staphylococcus aureus amino acid metabolism have recently gained traction as promising targets for the development of new antibiotics, however, not all aspects of this process are understood. The ATP-grasp superfamily includes enzymes that predominantly catalyze the ATP-dependent ligation of various carboxylate and amine substrates. One subset, ʟ-amino acid ligases (LALs), primarily catalyze the formation of dipeptide products in Gram-positive bacteria, however, their involvement in S. aureus amino acid metabolism has not been investigated. Here, we present the characterization of the putative ATP-grasp enzyme (SAOUHSC_02373) from S. aureus NCTC 8325 and its identification as a novel LAL. First, we interrogated the activity of SAOUHSC_02373 against a panel of ʟ-amino acid substrates. As a result, we identified SAOUHSC_02373 as an LAL with high selectivity for ʟ-aspartate and ʟ-methionine substrates, specifically forming an ʟ-aspartyl–ʟ-methionine dipeptide. Thus, we propose that SAOUHSC_02373 be assigned as ʟ-aspartate–ʟ-methionine ligase (LdmS). To further understand this unique activity, we investigated the mechanism of LdmS by X-ray crystallography, molecular modeling, and site-directed mutagenesis. Our results suggest that LdmS shares a similar mechanism to other ATP-grasp enzymes but possesses a distinctive active site architecture that confers selectivity for the ʟ-Asp and ʟ-Met substrates. Phylogenetic analysis revealed LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Subsequent genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with control of Met and Cys metabolism. Together, these findings support a role for LdmS in Staphylococcal sulfur amino acid metabolism.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Aimee J Horsfall
- Institute for Photonics and Advanced Sensing, (IPAS), School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jack Klose
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Institute for Photonics and Advanced Sensing, (IPAS), School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Tara L Pukala
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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3
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Zhu W, Radadiya A, Bisson C, Wenzel S, Nordin BE, Martínez-Márquez F, Imasaki T, Sedelnikova SE, Coricello A, Baumann P, Berry AH, Nomanbhoy TK, Kozarich JW, Jin Y, Rice DW, Takagi Y, Richards NGJ. High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity. Commun Biol 2019; 2:345. [PMID: 31552298 PMCID: PMC6748925 DOI: 10.1038/s42003-019-0587-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Expression of human asparagine synthetase (ASNS) promotes metastatic progression and tumor cell invasiveness in colorectal and breast cancer, presumably by altering cellular levels of L-asparagine. Human ASNS is therefore emerging as a bona fide drug target for cancer therapy. Here we show that a slow-onset, tight binding inhibitor, which exhibits nanomolar affinity for human ASNS in vitro, exhibits excellent selectivity at 10 μM concentration in HCT-116 cell lysates with almost no off-target binding. The high-resolution (1.85 Å) crystal structure of human ASNS has enabled us to identify a cluster of negatively charged side chains in the synthetase domain that plays a key role in inhibitor binding. Comparing this structure with those of evolutionarily related AMP-forming enzymes provides insights into intermolecular interactions that give rise to the observed binding selectivity. Our findings demonstrate the feasibility of developing second generation human ASNS inhibitors as lead compounds for the discovery of drugs against metastasis. Wen Zhu et al. report the crystal structure of human asparagine synthetase at a 1.85 Å resolution, enabling computational analysis of inhibitor binding. They also find new insights into the intermolecular interactions contributing to binding specificity of inhibitors.
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Affiliation(s)
- Wen Zhu
- 1School of Chemistry, Cardiff University, Cardiff, UK.,8Present Address: Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA USA
| | | | - Claudine Bisson
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,8Present Address: Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA USA
| | - Sabine Wenzel
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Brian E Nordin
- 4ActivX Biosciences, Inc, La Jolla, CA USA.,Present Address: Vividion Therapeutics, San Diego, CA USA
| | - Francisco Martínez-Márquez
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Tsuyoshi Imasaki
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA.,5Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Svetlana E Sedelnikova
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | | | - Alexandria H Berry
- 6Department of Biology, California Institute of Technology, Pasadena, CA USA
| | | | | | - Yi Jin
- 1School of Chemistry, Cardiff University, Cardiff, UK
| | - David W Rice
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Yuichiro Takagi
- 3Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Nigel G J Richards
- 1School of Chemistry, Cardiff University, Cardiff, UK.,7Foundation for Applied Molecular Evolution, Alachua, FL USA
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4
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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5
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Pham VH, Maaroufi H, Balg C, Blais SP, Messier N, Roy PH, Otis F, Voyer N, Lapointe J, Chênevert R. Inhibition ofHelicobacter pyloriGlu-tRNAGlnamidotransferase by novel analogues of the putative transamidation intermediate. FEBS Lett 2016; 590:3335-3345. [DOI: 10.1002/1873-3468.12380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Van Hau Pham
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie; Université Laval; Québec Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
| | - Christian Balg
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
| | - Sébastien P. Blais
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie; Université Laval; Québec Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
| | - Nancy Messier
- CHU de Québec; Centre de Recherche en Infectiologie; Université Laval; Québec Canada
| | - Paul H. Roy
- CHU de Québec; Centre de Recherche en Infectiologie; Université Laval; Québec Canada
| | - François Otis
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
| | - Normand Voyer
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
| | - Jacques Lapointe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie; Université Laval; Québec Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Canada
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
| | - Robert Chênevert
- The Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO); Université Laval; Québec Canada
- Département de Chimie, Faculté des Sciences et de Génie; Université Laval; Québec Canada
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6
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Chang YC, Weng CM, Shaikh T, Hong FE. Magnesium Halide-promoted Ring-opening Reaction of Cyclic Ether in the Presence of Phosphine Halide. J CHIN CHEM SOC-TAIP 2015. [DOI: 10.1002/jccs.201500154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Ding W, Li Y, Zhang Q. Substrate-Controlled Stereochemistry in Natural Product Biosynthesis. ACS Chem Biol 2015; 10:1590-8. [PMID: 25844528 DOI: 10.1021/acschembio.5b00104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Enzymes are generally believed to be highly regio- and stereoselective catalysts that strictly control the reaction coordinates and dominate the final catalytic outcomes. However, recent studies have started to suggest that substrates sometimes play key roles in determining the product selectivity in enzyme catalysis. Here, we highlight several enzymatic reactions in which the stereoselectivity is, at least in large part, governed by the intrinsic properties of the substrate rather than by characteristics of the enzyme. These reactions are involved in the biosynthesis of different classes of natural products, including lanthipeptides, sactipeptides, and polyketides. Understanding the mechanism of substrate-controlled stereospecificity may not only expand our knowledge of enzyme catalysis and enzyme evolution but also guide bioengineering efforts to produce novel valuable products.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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8
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Schiebel J, Chang A, Merget B, Bommineni GR, Yu W, Spagnuolo LA, Baxter MV, Tareilus M, Tonge PJ, Kisker C, Sotriffer CA. An ordered water channel in Staphylococcus aureus FabI: unraveling the mechanism of substrate recognition and reduction. Biochemistry 2015; 54:1943-55. [PMID: 25706582 DOI: 10.1021/bi5014358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
One third of all drugs in clinical use owe their pharmacological activity to the functional inhibition of enzymes, highlighting the importance of enzymatic targets for drug development. Because of the close relationship between inhibition and catalysis, understanding the recognition and turnover of enzymatic substrates is essential for rational drug design. Although the Staphylococcus aureus enoyl-acyl carrier protein reductase (saFabI) involved in bacterial fatty acid biosynthesis constitutes a very promising target for the development of novel, urgently needed anti-staphylococcal agents, the substrate binding mode and catalytic mechanism remained unclear for this enzyme. Using a combined crystallographic, kinetic, and computational approach, we have explored the chemical properties of the saFabI binding cavity, obtaining a consistent mechanistic model for substrate binding and turnover. We identified a water-molecule network linking the active site with a water basin inside the homo-tetrameric protein, which seems to be crucial for the closure of the flexible substrate binding loop as well as for an effective hydride and proton transfer during catalysis. On the basis of our results, we also derive a new model for the FabI-ACP complex that reveals how the ACP-bound acyl-substrate is injected into the FabI binding crevice. These findings support the future development of novel FabI inhibitors that target the FabI-ACP interface leading to the disruption of the interaction between these two proteins.
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Affiliation(s)
- Johannes Schiebel
- †Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany.,‡Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Josef-Schneider-Str. 2, D-97080 Wuerzburg, Germany
| | | | - Benjamin Merget
- †Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | | | | | | | | | - Mona Tareilus
- ‡Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Josef-Schneider-Str. 2, D-97080 Wuerzburg, Germany
| | | | - Caroline Kisker
- ‡Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, Josef-Schneider-Str. 2, D-97080 Wuerzburg, Germany
| | - Christoph A Sotriffer
- †Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
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9
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Point V, Malla RK, Diomande S, Martin BP, Delorme V, Carriere F, Canaan S, Rath NP, Spilling CD, Cavalier JF. Synthesis and kinetic evaluation of cyclophostin and cyclipostins phosphonate analogs as selective and potent inhibitors of microbial lipases. J Med Chem 2012; 55:10204-19. [PMID: 23095026 DOI: 10.1021/jm301216x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new series of customizable diastereomeric cis- and trans-monocyclic enol-phosphonate analogs to Cyclophostin and Cyclipostins were synthesized. Their potencies and mechanisms of inhibition toward six representative lipolytic enzymes belonging to distinct lipase families were examined. With mammalian gastric and pancreatic lipases no inhibition occurred with any of the compounds tested. Conversely, Fusarium solani Cutinase and lipases from Mycobacterium tuberculosis (Rv0183 and LipY) were all fully inactivated. The best inhibitors displayed a cis conformation (H and OMe) and exhibited higher inhibitory activities than the lipase inhibitor Orlistat toward the same enzymes. Our results have revealed that chemical group at the γ-carbon of the phosphonate ring strongly impacts the inhibitory efficiency, leading to a significant improvement in selectivity toward a target lipase over another. The powerful and selective inhibition of microbial (fungal and mycobacterial) lipases suggests that these seven-membered monocyclic enol-phosphonates should provide useful leads for the development of novel and highly selective antimicrobial agents.
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Affiliation(s)
- Vanessa Point
- CNRS - Aix-Marseille Université , Enzymologie Interfaciale et Physiologie de la Lipolyse, UMR 7282, 31 chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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10
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Ašler IL, Kovačić F, Marchetti-Deschmann M, Allmaier G, Štefanić Z, Kojić-Prodić B. Inhibition of extracellular lipase from Streptomyces rimosus with 3,4-dichloroisocoumarin. J Enzyme Inhib Med Chem 2012; 28:1094-104. [DOI: 10.3109/14756366.2012.716834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ivana Leščić Ašler
- Rudjer Bošković Institute, Department for Physical Chemistry,
Zagreb, Croatia
| | - Filip Kovačić
- Institute of Molecular Enzyme Technology, Heinrich-Heine University Düsseldorf, Research Center Jülich,
Jülich, Germany
| | | | - Günter Allmaier
- Vienna University of Technology, Institute for Chemical Technologies and Analytics,
Vienna, Austria
| | - Zoran Štefanić
- Rudjer Bošković Institute, Department for Physical Chemistry,
Zagreb, Croatia
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11
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Ikeuchi H, Ahn YM, Otokawa T, Watanabe B, Hegazy L, Hiratake J, Richards NGJ. A sulfoximine-based inhibitor of human asparagine synthetase kills L-asparaginase-resistant leukemia cells. Bioorg Med Chem 2012; 20:5915-27. [PMID: 22951255 DOI: 10.1016/j.bmc.2012.07.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/19/2012] [Accepted: 07/24/2012] [Indexed: 11/27/2022]
Abstract
An adenylated sulfoximine transition-state analogue 1, which inhibits human asparagine synthetase (hASNS) with nanomolar potency, has been reported to suppress the proliferation of an l-asparagine amidohydrolase (ASNase)-resistant MOLT-4 leukemia cell line (MOLT-4R) when l-asparagine is depleted in the medium. We now report the synthesis and biological activity of two new sulfoximine analogues of 1 that have been studied as part of systematic efforts to identify compounds with improved cell permeability and/or metabolic stability. One of these new analogues, an amino sulfoximine 5 having no net charge at cellular pH, is a better hASNS inhibitor (K(I)(∗)=8 nM) than 1 and suppresses proliferation of MOLT-4R cells at 10-fold lower concentration (IC(50)=0.1mM). More importantly, and in contrast to the lead compound 1, the presence of sulfoximine 5 at concentrations above 0.25 mM causes the death of MOLT-4R cells even when ASNase is absent in the culture medium. The amino sulfoximine 5 exhibits different dose-response behavior when incubated with an ASNase-sensitive MOLT-4 cell line (MOLT-4S), supporting the hypothesis that sulfoximine 5 exerts its effect by inhibiting hASNS in the cell. Our work provides further evidence for the idea that hASNS represents a chemotherapeutic target for the treatment of leukemia, and perhaps other cancers, including those of the prostate.
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Affiliation(s)
- Hideyuki Ikeuchi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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12
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Lagos CF, Araya-Secchi R, Thomas P, Pérez-Acle T, Tapia RA, Salas CO. Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione. J Mol Model 2012; 18:2055-64. [DOI: 10.1007/s00894-011-1224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 08/11/2011] [Indexed: 11/28/2022]
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13
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Fawaz MV, Topper M, Firestine SM. The ATP-grasp enzymes. Bioorg Chem 2011; 39:185-91. [PMID: 21920581 PMCID: PMC3243065 DOI: 10.1016/j.bioorg.2011.08.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/12/2011] [Accepted: 08/13/2011] [Indexed: 12/17/2022]
Abstract
The ATP-grasp enzymes consist of a superfamily of 21 proteins that contain an atypical ATP-binding site, called the ATP-grasp fold. The ATP-grasp fold is comprised of two α+β domains that "grasp" a molecule of ATP between them and members of the family typically have an overall structural design containing three common conserved focal domains. The founding members of the family consist of biotin carboxylase, d-ala-d-ala ligase and glutathione synthetase, all of which catalyze the ATP-assisted reaction of a carboxylic acid with a nucleophile via the formation of an acylphosphate intermediate. While most members of the superfamily follow this mechanistic pathway, studies have demonstrated that two enzymes catalyze only the phosphoryl transfer step and thus are kinases instead of ligases. Members of the ATP-grasp superfamily are found in several metabolic pathways including de novo purine biosynthesis, gluconeogenesis, and fatty acid synthesis. Given the critical nature of these enzymes, researchers have actively sought the development of potent inhibitors of several members of the superfamily as antibacterial and anti-obseity agents. In this review, we will discuss the structure, function, mechanism, and inhibition of the ATP-grasp enzymes.
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Affiliation(s)
| | | | - Steven M. Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201
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14
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Ašler IL, Pigac J, Vujaklija D, Luić M, Štefanić Z. Crystallization and preliminary X-ray diffraction studies of a complex of extracellular lipase from Streptomyces rimosus with the inhibitor 3,4-dichloroisocoumarin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1378-81. [PMID: 22102236 DOI: 10.1107/s1744309111032222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 08/09/2011] [Indexed: 11/10/2022]
Abstract
A recombinant lipase (triacylglycerol acylhydrolase; EC 3.1.1.3) from the bacterium Streptomyces rimosus was inhibited by the serine protease inhibitor 3,4-dichloroisocoumarin and crystallized by the hanging-drop vapour-diffusion method at 291 K. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 38.1, b = 78.7, c = 56.6 Å, β = 104.5° and probably two molecules in the asymmetric unit. Diffraction data were collected to 1.7 Å resolution using synchrotron radiation on the XRD beamline of the Elettra synchrotron, Trieste, Italy.
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Affiliation(s)
- Ivana Leščić Ašler
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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15
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Synthesis of 3,5-diazabicyclo [5.1.0] octenes. A new platform to mimic glycosidase transition states. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Ikeuchi H, Meyer ME, Ding Y, Hiratake J, Richards NG. A critical electrostatic interaction mediates inhibitor recognition by human asparagine synthetase. Bioorg Med Chem 2009; 17:6641-50. [DOI: 10.1016/j.bmc.2009.07.071] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 07/26/2009] [Accepted: 07/28/2009] [Indexed: 12/01/2022]
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17
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Zarnowski R, Cooper KG, Brunold LS, Calaycay J, Woods JP. Histoplasma capsulatum secreted gamma-glutamyltransferase reduces iron by generating an efficient ferric reductant. Mol Microbiol 2008; 70:352-68. [PMID: 18761625 DOI: 10.1111/j.1365-2958.2008.06410.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The intracellular fungal pathogen Histoplasma capsulatum (Hc) resides in mammalian macrophages and causes respiratory and systemic disease. Iron limitation is an important host antimicrobial defence, and iron acquisition is critical for microbial pathogenesis. Hc displays several iron acquisition mechanisms, including secreted glutathione-dependent ferric reductase activity (GSH-FeR). We purified this enzyme from culture supernatant and identified a novel extracellular iron reduction strategy involving gamma-glutamyltransferase (Ggt1) activity. The 320 kDa complex was composed of glycosylated protein subunits of about 50 and 37 kDa. The purified enzyme exhibited gamma-glutamyl transfer activity as well as iron reduction activity in the presence of glutathione. We cloned and manipulated expression of the encoding gene. Overexpression or RNAi silencing affected both GGT and GSH-FeR activities concurrently. Enzyme inhibition experiments showed that the activity is complex and involves two reactions. First, Ggt1 initiates enzymatic breakdown of GSH by cleavage of the gamma-glutamyl bond and release of cysteinylglycine. Second, the thiol group of the released dipeptide reduces ferric to ferrous iron. A combination of kinetic properties of both reactions resulted in efficient iron reduction over a broad pH range. Our findings provide novel insight into Hc iron acquisition strategies and reveal a unique aspect of Ggt1 function in this dimorphic mycopathogen.
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Affiliation(s)
- Robert Zarnowski
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA.
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18
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Fyfe PK, Oza SL, Fairlamb AH, Hunter WN. Leishmania trypanothione synthetase-amidase structure reveals a basis for regulation of conflicting synthetic and hydrolytic activities. J Biol Chem 2008; 283:17672-80. [PMID: 18420578 PMCID: PMC2427367 DOI: 10.1074/jbc.m801850200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/14/2008] [Indexed: 11/06/2022] Open
Abstract
The bifunctional trypanothione synthetase-amidase catalyzes biosynthesis and hydrolysis of the glutathione-spermidine adduct trypanothione, the principal intracellular thiol-redox metabolite in parasitic trypanosomatids. These parasites are unique with regard to their reliance on trypanothione to determine intracellular thiol-redox balance in defense against oxidative and chemical stress and to regulate polyamine levels. Enzymes involved in trypanothione biosynthesis provide essential biological activities, and those absent from humans or for which orthologues are sufficiently distinct are attractive targets to underpin anti-parasitic drug discovery. The structure of Leishmania major trypanothione synthetase-amidase, determined in three crystal forms, reveals two catalytic domains. The N-terminal domain, a cysteine, histidine-dependent amidohydrolase/peptidase amidase, is a papain-like cysteine protease, and the C-terminal synthetase domain displays an ATP-grasp family fold common to C:N ligases. Modeling of substrates into each active site provides insight into the specificity and reactivity of this unusual enzyme, which is able to catalyze four reactions. The domain orientation is distinct from that observed in a related bacterial glutathionylspermidine synthetase. In trypanothione synthetase-amidase, the interactions formed by the C terminus, binding in and restricting access to the amidase active site, suggest that the balance of ligation and hydrolytic activity is directly influenced by the alignment of the domains with respect to each other and implicate conformational changes with amidase activity. The potential inhibitory role of the C terminus provides a mechanism to control relative levels of the critical metabolites, trypanothione, glutathionylspermidine, and spermidine in Leishmania.
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Affiliation(s)
- Paul K Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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Balg C, Huot JL, Lapointe J, Chênevert R. Inhibition of Helicobacter pylori Aminoacyl-tRNA Amidotransferase by Puromycin Analogues. J Am Chem Soc 2008; 130:3264-5. [DOI: 10.1021/ja7100714] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christian Balg
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| | - Jonathan L. Huot
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| | - Jacques Lapointe
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
| | - Robert Chênevert
- Département de Chimie and Département de Biochimie et de Microbiologie, Centre de Recherche sur la Fonction, la Structure et l'Ingénierie des Protéines (CREFSIP), Faculté des Sciences et de Génie, Université Laval, Québec, Canada, G1K 7P4
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Torelli AT, Krucinska J, Wedekind JE. A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. RNA (NEW YORK, N.Y.) 2007; 13:1052-70. [PMID: 17488874 PMCID: PMC1894929 DOI: 10.1261/rna.510807] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.
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Affiliation(s)
- Andrew T Torelli
- Department of Biochemistry and Biophysics, Rochester, NY 14642, USA
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Abrunhosa-Thomas I, Sellers CE, Montchamp JL. Alkylation of H-phosphinate esters under basic conditions. J Org Chem 2007; 72:2851-6. [PMID: 17352490 PMCID: PMC2525801 DOI: 10.1021/jo062436o] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient and general procedure was developed for the direct alkylation of H-phosphinate esters with LHMDS at low temperature. The simplicity of the reaction allows the use of various H-phosphinate esters and takes place with a wide range of electrophiles. The approach can be employed to access some GABA analogues or precursors to GABA analogues. The isolated yields are moderate to good. This is the first report of an alkylation with a secondary iodide or a primary chloride.
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Affiliation(s)
| | - Claire E. Sellers
- Department of Chemistry, TCU Box 298860, Texas Christian University, Fort, Worth, Texas 76129
| | - Jean-Luc Montchamp
- Department of Chemistry, TCU Box 298860, Texas Christian University, Fort, Worth, Texas 76129
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22
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Pai CH, Chiang BY, Ko TP, Chou CC, Chong CM, Yen FJ, Chen S, Coward JK, Wang AHJ, Lin CH. Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. EMBO J 2006; 25:5970-82. [PMID: 17124497 PMCID: PMC1698887 DOI: 10.1038/sj.emboj.7601440] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 10/12/2006] [Indexed: 01/22/2023] Open
Abstract
Most organisms use glutathione to regulate intracellular thiol redox balance and protect against oxidative stress; protozoa, however, utilize trypanothione for this purpose. Trypanothione biosynthesis requires ATP-dependent conjugation of glutathione (GSH) to the two terminal amino groups of spermidine by glutathionylspermidine synthetase (GspS) and trypanothione synthetase (TryS), which are considered as drug targets. GspS catalyzes the penultimate step of the biosynthesis-amide bond formation between spermidine and the glycine carboxylate of GSH. We report herein five crystal structures of Escherichia coli GspS in complex with substrate, product or inhibitor. The C-terminal of GspS belongs to the ATP-grasp superfamily with a similar fold to the human glutathione synthetase. GSH is likely phosphorylated at one of two GSH-binding sites to form an acylphosphate intermediate that then translocates to the other site for subsequent nucleophilic addition of spermidine. We also identify essential amino acids involved in the catalysis. Our results constitute the first structural information on the biochemical features of parasite homologs (including TryS) that underlie their broad specificity for polyamines.
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Affiliation(s)
- Chien-Hua Pai
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
- Institute of Biochemistry, National Yang-Ming University, Taipei, Taiwan
| | - Bing-Yu Chiang
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Tzu- Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
| | | | - Cheong-Meng Chong
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
| | - Fang-Jiun Yen
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
| | - Shoujun Chen
- Departments of Medicinal Chemistry & Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - James K Coward
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan-Kang, Taipei 11529, Taiwan. Tel.: +886 2 2788 1981; Fax: +886 2 2788 2043; E-mail:
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Nan-Kang, Taipei, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan-Kang, Taipei 11529, Taiwan. Tel.: +886 2 2789 0110; Fax: +886 2 4705; E-mail:
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