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El Sahili A, Li SZ, Lang J, Virus C, Planamente S, Ahmar M, Guimaraes BG, Aumont-Nicaise M, Vigouroux A, Soulère L, Reader J, Queneau Y, Faure D, Moréra S. A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. PLoS Pathog 2015; 11:e1005071. [PMID: 26244338 PMCID: PMC4526662 DOI: 10.1371/journal.ppat.1005071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022] Open
Abstract
Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3'-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs.
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Affiliation(s)
- Abbas El Sahili
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Si-Zhe Li
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - Julien Lang
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Cornelia Virus
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sara Planamente
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Mohammed Ahmar
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | | | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), Protein-Protein Interaction Platform, CNRS CEA University Paris-Sud, Orsay, France
| | - Armelle Vigouroux
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
| | - Laurent Soulère
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
| | - John Reader
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yves Queneau
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, ICBMS, Université de Lyon, INSA Lyon, UMR 5246, CNRS, Université Lyon 1, INSA Lyon, CPE-Lyon, Bât J. Verne, Villeurbanne, France
- * E-mail: (YQ); (DF); (SM)
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
| | - Solange Moréra
- Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France
- * E-mail: (YQ); (DF); (SM)
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Abstract
Explorations of the therapeutic potential of heparin mimetics, anionic compounds that are analogues of glycosaminoglycans (GAGs), have gone hand-in-hand with the emergence of understanding as to the role of GAGs in many essential biological processes. A myriad of structurally different heparin mimetics have been prepared and examined in many diverse applications. They range in complexity from heterogeneous polysaccharides that have been chemically sulphated to well-defined compounds, designed in part to mimic the natural ligand, but with binding specificity and potency increased by conjugation to non-carbohydrate pharmacophores. The maturity of the field is illustrated by the seven heparin mimetics that have achieved marketing approval and there are several more in late-stage clinical development. An overview of the structural determinants of heparin mimetics is presented together with an indication of their activities. The challenges in developing heparin mimetics as drugs, specificity and potential toxicity issues, are highlighted. Finally, the development path of three structurally very different mimetics, PI-88(®), GMI-1070 and RGTAs, each of which is in clinical trials, is described.
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Fylaktakidou KC, Duarte CD, Koumbis AE, Nicolau C, Lehn JM. Polyphosphates and Pyrophosphates of Hexopyranoses as Allosteric Effectors of Human Hemoglobin: Synthesis, Molecular Recognition, and Effect on Oxygen Release. ChemMedChem 2010; 6:153-68. [DOI: 10.1002/cmdc.201000366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Amigues E, Hardacre C, Keane G, Migaud M, O'Neill M. Ionic liquids—media for unique phosphorus chemistry. Chem Commun (Camb) 2006:72-4. [PMID: 16353096 DOI: 10.1039/b509248e] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionic liquids have been shown to offer hitherto unseen control as both a storage solvent for PCl3 and POCl3 and reaction media for fluorination and mixed anhydride formation under benign conditions.
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Affiliation(s)
- Eric Amigues
- QUILL and School of Chemistry, Queens University Belfast, Belfast, Northern Ireland BT9 5AG
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Gama CI, Hsieh-Wilson LC. Chemical approaches to deciphering the glycosaminoglycan code. Curr Opin Chem Biol 2005; 9:609-19. [PMID: 16242378 DOI: 10.1016/j.cbpa.2005.10.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 10/05/2005] [Indexed: 11/27/2022]
Abstract
Glycosaminoglycans are sulfated biopolymers with rich chemical diversity and complex functions in vivo, contributing to processes ranging from cell growth and neuronal development to viral invasion and neurodegenerative disease. Recent studies suggest that glycosaminoglycans may encode information in the form of a 'sulfation code,' whereby discrete modifications to the polysaccharide backbone may direct the location or activities of proteins.
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Affiliation(s)
- Cristal I Gama
- Howard Hughes Medical Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Monien BH, Cheang KI, Desai UR. Mechanism of Poly(acrylic acid) Acceleration of Antithrombin Inhibition of Thrombin: Implications for the Design of Novel Heparin Mimics. J Med Chem 2005; 48:5360-8. [PMID: 16078853 DOI: 10.1021/jm0503648] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bridging mechanism of antithrombin inhibition of thrombin is a dominant mechanism contributing a massive approximately 2500-fold acceleration in the reaction rate and is also a key reason for the clinical usage of heparin. Our recent study of the antithrombin-activating properties of a carboxylic acid-based polymer, poly(acrylic acid) (PAA), demonstrated a surprisingly high acceleration in thrombin inhibition (Monien, B. H.; Desai, U. R. J. Med. Chem. 2005, 48, 1269). To better understand this interesting phenomenon, we have studied the mechanism of PAA-dependent acceleration in antithrombin inhibition of thrombin. Competitive binding studies with low-affinity heparin and a heparin tetrasaccharide suggest that PAA binds antithrombin in both the pentasaccharide- and the extended heparin-binding sites, and these results are corroborated by molecular modeling. The salt-dependence of the K(D) of the PAA-antithrombin interaction shows the formation of five ionic interactions. In contrast, the contribution of nonionic forces is miniscule, resulting in an interaction that is significantly weaker than that observed for heparins. A bell-shaped profile of the observed rate constant for antithrombin inhibition of thrombin as a function of PAA concentration was observed, suggesting that inhibition proceeds through the "bridging" mechanism. The knowledge gained in this mechanistic study highlights important rules for the rational design of orally available heparin mimics.
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Affiliation(s)
- Bernhard H Monien
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 410 N. 12th Street, Richmond, VA 23298, USA
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Monien BH, Desai UR. Antithrombin Activation by Nonsulfated, Non-Polysaccharide Organic Polymer. J Med Chem 2005; 48:1269-73. [PMID: 15715496 DOI: 10.1021/jm0492960] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accelerated antithrombin inhibition of procoagulant enzymes has been exclusively achieved with polysulfated polysaccharides. We reasoned that antithrombin activation should be possible with nonsulfated activators based only on carboxylic acid groups. As a proof of the principle, linear poly(acrylic acid)s were found to bind to antithrombin and accelerate inhibition of factor Xa and thrombin. Our work demonstrates that molecules completely devoid of sulfate groups can activate antithrombin effectively and, more importantly, suggests that it may be possible to develop orally bioavailable, carboxylate-based antithrombin activators.
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Affiliation(s)
- Bernhard H Monien
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298-0540, USA
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Rele SM, Iyer SS, Baskaran S, Chaikof EL. Design and Synthesis of Dimeric Heparinoid Mimetics. J Org Chem 2004; 69:9159-70. [PMID: 15609950 DOI: 10.1021/jo049092r] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic oligosaccharide constructs exhibiting tailored and well-defined heparan sulfate (HS) like sequences offer the potential to modulate dynamic HS-dependent biomolecular recognition processes. We report an efficient strategy for the generation of HS-like fragments [GlcA-beta-(1,4)-GlcNAc] and related dimerized (gemini) disaccharides (4a and 4b) via n-pentenyl glycoside formation. When a convergent synthetic approach was utilized, construction of target molecules was achieved through a combination of chemoselective protection/deprotection protocols, imidate and n-pentenyl glycosylations, and functional group manipulations followed by ozonolysis and reductive amination. For example, glycosylation of a 2-azido glycoside (25) with a trichloroacetimidate glucuronic acid donor (13), using a catalytic amount of TMSOTf, furnished heparin-like disaccharides (28a and 28b) that were equipped with an n-pentenyl tether at the anomeric end. In turn, heparinoid-like gemini disaccharides (4a and 4b) were produced by selective transformation of the olefinic unit in the n-pentenyl glycoside to the four-carbon aldehyde followed by reductive amination with ethylenediamine. The described synthetic approach provides access to structural variants of small heparinoid oligomers as versatile building blocks for generating novel HS mimetic pharmacotherapeutics, diagnostic reagents, and biomaterials.
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Affiliation(s)
- Shyam M Rele
- Department of Surgery, Emory University, Atlanta, Georgia 30322, USA.
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Poletti L, Lay L. Chemical Contributions to Understanding Heparin Activity: Synthesis of Related Sulfated Oligosaccharides. European J Org Chem 2003. [DOI: 10.1002/ejoc.200200721] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura Poletti
- Dipartimento di Chimica Organica e Industriale and Centro Interdisciplinare Studi bio‐molecolari e applicazioni Industriali (CISI), Università degli Studi di Milano, and CNR (Istituto di Scienze e Tecnologie Molecolari), Via G. Venezian 21, 20133 Milano, Italy, Fax: (internat.) + 39‐02/50314061
| | - Luigi Lay
- Dipartimento di Chimica Organica e Industriale and Centro Interdisciplinare Studi bio‐molecolari e applicazioni Industriali (CISI), Università degli Studi di Milano, and CNR (Istituto di Scienze e Tecnologie Molecolari), Via G. Venezian 21, 20133 Milano, Italy, Fax: (internat.) + 39‐02/50314061
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Abstract
Clinically used anticoagulants are inhibitors of enzymes involved in the coagulation pathway, primarily thrombin and factor Xa. These agents can be either direct or indirect inhibitors of clotting enzymes. Heparin-based anticoagulants are indirect inhibitors that enhance the proteinase inhibitory activity of a natural anticoagulant, antithrombin. Despite its phenomenal success, current anticoagulation therapy suffers from the risk of serious bleeding. The need for safer and more effective antithrombotic agents clearly exists. The past decade has seen enormous effort directed toward discovering and/or designing new molecules with anticoagulant activity. These new molecules can be classified into (a). antithrombin and its mutants, (b). natural polysaccharides, (c). synthetic modified heparins and heparin-mimics, (d). synthetic oligosaccharides, and (e). synthetic non-sugar antithrombin activators. This review focuses on these efforts in designing or discovering new molecules that act through the antithrombin pathway of anticoagulation.
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Affiliation(s)
- Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, USA.
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Rzepecki PW, Prestwich GD. Synthesis of hybrid lipid probes: derivatives of phosphatidylethanolamine-extended phosphatidylinositol 4,5-bisphosphate (Pea-PIP(2)). J Org Chem 2002; 67:5454-60. [PMID: 12153242 DOI: 10.1021/jo011185a] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The total asymmetric synthesis of a novel hybrid lipid possessing a 2,3-diacylthreitol backbone, rather than a 1,2-diacylglycerol backbone, is described. The title compound, Pea-PIP(2), possesses a phosphatidylethanolamine (PE) headgroup at the 1-position and a phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)) headgroup at the 4-position. Reporters (biotin, fluorophores, spin label) were covalently attached to the free amino group of the PE, such that these reporters were targeted to the lipid-water interface. The diacyl moieties allow incorporation of Pea-PIP(2) into a lipid bilayer, while the PtdIns(4,5)P(2) moiety in the aqueous layer was specifically recognized by PtdIns(4,5)P(2)-specific binding proteins.
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Affiliation(s)
- Piotr W Rzepecki
- Department of Medicinal Chemistry, The University of Utah, 419 Wakara Way, Suite 205, Salt Lake City, Utah 84108, USA
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Gunnarsson GT, Desai UR. Designing small, nonsugar activators of antithrombin using hydropathic interaction analyses. J Med Chem 2002; 45:1233-43. [PMID: 11881992 DOI: 10.1021/jm020012q] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Conformational activation of antithrombin is a critical mechanism for the inhibition of factor Xa, a proteinase of the blood coagulation cascade, and is typically achieved with heparin, a polyanionic polysaccharide clinically used for anticoagulation. Although numerous efforts have been directed toward the design of better activators, a fundamental tenet of these studies has been the assumed requirement of an oligo- or a polysaccharide backbone. We demonstrate here a concept that small nonsaccharidic nonpolymeric molecules may be rationally designed to interact with and activate antithrombin for enhanced inhibition of factor Xa. The rational design strategy is based on a study of complexes of natural and mutant antithrombins with heparin-based oligosaccharides using hydropathic interaction (HINT) technique, a quantitative computerized tool for analysis of molecular interactions. A linear correlation was observed between the free energy of binding for antithrombinminus signoligosaccharide complexes and the HINT score over a wide range of approximately 13 kcal/mol, indicating strong predictive capability of the HINT technique. Using this approach, a small, nonsugar, aromatic molecule, (minus sign)-epicatechin sulfate (ECS), was designed to mimic the nonreducing end trisaccharide unit DEF of the sequence specific heparin pentasaccharide DEFGH. HINT suggested a comparable antithrombin-binding geometry and interaction profile for ECS and trisaccharide DEF. Biochemical studies indicated that ECS binds antithrombin with equilibrium dissociation constants of 10.5 and 66 microM at pH 6.0, I 0.025, and pH 7.4, I 0.035, respectively, that compare favorably with 2 and 80 microM observed for the natural activator DEF. ECS accelerates the antithrombin inhibition of factor Xa nearly 8-fold demonstrating for the first time that conformational activation of antithrombin is feasible with appropriately designed small nonsugar organic molecules. The results present unique opportunities for de novo activator design based on this first-generation lead.
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Affiliation(s)
- Gunnar T Gunnarsson
- Department of Medicinal Chemistry, Virginia Commonwealth University, 410 North 12th Street, P.O. Box 980540, Richmond, Virginia 23298, USA
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