51
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Madge PD, Maggioni A, Pascolutti M, Amin M, Waespy M, Bellette B, Thomson RJ, Kelm S, von Itzstein M, Haselhorst T. Structural characterisation of high affinity Siglec-2 (CD22) ligands in complex with whole Burkitt's lymphoma (BL) Daudi cells by NMR spectroscopy. Sci Rep 2016; 6:36012. [PMID: 27808110 PMCID: PMC5093622 DOI: 10.1038/srep36012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 10/10/2016] [Indexed: 12/13/2022] Open
Abstract
Siglec-2 undergoes constitutive endocytosis and is a drug target for autoimmune diseases and B cell-derived malignancies, including hairy cell leukaemia, marginal zone lymphoma, chronic lymphocytic leukaemia and non-Hodgkin's lymphoma (NHL). An alternative to current antibody-based therapies is the use of liposomal nanoparticles loaded with cytotoxic drugs and decorated with Siglec-2 ligands. We have recently designed the first Siglec-2 ligands (9-biphenylcarboxamido-4-meta-nitrophenyl-carboxamido-Neu5Acα2Me, 9-BPC-4-mNPC-Neu5Acα2Me) with simultaneous modifications at C-4 and C-9 position. In the current study we have used Saturation Transfer Difference (STD) NMR spectroscopy to monitor the binding of 9-BPC-4-mNPC-Neu5Acα2Me to Siglec-2 present on intact Burkitt's lymphoma Daudi cells. Pre-treatment of cells with periodate resulted in significantly higher STD NMR signal intensities for 9-BPC-4-mNPC-Neu5Acα2Me as the cells were more susceptible to ligand binding because cis-binding on the cell surface was removed. Quantification of STD NMR effects led to a cell-derived binding epitope of 9-BPC-4-mNPC-Neu5Acα2Me that facilitated the design and synthesis of C-2, C-3, C-4 and C-9 tetra-substituted Siglec-2 ligands showing an 88-fold higher affinity compared to 9-BPC-Neu5Acα2Me. This is the first time a NMR-based binding study of high affinity Siglec-2 (CD22) ligands in complex with whole Burkitt's lymphoma Daudi cells has been described that might open new avenues in developing tailored therapeutics and personalised medicine.
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Affiliation(s)
- Paul D Madge
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Andrea Maggioni
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Mauro Pascolutti
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Moein Amin
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Mario Waespy
- Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, 28334 Bremen, Germany
| | - Bernadette Bellette
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Robin J Thomson
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Sørge Kelm
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia.,Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, 28334 Bremen, Germany
| | - Mark von Itzstein
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
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52
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Gossert AD, Jahnke W. NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:82-125. [PMID: 27888841 DOI: 10.1016/j.pnmrs.2016.09.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 05/12/2023]
Abstract
Protein-ligand interactions are at the heart of drug discovery research. NMR spectroscopy is an excellent technology to identify and validate protein-ligand interactions. A plethora of NMR methods are available which are powerful, robust and information-rich, but also have pitfalls and limitations. In this review, we will focus on how to choose between different experiments, and assess their strengths and liabilities. We introduce the concept of the validation cross, which helps to categorize experiments according to their information content and to simplify the choice of the right experiment in order to address a specific question. Additionally, we will provide the framework for drawing correct conclusions from experimental results in order to accurately evaluate such interactions. Out of scope for this review are methods for subsequent characterization of the interaction such as quantitative KD determination, binding mode analysis, or structure determination.
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Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland.
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland
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53
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Li S, Ahmed L, Zhang R, Pan Y, Matsunami H, Burger JL, Block E, Batista VS, Zhuang H. Smelling Sulfur: Copper and Silver Regulate the Response of Human Odorant Receptor OR2T11 to Low-Molecular-Weight Thiols. J Am Chem Soc 2016; 138:13281-13288. [PMID: 27659093 DOI: 10.1021/jacs.6b06983] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mammalian survival depends on ultrasensitive olfactory detection of volatile sulfur compounds, since these compounds can signal the presence of rancid food, O2 depleted atmospheres, and predators (through carnivore excretions). Skunks exploit this sensitivity with their noxious spray. In commerce, natural and liquefied gases are odorized with t-BuSH and EtSH, respectively, as warnings. The 100-million-fold difference in olfactory perception between structurally similar EtSH and EtOH has long puzzled those studying olfaction. Mammals detect thiols and other odorants using odorant receptors (ORs), members of the family of seven transmembrane G-protein-coupled receptors (GPCRs). Understanding the regulator cofactors and response of ORs is particularly challenging due to the lack of X-ray structural models. Here, we combine computational modeling and site-directed mutagenesis with saturation transfer difference (STD) NMR spectroscopy and measurements of the receptor response profiles. We find that human thiol receptor OR2T11 responds specifically to gas odorants t-BuSH and EtSH requiring ionic copper for its robust activation and that this role of copper is mimicked by ionic and nanoparticulate silver. While copper is both an essential nutrient for life and, in excess, a hallmark of various pathologies and neurodegenerative diseases, its involvement in human olfaction has not been previously demonstrated. When screened against a series of alcohols, thiols, sulfides, and metal-coordinating ligands, OR2T11 responds with enhancement by copper to the mouse semiochemical CH3SCH2SH and derivatives, to four-membered cyclic sulfide thietane and to one- to four-carbon straight- and branched-chain and five-carbon branched-chain thiols but not to longer chain thiols, suggesting compact receptor dimensions. Alcohols are unreactive.
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Affiliation(s)
- Shengju Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiaotong University School of Medicine , Shanghai 200025, China
| | - Lucky Ahmed
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Ruina Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiaotong University School of Medicine , Shanghai 200025, China
| | - Yi Pan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiaotong University School of Medicine , Shanghai 200025, China
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology and Department of Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Jessica L Burger
- Applied Chemicals and Materials Division, National Institute of Standards and Technology , Boulder, Colorado 80305, United States
| | - Eric Block
- Department of Chemistry, University at Albany, State University of New York , Albany, New York 12222, United States
| | - Victor S Batista
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Hanyi Zhuang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiaotong University School of Medicine , Shanghai 200025, China.,Institute of Health Sciences, Shanghai Jiaotong University School of Medicine/Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences , Shanghai 200031, China
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54
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Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG. Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochem Pharmacol 2016; 118:96-108. [PMID: 27531061 DOI: 10.1016/j.bcp.2016.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/12/2016] [Indexed: 12/21/2022]
Abstract
The P-glycoprotein (Pgp) transporter plays a central role in drug disposition by effluxing a chemically diverse range of drugs from cells through conformational changes and ATP hydrolysis. A number of drugs are known to activate ATP hydrolysis of Pgp, but coupling between ATP and drug binding is not well understood. The cardiovascular drug verapamil is one of the most widely studied Pgp substrates and therefore, represents an ideal drug to investigate the drug-induced ATPase activation of Pgp. As previously noted, verapamil-induced Pgp-mediated ATP hydrolysis kinetics was biphasic at saturating ATP concentrations. However, at subsaturating ATP concentrations, verapamil-induced ATPase activation kinetics became monophasic. To further understand this switch in kinetic behavior, the Pgp-coupled ATPase activity kinetics was checked with a panel of verapamil and ATP concentrations and fit with the substrate inhibition equation and the kinetic fitting software COPASI. The fits suggested that cooperativity between ATP and verapamil switched between low and high verapamil concentration. Fluorescence spectroscopy of Pgp revealed that cooperativity between verapamil and a non-hydrolyzable ATP analog leads to distinct global conformational changes of Pgp. NMR of Pgp reconstituted in liposomes showed that cooperativity between verapamil and the non-hydrolyzable ATP analog modulate each other's interactions. This information was used to produce a conformationally-gated model of drug-induced activation of Pgp-mediated ATP hydrolysis.
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Affiliation(s)
- Kaitlyn V Ledwitch
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Morgan E Gibbs
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Robert W Barnes
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Arthur G Roberts
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States.
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55
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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56
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Burger JL, Jeerage KM, Bruno TJ. Direct nuclear magnetic resonance observation of odorant binding to mouse odorant receptor MOR244-3. Anal Biochem 2016; 502:64-72. [PMID: 27019154 DOI: 10.1016/j.ab.2016.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/01/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Mammals are able to perceive and differentiate a great number of structurally diverse odorants through the odorant's interaction with odorant receptors (ORs), proteins found within the cell membrane of olfactory sensory neurons. The natural gas industry has used human olfactory sensitivity to sulfur compounds (thiols, sulfides, etc.) to increase the safety of fuel gas transport, storage, and use through the odorization of this product. In the United States, mixtures of sulfur compounds are used, but the major constituent of odorant packages is 2-methylpropane-2-thiol, also known as tert-butyl mercaptan. It has been fundamentally challenging to understand olfaction and odorization due to the low affinity of odorous ligands to the ORs and the difficulty in expressing a sufficient number of OR proteins. Here, we directly observed the binding of tert-butyl mercaptan and another odiferous compound, cis-cyclooctene, to mouse OR MOR244-3 on living cells by saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy. This effort lays the groundwork for resolving molecular mechanisms responsible for ligand binding and resulting signaling, which in turn will lead to a clearer understanding of odorant recognition and competition.
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Affiliation(s)
- Jessica L Burger
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO, 80305, USA.
| | - Kavita M Jeerage
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO, 80305, USA
| | - Thomas J Bruno
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO, 80305, USA
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57
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Benoni R, Pertinhez TA, Spyrakis F, Davalli S, Pellegrino S, Paredi G, Pezzotti A, Bettati S, Campanini B, Mozzarelli A. Structural insight into the interaction ofO-acetylserine sulfhydrylase with competitive, peptidic inhibitors by saturation transfer difference-NMR. FEBS Lett 2016; 590:943-53. [DOI: 10.1002/1873-3468.12126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Thelma A. Pertinhez
- Department of Oncology and Advanced Techniques; Arcispedale Santa Maria Nuova-IRCCS; Reggio Emilia Italy
| | | | | | - Sara Pellegrino
- Department of Pharmaceutical Sciences; Section of General and Organic Chemistry ‘A. Marchesini’; University of Milan; Italy
| | | | | | - Stefano Bettati
- Department of Neurosciences; University of Parma; Italy
- National Institute for Biostructures and Biosystems; Rome Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy; University of Parma; Italy
- National Institute for Biostructures and Biosystems; Rome Italy
- Institute of Biophysics; CNR; Pisa Italy
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58
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Vasile F, Menchi G, Lenci E, Guarna A, Potenza D, Trabocchi A. Insight to the binding mode of triazole RGD-peptidomimetics to integrin-rich cancer cells by NMR and molecular modeling. Bioorg Med Chem 2016; 24:989-94. [DOI: 10.1016/j.bmc.2016.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 12/20/2022]
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59
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Abstract
The majority of therapeutics target membrane proteins, accessible on the surface of cells, to alter cellular signaling. Cells use membrane proteins to transduce signals into cells, transport ions and molecules, bind cells to a surface or substrate, and catalyze reactions. Newly devised technologies allow us to drug conventionally "undruggable" regions of membrane proteins, enabling modulation of protein-protein, protein-lipid, and protein-nucleic acid interactions. In this review, we survey the state of the art of high-throughput screening and rational design in drug discovery, and we evaluate the advances in biological understanding and technological capacity that will drive pharmacotherapy forward against unorthodox membrane protein targets.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry.,BioFrontiers Institute, and.,Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Aaron D Flynn
- BioFrontiers Institute, and.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309; ,
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60
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Unravelling the complex drug-drug interactions of the cardiovascular drugs, verapamil and digoxin, with P-glycoprotein. Biosci Rep 2016; 36:BSR20150317. [PMID: 26823559 PMCID: PMC4793304 DOI: 10.1042/bsr20150317] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 01/22/2016] [Indexed: 02/06/2023] Open
Abstract
P-glycoprotein (Pgp) plays a major role in promoting drug–drug interactions (DDIs) with verapamil and digoxin. In the present study, we present a comprehensive molecular and mechanistic model of Pgp DDIs encompassing drug binding, ATP hydrolysis, transport and conformational changes. Drug–drug interactions (DDIs) and associated toxicity from cardiovascular drugs represents a major problem for effective co-administration of cardiovascular therapeutics. A significant amount of drug toxicity from DDIs occurs because of drug interactions and multiple cardiovascular drug binding to the efflux transporter P-glycoprotein (Pgp), which is particularly problematic for cardiovascular drugs because of their relatively low therapeutic indexes. The calcium channel antagonist, verapamil and the cardiac glycoside, digoxin, exhibit DDIs with Pgp through non-competitive inhibition of digoxin transport, which leads to elevated digoxin plasma concentrations and digoxin toxicity. In the present study, verapamil-induced ATPase activation kinetics were biphasic implying at least two verapamil-binding sites on Pgp, whereas monophasic digoxin activation of Pgp-coupled ATPase kinetics suggested a single digoxin-binding site. Using intrinsic protein fluorescence and the saturation transfer double difference (STDD) NMR techniques to probe drug–Pgp interactions, verapamil was found to have little effect on digoxin–Pgp interactions at low concentrations of verapamil, which is consistent with simultaneous binding of the drugs and non-competitive inhibition. Higher concentrations of verapamil caused significant disruption of digoxin–Pgp interactions that suggested overlapping and competing drug-binding sites. These interactions correlated to drug-induced conformational changes deduced from acrylamide quenching of Pgp tryptophan fluorescence. Also, Pgp-coupled ATPase activity kinetics measured with a range of verapamil and digoxin concentrations fit well to a DDI model encompassing non-competitive and competitive inhibition of digoxin by verapamil. The results and previous transport studies were combined into a comprehensive model of verapamil–digoxin DDIs encompassing drug binding, ATP hydrolysis, transport and conformational changes.
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61
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Farina B, de Paola I, Russo L, Capasso D, Liguoro A, Gatto AD, Saviano M, Pedone PV, Di Gaetano S, Malgieri G, Zaccaro L, Fattorusso R. A Combined NMR and Computational Approach to Determine the RGDechi-hCit-αv β3 Integrin Recognition Mode in Isolated Cell Membranes. Chemistry 2015; 22:681-93. [PMID: 26548575 DOI: 10.1002/chem.201503126] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 11/07/2022]
Abstract
The critical role of integrins in tumor progression and metastasis has stimulated intense efforts to identify pharmacological agents that can modulate integrin function. In recent years, αv β3 and αv β5 integrin antagonists were demonstrated to be effective in blocking tumor progression. RGDechi-hCit, a chimeric peptide containing a cyclic RGD motif linked to an echistatin C-terminal fragment, is able to recognize selectively αv β3 integrin both in vitro and in vivo. High-resolution molecular details of the selective αv β3 recognition of the peptide are certainly required, nonetheless RGDechi-hCit internalization limited the use of classical in cell NMR experiments. To overcome such limitations, we used WM266 isolated cellular membranes to accomplish a detailed NMR interaction study that, combined with a computational analysis, provides significant structural insights into αv β3 molecular recognition by RGDechi-hCit. Remarkably, on the basis of the identified molecular determinants, we design a RGDechi-hCit mutant that is selective for αv β5 integrin.
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Affiliation(s)
- Biancamaria Farina
- Dipatimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi Napoli, Via Vivaldi 46, 81100, Caserta (Italy).,Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples (Italy)
| | - Ivan de Paola
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples (Italy)
| | - Luigi Russo
- Dipatimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi Napoli, Via Vivaldi 46, 81100, Caserta (Italy)
| | - Domenica Capasso
- Dipartimento di Farmacia, Università di Napoli Federico II, Via Mezzocannone 16, 80134 Naples (Italy)
| | - Annamaria Liguoro
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples (Italy)
| | - Annarita Del Gatto
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples (Italy)
| | - Michele Saviano
- Istituto di Cristallografia, CNR, Via Amendola 122/O, 70126 Bari (Italy)
| | - Paolo V Pedone
- Dipatimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi Napoli, Via Vivaldi 46, 81100, Caserta (Italy)
| | - Sonia Di Gaetano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples (Italy)
| | - Gaetano Malgieri
- Dipatimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi Napoli, Via Vivaldi 46, 81100, Caserta (Italy)
| | - Laura Zaccaro
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples (Italy).
| | - Roberto Fattorusso
- Dipatimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi Napoli, Via Vivaldi 46, 81100, Caserta (Italy).
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62
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Marchetti R, Dillon MJ, Burtnick MN, Hubbard MA, Kenfack MT, Blériot Y, Gauthier C, Brett PJ, AuCoin DP, Lanzetta R, Silipo A, Molinaro A. Burkholderia pseudomallei Capsular Polysaccharide Recognition by a Monoclonal Antibody Reveals Key Details toward a Biodefense Vaccine and Diagnostics against Melioidosis. ACS Chem Biol 2015. [PMID: 26198038 DOI: 10.1021/acschembio.5b00502] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Burkholderia pseudomallei is the bacterium responsible for melioidosis, an infectious disease with high mortality rates. Since melioidosis is a significant public health concern in endemic regions and the organism is currently classified as a potential biothreat agent, the development of effective vaccines and rapid diagnostics is a priority. The capsular polysaccharide (CPS) expressed by B. pseudomallei is a highly conserved virulence factor and a protective antigen. Because of this, CPS is considered an attractive antigen for use in the development of both vaccines and diagnostics. In the present study, we describe the interactions of CPS with the murine monoclonal antibody (mAb) 4C4 using a multidisciplinary approach including organic synthesis, molecular biology techniques, surface plasmon resonance, and nuclear magnetic spectroscopy. Using these methods, we determined the mode of binding between mAb 4C4 and native CPS or ad hoc synthesized capsular polysaccharide fragments. Interestingly, we demonstrated that the O-acetyl moiety of CPS is essential for the interaction of the CPS epitope with mAb 4C4. Collectively, our results provide important insights into the structural features of B. pseudomallei CPS that enable antibody recognition that may help the rational design of CPS-based vaccine candidates. In addition, our findings confirm that the mAb 4C4 is suitable for use in an antibody-based detection assay for diagnosis of B. pseudomallei infections.
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Affiliation(s)
- Roberta Marchetti
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
| | - Michael J. Dillon
- Department
of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada 89557, United States
| | - Mary N. Burtnick
- Department
of Microbiology and Immunology, University of South Alabama, Mobile, Alabama 36688, United States
| | - Mark A. Hubbard
- Department
of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada 89557, United States
| | - Marielle Tamigney Kenfack
- Université de Poitiers, Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073 Poitiers Cedex-9, France
| | - Yves Blériot
- Université de Poitiers, Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073 Poitiers Cedex-9, France
| | - Charles Gauthier
- Université de Poitiers, Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073 Poitiers Cedex-9, France
| | - Paul J. Brett
- Department
of Microbiology and Immunology, University of South Alabama, Mobile, Alabama 36688, United States
| | - David P. AuCoin
- Department
of Microbiology and Immunology, University of Nevada School of Medicine, Reno, Nevada 89557, United States
| | - Rosa Lanzetta
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
| | - Alba Silipo
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
| | - Antonio Molinaro
- Department
of Chemical Sciences, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, I-80126, Naples, Italy
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63
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Mazzei P, Piccolo A. Interactions between natural organic matter and organic pollutants as revealed by NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:667-678. [PMID: 25783763 DOI: 10.1002/mrc.4209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Natural organic matter (NOM) plays a critical role in regulating the transport and the fate of organic contaminants in the environment. NMR spectroscopy is a powerful technique for the investigation of the sorption and binding mechanisms between NOM and pollutants, as well as their mutual chemical transformations. Despite NMR relatively low sensibility but due to its wide versatility to investigating samples in the liquid, gel, and solid phases, NMR application to environmental NOM-pollutants relations enables the achievement of specific and complementary molecular information. This report is a brief outline of the potentialities of the different NMR techniques and pulse sequences to elucidate the interactions between NOM and organic pollutants, with and without their labeling with nuclei that enhance NMR sensitivity.
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Affiliation(s)
- Pierluigi Mazzei
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055, Portici, Italy
| | - Alessandro Piccolo
- Centro Interdipartimentale per la Risonanza Magnetica Nucleare per l'Ambiente, l'Agro-Alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055, Portici, Italy
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64
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Cox BD, Mehta AK, DiRaddo JO, Liotta DC, Wilson LJ, Snyder JP. Structural analysis of CXCR4 - Antagonist interactions using saturation-transfer double-difference NMR. Biochem Biophys Res Commun 2015; 466:28-32. [PMID: 26301631 DOI: 10.1016/j.bbrc.2015.08.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 08/19/2015] [Indexed: 11/15/2022]
Abstract
CXCR4 is a GPCR involved in leukocyte trafficking. Small molecule antagonists of the receptor may treat inflammatory disease, cancer and HIV. Here we probe the binding of a tetrahydroisoquinoline-based antagonist (TIQ-10) to CXCR4 using saturation transfer double-difference (STDD) NMR. STDD spectra were acquired using extracts from Chinese Hamster Ovary cells expressing membrane-embedded CXCR4. The experiments demonstrate competitive binding between TIQ-10 and established antagonists and provide the TIQ-10 - CXCR4 binding epitope. Molecular modeling of TIQ-10 into the binding pocket provides a pose consistent with STDD-derived interactions. This study paves the way for future investigations of GPCR-ligand interactions in a biological milieu for use in chemical biology, biochemistry, structural biology, and rational drug design.
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Affiliation(s)
- Bryan D Cox
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - Anil K Mehta
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - John O DiRaddo
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - Dennis C Liotta
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - Lawrence J Wilson
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA
| | - James P Snyder
- Emory University, Department of Chemistry, 1515 Dickey Dr., Atlanta, GA 30322, USA.
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65
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Aguirre C, Cala O, Krimm I. Overview of Probing Protein‐Ligand Interactions Using NMR. ACTA ACUST UNITED AC 2015; 81:17.18.1-17.18.24. [DOI: 10.1002/0471140864.ps1718s81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Olivier Cala
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
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66
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Sorge JL, Wagstaff JL, Rowe ML, Williamson RA, Howard MJ. Q2DSTD NMR deciphers epitope-mapping variability for peptide recognition of integrin αvβ6. Org Biomol Chem 2015; 13:8001-7. [PMID: 26119198 PMCID: PMC4541471 DOI: 10.1039/c5ob01237f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integrin αvβ6 is a cell surface arginine-glycine-aspartic acid (RGD)-specific heterodimeric glycoprotein that is only expressed on epithelia during processes of tissue remodelling, including cancer. The specificity and molecular nature of interactions toward this integrin are poorly understood and new insights into such processes are important to cell biologists and pharmaceutical drug discovery. This study demonstrates the application of quantitative two-dimensional saturation transfer (Q2DSTD) NMR to obtain precise details of peptide interactions with integrin αvβ6 and their correlation to specificity for the integrin. This approach highlights subtle but significant differences in ligand contact by three related 21-mer peptides: FMDV2, an αvβ6 specific peptide and DBD1 and LAP2T1 peptides that bind many αv integrins in addition to αvβ6. FMDV2 and DBD1 differ only by the cyclisation of DBD1; a process that removes αvβ6 specificity. Q2DSTD NMR demonstrates these peptides experience significantly different interactions with the integrin; FMDV contacts primarily through four residues: 6Leu, 10Leu, 12Val and 13Leu, whereas DBD1 and LAP2T1 have more widespread contacts across their sequences. Q2DSTD NMR combined two-dimensional STD with quantitation by considering the relaxation of the ligand (CRL) to provide precise ligand contact information. This study also examines the role of CRL in the Q2DSTD process and how quantitation modifies STD data and unravels epitope-mapping variability to provide precise results that differentiate interactions at the atomic level for each peptide.
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Affiliation(s)
- Jessica L Sorge
- School of Biosciences, University of Kent, Canterbury, Kent, UK.
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67
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Marchetti R, Molinaro A, Silipo A. NMR as a Tool to Unveil the Molecular Basis of Glycan-mediated Host–Pathogen Interactions. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nature of the relationship between microbes and hosts spans the broad spectrum from beneficial (symbiosis) to pathogenic (disease); one of the key factors determining the establishment of any type of host–microbe interaction is the pattern of glycoconjugates exposed on cell surfaces, many known as virulence factors since they are pivotal for adhesion to host tissue, immunoevasion and immunosuppression, causing disease in the host. The recognition of these pathogen glycostructures by specific host receptors is an important means of immune defense. In this context, NMR represents a valuable tool to investigate the conformational properties of both host/pathogen signaling molecules and to disclose their interaction at a molecular level. This chapter provides an overview of several protein–carbohydrate interaction systems studied by NMR, and their implications in human and plant diseases.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
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68
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Ardá A, Canales A, Cañada FJ, Jiménez-Barbero J. Carbohydrate–Protein Interactions: A 3D View by NMR. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
NMR spectroscopy is a key tool for carbohydrate research. In studies with complex oligosaccharides there are limits to the amount of relevant structural information provided by these observables due to problems of signal overlapping, strong coupling and/or the scarcity of the key NOE information. Thus, there is an increasing need for additional parameters with structural information, such as residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) or pseudo contact shifts (PCSs). Carbohydrates are rather flexible molecules. Therefore, NMR observables do not always correlate with a single conformer but with an ensemble of low free-energy conformers that can be accessed by thermal fluctuations. Depending on the system under study, different NMR approaches can be followed to characterize protein–carbohydrate interactions: the standard methodologies can usually be classified as “ligand-based” or “receptor-based”. The selection of the proper methodology is usually determined by the size of the receptor, the dissociation constant of the complex (KD), the availability of the labelled protein (15N, 13C) and the access to soluble receptors at enough concentration for NMR measurements.
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Affiliation(s)
- Ana Ardá
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Angeles Canales
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - F. Javier Cañada
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, CIB-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- CIC bioGUNE, Parque Tecnológico de Bizkaia Edif. 801A-1 48160 Derio-Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
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69
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van de Weerd R, Berbís MA, Sparrius M, Maaskant JJ, Boot M, Paauw NJ, de Vries N, Boon L, Baba O, Cañada FJ, Geurtsen J, Jiménez-Barbero J, Appelmelk BJ. A murine monoclonal antibody to glycogen: characterization of epitope-fine specificity by saturation transfer difference (STD) NMR spectroscopy and its use in mycobacterial capsular α-glucan research. Chembiochem 2015; 16:977-89. [PMID: 25766777 DOI: 10.1002/cbic.201402713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a major pathogen responsible for 1.5 million deaths annually. This bacterium is characterized by a highly unusual and impermeable cell envelope, which plays a key role in mycobacterial survival and virulence. Although many studies have focused on the composition and functioning of the mycobacterial cell envelope, the capsular α-glucan has received relatively minor attention. Here we show that a murine monoclonal antibody (Mab) directed against glycogen cross-reacts with mycobacterial α-glucans, polymers of α(1-4)-linked glucose residues with α(1-6)-branch points. We identified the Mab epitope specificity by saturation transfer difference NMR and show that the α(1-4)-linked glucose residues are important in glucan-Mab interaction. The minimal epitope is formed by (linear) maltotriose. Notably, a Mycobacterium mutant lacking the branching enzyme GlgB does not react with the Mab; this suggests that the α(1-6)-branches form part of the epitope. These seemingly conflicting data can be explained by the fact that in the mutant the linear form of the α-glucan (amylose) is insoluble. This Mab was subsequently used to develop several techniques helpful in capsular α-glucan research. By using a capsular glucan-screening methodology based on this Mab we were able to identify several unknown genes involved in capsular α-glucan biogenesis. Additionally, we developed two methods for the detection of capsular α-glucan levels. This study therefore opens new ways to study capsular α-glucan and to identify possible targets for further research.
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Affiliation(s)
- Robert van de Weerd
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam (The Netherlands)
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70
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Dureau R, Gicquel M, Artur I, Guégan JP, Carboni B, Ferrières V, Berrée F, Legentil L. Synthesis and evaluation of 1,2-trans alkyl galactofuranoside mimetics as mycobacteriostatic agents. Org Biomol Chem 2015; 13:4940-52. [DOI: 10.1039/c5ob00296f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The strong interaction of an octyl chain with M. smegmatis cells was paired with high specificity of the galactofuranose ring against mycobacteria growth.
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Affiliation(s)
- Rémy Dureau
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
- France
| | - Maxime Gicquel
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
- France
| | - Isabelle Artur
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
- France
| | - Jean-Paul Guégan
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
- France
| | - Bertrand Carboni
- Institut des Sciences Chimiques de Rennes
- UMR 6226 CNRS – Université de Rennes1
- 35042 Rennes Cedex
- France
- Université européenne de Bretagne
| | - Vincent Ferrières
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
- France
| | - Fabienne Berrée
- Institut des Sciences Chimiques de Rennes
- UMR 6226 CNRS – Université de Rennes1
- 35042 Rennes Cedex
- France
- Université européenne de Bretagne
| | - Laurent Legentil
- Ecole Nationale Supérieure de Chimie de Rennes
- CNRS
- UMR 6226
- 35708 Rennes Cedex 7
- France
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Abstract
Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (<300-350 Da) and lower initial potency but higher ligand efficiency when compared to those from high-throughput screening. NMR spectroscopy has been widely used for FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.
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72
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Blaum BS, Hannan JP, Herbert AP, Kavanagh D, Uhrín D, Stehle T. Structural basis for sialic acid-mediated self-recognition by complement factor H. Nat Chem Biol 2014; 11:77-82. [PMID: 25402769 DOI: 10.1038/nchembio.1696] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 10/02/2014] [Indexed: 12/25/2022]
Abstract
The serum protein complement factor H (FH) ensures downregulation of the complement alternative pathway, a branch of innate immunity, upon interaction with specific glycans on host cell surfaces. Using ligand-based NMR, we screened a comprehensive set of sialylated glycans for binding to FH and solved the crystal structure of a ternary complex formed by the two C-terminal domains of FH, a sialylated trisaccharide and the complement C3b thioester-containing domain. Key residues in the sialic acid binding site are conserved from mice to men, and residues linked to atypical hemolytic uremic syndrome cluster within this binding site, suggesting a possible role for sialic acid as a host marker also in other mammals and a critical role in human renal complement homeostasis. Unexpectedly, the FH sialic acid binding site is structurally homologous to the binding sites of two evolutionarily unrelated proteins. The crystal structure also advances our understanding of bacterial immune evasion strategies.
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Affiliation(s)
- Bärbel S Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Jonathan P Hannan
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - David Kavanagh
- Institute of Genetic Medicine, International Centre for Life, Newcastle upon Tyne, UK
| | - Dušan Uhrín
- The School of Chemistry, University of Edinburgh, Scotland, UK
| | - Thilo Stehle
- 1] Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany. [2] Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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73
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Diana D, Russomanno A, De Rosa L, Di Stasi R, Capasso D, Di Gaetano S, Romanelli A, Russo L, D'Andrea LD, Fattorusso R. Functional binding surface of a β-hairpin VEGF receptor targeting peptide determined by NMR spectroscopy in living cells. Chemistry 2014; 21:91-5. [PMID: 25378243 DOI: 10.1002/chem.201403335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 12/22/2022]
Abstract
In this study, the functional interaction of HPLW peptide with VEGFR2 (Vascular Endothelial Growth Factor Receptor 2) was determined by using fast (15)N-edited NMR spectroscopic experiments. To this aim, (15)N uniformly labelled HPLW has been added to Porcine Aortic Endothelial Cells. The acquisition of isotope-edited NMR spectroscopic experiments, including (15)N relaxation measurements, allowed a precise characterization of the in-cell HPLW epitope recognized by VEGFR2.
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Affiliation(s)
- Donatella Diana
- Istituto di Biostrutture e Bioimmagini, C.N.R., via Mezzocannone 16, 80134, Napoli (Italy)
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74
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Albohy A, Richards MR, Cairo CW. Mapping substrate interactions of the human membrane-associated neuraminidase, NEU3, using STD NMR. Glycobiology 2014; 25:284-93. [DOI: 10.1093/glycob/cwu109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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75
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Abstract
Ever since scientists realized that cells are the basic building blocks of all life, they have been developing tools to look inside them to reveal the architectures and mechanisms that define their biological functions. Whereas "looking into cells" is typically said in reference to optical microscopy, high-resolution in-cell and on-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful method that offers exciting new possibilities for structural and functional studies in and on live cells. In contrast to conventional imaging techniques, in- and on-cell NMR methods do not provide spatial information on cellular biomolecules. Instead, they enable atomic-resolution insights into the native cell states of proteins, nucleic acids, glycans, and lipids. Here we review recent advances and developments in both fields and discuss emerging concepts that have been delineated with these methods.
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Affiliation(s)
- Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, Maryland 20852-1448;
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76
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Lerche MH, Jensen PR, Karlsson M, Meier S. NMR insights into the inner workings of living cells. Anal Chem 2014; 87:119-32. [PMID: 25084065 DOI: 10.1021/ac501467x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mathilde H Lerche
- Albeda Research , Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
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77
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In vivo ultrasound molecular imaging of inflammatory thrombosis in arteries with cyclic Arg-Gly-Asp-modified microbubbles targeted to glycoprotein IIb/IIIa. Invest Radiol 2014; 48:803-12. [PMID: 23857134 DOI: 10.1097/rli.0b013e318298652d] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Ultrasound molecular imaging has the potential to detect activated platelets, thus identifying atherosclerotic plaque instability before onset of serious clinical events. However, it has not been well defined in inflammatory arterial thrombosis. We hypothesized that microbubbles (MBs) target glycoprotein IIb/IIIa (GP IIb/IIIa) could achieve a noninvasive in vivo detection of inflammatory thrombosis in large arteries through contrast-enhanced ultrasound (CEU) imaging. MATERIALS AND METHODS Lipid shell-based gas-filled MBs were modified covalently with a cyclic Arg-Gly-Asp (RGD) peptide (MB-cRGD) targeted to activated GP IIb/IIIa or a negative control peptide (MB-CON) via thiol-maleimide coupling. Adherence of MB-cRGD and MB-CON to GP IIb/IIIa was determined in vitro by using a parallel plate flow chamber at variable shear stress (0.5-8 dynes/cm2). Inflammatory platelet thrombosis was induced by periadvential application of arachidonic acid (AA) to one of the bilateral carotids of C57BL/6 mice (n = 20) and confirmed through intravital fluorescence microscopy. Attachment of MBs was determined in vivo with CEU imaging of bilateral carotids in the AA application mice with (n = 10) or without (n = 10) pretreatment of GP IIb/IIIa antagonist. The expression of integrin GP IIb/IIIa was assessed through immunohistochemistry. RESULTS Microbubble-cRGD but not MB-CON had excellent affinity to GP IIb/IIIa under all shear stress conditions. Successful inflammatory platelet activation and thrombosis in AA application carotids were noted through intravital fluorescence microscopy. Contrast video intensity from adhered MB-cRGD in the thrombi was significantly higher than that from MB-CON (P < 0.05). Video intensity of MB-cRGD in the thrombi was suppressed significantly by preblocking with GP IIb/IIIa antagonist (P < 0.05) but not for MB-CON. Immunohistochemical finding demonstrates that expression of integrin GP IIb/IIIa in the thrombi was abundant; it was inhibited significantly through pretreatment with GP IIb/IIIa antagonist (P < 0.05). CONCLUSIONS Cyclic RGD-modified MBs targeted to GP IIb/IIIa with CEU are capable of detecting inflammation-activated platelets and thrombosis in large arteries, thus providing a potential tool for identification of vulnerable atherosclerotic plaques.
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78
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Mondal M, Radeva N, Köster H, Park A, Potamitis C, Zervou M, Klebe G, Hirsch AKH. Strukturbasiertes Design von Hemmstoffen der Aspartylprotease Endothiapepsin mittels dynamischer kombinatorischer Chemie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309682] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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79
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Mondal M, Radeva N, Köster H, Park A, Potamitis C, Zervou M, Klebe G, Hirsch AKH. Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry. Angew Chem Int Ed Engl 2014; 53:3259-63. [PMID: 24532096 DOI: 10.1002/anie.201309682] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Indexed: 12/19/2022]
Abstract
Structure-based design (SBD) can be used for the design and/or optimization of new inhibitors for a biological target. Whereas de novo SBD is rarely used, most reports on SBD are dealing with the optimization of an initial hit. Dynamic combinatorial chemistry (DCC) has emerged as a powerful strategy to identify bioactive ligands given that it enables the target to direct the synthesis of its strongest binder. We have designed a library of potential inhibitors (acylhydrazones) generated from five aldehydes and five hydrazides and used DCC to identify the best binder(s). After addition of the aspartic protease endothiapepsin, we characterized the protein-bound library member(s) by saturation-transfer difference NMR spectroscopy. Cocrystallization experiments validated the predicted binding mode of the two most potent inhibitors, thus demonstrating that the combination of de novo SBD and DCC constitutes an efficient starting point for hit identification and optimization.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen (The Netherlands) http://www.rug.nl/research/bio-organic-chemistry/hirsch/
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80
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Alkyl galactofuranosides strongly interact with Leishmania donovani membrane and provide antileishmanial activity. Antimicrob Agents Chemother 2014; 58:2156-66. [PMID: 24468785 DOI: 10.1128/aac.01350-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We investigated the in vitro effects of four alkyl-galactofuranoside derivatives, i.e., octyl-β-D-galactofuranoside (compound 1), 6-amino-β-D-galactofuranoside (compound 2), 6-N-acetamido-β-D-galactofuranoside (compound 3), and 6-azido-β-D-galactofuranoside (compound 4), on Leishmania donovani. Their mechanism of action was explored using electron paramagnetic resonance spectroscopy (EPR) and nuclear magnetic resonance (NMR), and ultrastructural alterations were analyzed by transmission electron microscopy (TEM). Compound 1 showed the most promising effects by inhibiting promastigote growth at a 50% inhibitory concentration (IC50) of 8.96±2.5 μM. All compounds exhibit low toxicity toward human macrophages. Compound 1 had a higher selectivity index than the molecule used for comparison, i.e., miltefosine (159.7 versus 37.9, respectively). EPR showed that compound 1 significantly reduced membrane fluidity compared to control promastigotes and to compound 3. The furanose ring was shown to support this effect, since the isomer galactopyranose had no effect on parasite membrane fluidity or growth. NMR showed a direct interaction of all compounds (greatest with compound 1, followed by compounds 2, 3, and 4, in descending order) with the promastigote membrane and with octyl-galactopyranose and octanol, providing evidence that the n-octyl chain was primarily involved in anchoring with the parasite membrane, followed by the putative crucial role of the furanose ring in the antileishmanial activity. A morphological analysis of compound 1-treated promastigotes by TEM revealed profound alterations in the parasite membrane and organelles, but this was not the case with compound 3. Quantification of annexin V binding by flow cytometry confirmed that compound 1 induced apoptosis in >90% of promastigotes. The effect of compound 1 was also assessed on intramacrophagic amastigotes and showed a reduction in amastigote growth associated with an increase of reactive oxygen species (ROS) production, thus validating its promising effect.
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81
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Hayafune M, Berisio R, Marchetti R, Silipo A, Kayama M, Desaki Y, Arima S, Squeglia F, Ruggiero A, Tokuyasu K, Molinaro A, Kaku H, Shibuya N. Chitin-induced activation of immune signaling by the rice receptor CEBiP relies on a unique sandwich-type dimerization. Proc Natl Acad Sci U S A 2014; 111:E404-13. [PMID: 24395781 PMCID: PMC3903257 DOI: 10.1073/pnas.1312099111] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Perception of microbe-associated molecular patterns (MAMPs) through pattern recognition receptors (PRRs) triggers various defense responses in plants. This MAMP-triggered immunity plays a major role in the plant resistance against various pathogens. To clarify the molecular basis of the specific recognition of chitin oligosaccharides by the rice PRR, CEBiP (chitin-elicitor binding protein), as well as the formation and activation of the receptor complex, biochemical, NMR spectroscopic, and computational studies were performed. Deletion and domain-swapping experiments showed that the central lysine motif in the ectodomain of CEBiP is essential for the binding of chitin oligosaccharides. Epitope mapping by NMR spectroscopy indicated the preferential binding of longer-chain chitin oligosaccharides, such as heptamer-octamer, to CEBiP, and also the importance of N-acetyl groups for the binding. Molecular modeling/docking studies clarified the molecular interaction between CEBiP and chitin oligosaccharides and indicated the importance of Ile122 in the central lysine motif region for ligand binding, a notion supported by site-directed mutagenesis. Based on these results, it was indicated that two CEBiP molecules simultaneously bind to one chitin oligosaccharide from the opposite side, resulting in the dimerization of CEBiP. The model was further supported by the observations that the addition of (GlcNAc)8 induced dimerization of the ectodomain of CEBiP in vitro, and the dimerization and (GlcNAc)8-induced reactive oxygen generation were also inhibited by a unique oligosaccharide, (GlcNβ1,4GlcNAc)4, which is supposed to have N-acetyl groups only on one side of the molecule. Based on these observations, we proposed a hypothetical model for the ligand-induced activation of a receptor complex, involving both CEBiP and Oryza sativa chitin-elicitor receptor kinase-1.
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Affiliation(s)
- Masahiro Hayafune
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Alba Silipo
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Miyu Kayama
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Yoshitake Desaki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Sakiko Arima
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy
| | - Ken Tokuyasu
- Food Resource Division, National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan
| | - Antonio Molinaro
- Department of Chemical Sciences, Universita di Napoli Federico II, I-80126 Naples, Italy; and
| | - Hanae Kaku
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
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82
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Unione L, Galante S, Díaz D, Cañada FJ, Jiménez-Barbero J. NMR and molecular recognition. The application of ligand-based NMR methods to monitor molecular interactions. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00138a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
NMR allows the monitoring of molecular recognition processes in solution. Nowadays, a plethora of NMR methods are available to deduce the key features of the interaction from both the ligand or the receptor points of view.
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Affiliation(s)
- Luca Unione
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - Silvia Galante
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - Dolores Díaz
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - F. Javier Cañada
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
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83
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Rösner HI, Kragelund BB. Structure and dynamic properties of membrane proteins using NMR. Compr Physiol 2013; 2:1491-539. [PMID: 23798308 DOI: 10.1002/cphy.c110036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Integral membrane proteins are one of the most challenging groups of macromolecules despite their apparent conformational simplicity. They manage and drive transport, circulate information, and participate in cellular movements via interactions with other proteins and through intricate conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches, a large variety of developments of well-established techniques are available providing insight into membrane protein flexibility, dynamics, and interactions. Inspired by the speed of development in the application of new strategies, by invention of methods to measure solvent accessibility and describe low-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability.
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Affiliation(s)
- Heike I Rösner
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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84
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Balazs YS, Lisitsin E, Carmiel O, Shoham G, Shoham Y, Schmidt A. Identifying critical unrecognized sugar-protein interactions in GH10 xylanases fromGeobacillus stearothermophilususing STD NMR. FEBS J 2013; 280:4652-65. [DOI: 10.1111/febs.12437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Yael S. Balazs
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Elina Lisitsin
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Oshrat Carmiel
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Gil Shoham
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Yuval Shoham
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Asher Schmidt
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
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85
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NMR-based analysis of protein-ligand interactions. Anal Bioanal Chem 2013; 406:943-56. [PMID: 23591643 DOI: 10.1007/s00216-013-6931-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
Abstract
Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.
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86
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Guzzetti I, Civera M, Vasile F, Araldi EM, Belvisi L, Gennari C, Potenza D, Fanelli R, Piarulli U. Determination of the binding epitope of RGD-peptidomimetics to αvβ3 and αIIbβ3 integrin-rich intact cells by NMR and computational studies. Org Biomol Chem 2013; 11:3886-93. [DOI: 10.1039/c3ob40540k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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87
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Abstract
Nuclear magnetic resonance (NMR) is well suited to probing the interactions between ligands and macromolecular receptors. It is a truly label-free technique, requiring only the presence of atoms (usually (1)H or (19)F) which give rise to observable resonances on either the ligand or the receptor. A number of parameters associated with these resonances can be used to distinguish rapidly tumbling compounds from ligands which bind to a macromolecular receptor. As such, NMR reports directly on the molecular components involved in the binding interaction whilst avoiding artifacts arising from the addition of an observable label. NMR is also unique amongst biophysical techniques in giving information on the chemical nature of almost all of the constituents present in the sample, thus allowing ready identification of sample, contaminants, degraded material and buffers. Solution phase NMR is also free of artifacts introduced by the presence of a solid support or matrix, although some interesting NMR techniques have been developed to identify ligand-receptor interactions in both solid and heterogeneous phase systems.NMR can readily report on molecular interactions across a wide range of affinities and timescales. Although NMR is not an inherently sensitive technique, the development of cryogenic probeheads over the past decade has dramatically increased the range of applicability of the technique and reduced the stringent sample requirements that used to be regarded as an "Achilles' heel" of NMR. The last, but by no means the least, NMR has the ability to determine structural information at atomic resolution; this has proved to be particularly useful when applied to those protein-ligand systems which cannot be readily crystallized.
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Affiliation(s)
- Ben Davis
- Vernalis Ltd (R&D), Great Abington, Cambridge, UK
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88
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Wagstaff JL, Taylor SL, Howard MJ. Recent developments and applications of saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy. ACTA ACUST UNITED AC 2013; 9:571-7. [DOI: 10.1039/c2mb25395j] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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89
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Proteasome allostery as a population shift between interchanging conformers. Proc Natl Acad Sci U S A 2012; 109:E3454-62. [PMID: 23150576 DOI: 10.1073/pnas.1213640109] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein degradation plays a critical role in cellular homeostasis, in regulating the cell cycle, and in the generation of peptides that are used in the immune response. The 20S proteasome core particle (CP), a barrel-like structure consisting of four heptameric protein rings stacked axially on top of each other, is central to this process. CP function is controlled by activator complexes that bind 75 Å away from sites catalyzing proteolysis, and biochemical data are consistent with an allosteric mechanism by which binding is communicated to distal active sites. However, little structural evidence has emerged from the high-resolution images of the CP. Using methyl TROSY NMR spectroscopy, we demonstrate that in solution, the CP interconverts between multiple conformations whose relative populations are shifted on binding of the 11S activator or mutation of residues that contact activators. These conformers differ in contiguous regions of structure that connect activator binding to the CP active sites, and changes in their populations lead to differences in substrate proteolysis patterns. Moreover, various active site modifications result in conformational changes to the activator binding site by modulating the relative populations of these same CP conformers. This distribution is also affected by the binding of a small-molecule allosteric inhibitor of proteolysis, chloroquine, suggesting an important avenue in the development of therapeutics for proteasome inhibition.
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90
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Abstract
Drug discovery on membrane proteins is still a difficult task, despite the recognized importance of membrane proteins as drug targets. Here, we present an overview of NMR methods available for structure-based drug design on membrane proteins. NMR spectroscopy is capable of identifying potential binders in screening and defining their relative binding constants, binding stoichiometry, conformation in the binding pocket and the relative binding orientation for binders of different series. Examples are given in the review highlighting the potential of NMR spectroscopy for future progress in drug discovery on membrane proteins.
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91
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Bhunia A, Bhattacharjya S, Chatterjee S. Applications of saturation transfer difference NMR in biological systems. Drug Discov Today 2012; 17:505-13. [DOI: 10.1016/j.drudis.2011.12.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 11/10/2011] [Accepted: 12/14/2011] [Indexed: 01/08/2023]
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92
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Johnson MA, Cartmell J, Weisser NE, Woods RJ, Bundle DR. Molecular recognition of Candida albicans (1->2)-β-mannan oligosaccharides by a protective monoclonal antibody reveals the immunodominance of internal saccharide residues. J Biol Chem 2012; 287:18078-90. [PMID: 22493450 DOI: 10.1074/jbc.m112.355578] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A self-consistent model of β-mannan oligosaccharides bound to a monoclonal antibody, C3.1, that protects mice against Candida albicans has been developed through chemical mapping, NMR spectroscopic, and computational studies. This antibody optimally binds di- and trisaccharide epitopes, whereas larger oligomers bind with affinities that markedly decrease with increasing chain length. The (1→2)-β-linked di-, tri-, and tetramannosides bind in helical conformations similar to the solution global minimum. Antibody recognition of the di- and trisaccharide is primarily dependent on the mannose unit at the reducing end, with the hydrophobic face of this sugar being tightly bound. Recognition of a tetrasaccharide involves a frameshift in the ligand interaction, shown by strong binding of the sugar adjacent to the reducing end. We show that frameshifting may also be deliberately induced by chemical modifications. Molecular recognition patterns similar to that of mAb C3.1, determined by saturation transfer difference-NMR, were also observed in polyclonal sera from rabbits immunized with a trisaccharide glycoconjugate. The latter observation points to the importance of internal residues as immunodominant epitopes in (1→2)-β-mannans and to the viability of a glycoconjugate vaccine composed of a minimal length oligosaccharide hapten.
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Affiliation(s)
- Margaret A Johnson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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93
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Kooijmans SAA, Vader P, van Dommelen SM, van Solinge WW, Schiffelers RM. Exosome mimetics: a novel class of drug delivery systems. Int J Nanomedicine 2012; 7:1525-41. [PMID: 22619510 PMCID: PMC3356169 DOI: 10.2147/ijn.s29661] [Citation(s) in RCA: 224] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of extracellular phospholipid vesicles as conveyors of cellular information has created excitement in the field of drug delivery. Biological therapeutics, including short interfering RNA and recombinant proteins, are prone to degradation, have limited ability to cross biological membranes, and may elicit immune responses. Therefore, delivery systems for such drugs are under intensive investigation. Exploiting extracellular vesicles as carriers for biological therapeutics is a promising strategy to overcome these issues and to achieve efficient delivery to the cytosol of target cells. Exosomes are a well studied class of extracellular vesicles known to carry proteins and nucleic acids, making them especially suitable for such strategies. However, the considerable complexity and the related high chance of off-target effects of these carriers are major barriers for translation to the clinic. Given that it is well possible that not all components of exosomes are required for their proper functioning, an alternative strategy would be to mimic these vesicles synthetically. By assembly of liposomes harboring only crucial components of natural exosomes, functional exosome mimetics may be created. The low complexity and use of well characterized components strongly increase the pharmaceutical acceptability of such systems. However, exosomal components that would be required for the assembly of functional exosome mimetics remain to be identified. This review provides insights into the composition and functional properties of exosomes, and focuses on components which could be used to enhance the drug delivery properties of exosome mimetics.
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Affiliation(s)
- Sander A A Kooijmans
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
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94
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95
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Use of NMR saturation transfer difference spectroscopy to study ligand binding to membrane proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 914:47-63. [PMID: 22976022 DOI: 10.1007/978-1-62703-023-6_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Detection of weak ligand binding to membrane-spanning proteins, such as receptor proteins at low physiological concentrations, poses serious experimental challenges. Saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy offers an excellent way to surmount these problems. As the name suggests, magnetization transferred from the receptor to its bound ligand is measured by directly observing NMR signals from the ligand itself. Low-power irradiation is applied to a (1)H NMR spectral region containing protein signals but no ligand signals. This irradiation spreads quickly throughout the membrane protein by the process of spin diffusion and saturates all protein (1)H NMR signals. (1)H NMR signals from a ligand bound transiently to the membrane protein become saturated and, upon dissociation, serve to decrease the intensity of the (1)H NMR signals measured from the pool of free ligand. The experiment is repeated with the irradiation pulse placed outside the spectral region of protein and ligand, a condition that does not lead to saturation transfer to the ligand. The two resulting spectra are subtracted to yield the difference spectrum. As an illustration of the methodology, we review here STD-NMR experiments designed to investigate binding of ligands to the human sweet taste receptor, a member of the large family of G-protein-coupled receptors. Sweetener molecules bind to the sweet receptor with low affinity but high specificity and lead to a variety of physiological responses.
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96
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Airoldi C, Giovannardi S, La Ferla B, Jiménez-Barbero J, Nicotra F. Saturation Transfer Difference NMR Experiments of Membrane Proteins in Living Cells under HR-MAS Conditions: The Interaction of the SGLT1 Co-transporter with Its Ligands. Chemistry 2011; 17:13395-9. [DOI: 10.1002/chem.201102181] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 12/13/2022]
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97
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STD-NMR: application to transient interactions between biomolecules—a quantitative approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1357-69. [DOI: 10.1007/s00249-011-0749-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 09/06/2011] [Indexed: 02/02/2023]
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98
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Bhunia A, Bhattacharjya S. Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Biopolymers 2011; 96:273-87. [PMID: 20683937 DOI: 10.1002/bip.21530] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High-resolution interactions studies of molecules with lipopolysaccharide (LPS) or endotoxin are important for health, diseases and environment. LPS is the major constituent of the outer layer of the outer membrane of the gram-negative bacteria. LPS provides an efficient barrier against permeation of variety of compounds including antibacterial agents and antimicrobial peptides. In the intensive care units, LPS is known for the fatal septic shock syndromes. Because of LPS toxicity, high affinity LPS sensors are sought-after for the assessment of the quality of water and pharmaceutical products. Therefore, elucidation of binding epitopes of LPS interacting molecules would be vital for the development of antimicrobial, antiendotoxic molecules. Polymyxin B (PMB), an antibacterial cyclic lipo-peptide, is well known for its LPS sequestering and neutralizing activities. Here, we have used saturation transfer difference (STD) NMR methods for characterizing interactions of PMB with LPS from E. coli 0111:B4 and P. aeruginosa. The dissociation constants of the LPS-PMB complexes were obtained from concentration dependent STD studies. Further a detailed epitope mapping of PMB has been carried out in E. coli 0111:B4 LPS micelles. Experiments including one-dimensional 1H STD, two-dimensional 1H-1H STD-TOCSY and naturalabundance 13C-1H STD-HSQC, are performed to determine the site(s) of interactions of PMB with endotoxin at atomic resolution. Our studies reveal that the hydrophobic sidechains of PMB including a part of the N-terminus lipidic tail demonstrate close contacts with LPS. In contrast, cyclic backbone structure of PMB has the lowest STD effects suggesting a rather loose association with endotoxin.
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Affiliation(s)
- Anirban Bhunia
- Biomolecular NMR and Drug Discovery Laboratory, School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551
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99
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Vega-Vázquez M, Cobas JC, Oliveira de Sousa FF, Martin-Pastor M. A NMR reverse diffusion filter for the simplification of spectra of complex mixtures and the study of drug receptor interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:464-468. [PMID: 21751249 DOI: 10.1002/mrc.2786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/29/2011] [Accepted: 05/31/2011] [Indexed: 05/31/2023]
Abstract
A reverse diffusion filter NMR experiment (Drev) is proposed for the study of small molecules in binding with macromolecules. The filtering efficiency of Drev to eliminate the signals of the macromolecule is shown to be superior to conventional transverse relaxation filters at least for macromolecules containing a significant fraction of flexible residues. The Drev filter was also a useful complement for ligand-based NMR screening in combination with saturation transfer difference experiments.
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Affiliation(s)
- M Vega-Vázquez
- Unidade de Resonancia Magnética, Edif. CACTUS, RIAIDT, Campus Vida, University of Santiago de Compostela, A Coruña 15706, Spain
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100
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Simpson AJ, McNally DJ, Simpson MJ. NMR spectroscopy in environmental research: from molecular interactions to global processes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:97-175. [PMID: 21397118 DOI: 10.1016/j.pnmrs.2010.09.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/17/2010] [Indexed: 05/30/2023]
Affiliation(s)
- André J Simpson
- Environmental NMR Center, Department of Chemistry, University of Toronto, Ontario, Canada.
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