Development of Methodologies for Identifying Nonspecific Ligand Interactions in Electrospray Ionization Mass Spectrometry PDF Download

Author: Nian Sun
Publisher:
ISBN:
Category : Electrospray ionization mass spectrometry
Languages : en
Pages : 178

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Author: Carolyn Leigh Mazzitelli
Publisher:
ISBN:
Category : DNA-ligand interactions
Languages : en
Pages : 390

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Book Description
Many anticancer and antibacterial therapies are based on the interaction of small molecule drugs with DNA. Increasing interest in the development of DNA-interactive agents has fostered the need for sensitive and versatile analytical techniques that are capable of characterizing the DNA/ligand interactions and are compatible with librarybased screening methods. Electrospray ionization mass spectrometry (ESI-MS) has emerged as a useful technique for the analysis of non-covalent complexes formed between DNA and small molecules due to its low sample consumption and fast analysis time. The work presented in this dissertation is aimed at exploring, optimizing, and validating ESI-MS methods for characterizing DNA-ligand interactions. ESI-MS is first used to assess the binding of threading bis-intercalators to duplexes containing different sequences to determine high affinity binding sites of the ligands. Preliminary DNAse footprinting experiments identified possible specific binding sites of the ligands and ESI-MS experiments revealed that the ligands bound to DNA duplexes containing the respective specific binding sequences. The metal-mediated binding of benzoxazole ligands with different side chains to duplex DNA is also examined. Cu2 and Ni were found to promote the most dramatic increase in ligand binding, and ligands exhibiting the most dramatic metal-mediated or metal-enhanced binding were also determined to be the most cytotoxic. The quadruplex DNA binding selectivity of perylene diimides is evaluated by screening the binding of the ligands to quadruplex, duplex and single strand DNA by ESI-MS. Three ligands, one containing basic side chains, one containing anionic sidechains, and one benzannulated compound were determined to be the most-quadruplex selective. The ESI-MS results correlated well with spectroscopic experiments. The relative gas-phase stabilities of different quadruplex DNA structures were investigated using molecular dynamics simulations and ESI-MS. The stabilities from the E[subscript 1/2] values generally paralleled the RMSD and relative free energies of the quadruplexes based on MD energy analysis. Finally an ESI-MS technique employing the KMnO4 reaction with DNA to determine conformational changes to the duplex structure upon ligand binding is detailed. Thymines in most intercalator/duplex complexes are more susceptible to oxidation by KMnO4 than those in duplex DNA. CAD and IRMPD experiments are used to identify the site of oxidation.

Author: Adetayo Musbau Mustapha
Publisher:
ISBN:
Category : Electrospray ionization mass spectrometry
Languages : en
Pages : 0

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Metal-ligand interactions are important in such diverse areas as environmental remediation, drug development, and biochemistry. Potentiometric and spectroscopic techniques, including UV-Visible, infrared, Raman, and NMR spectroscopies, are commonly used to investigate metal-ligand interactions. However, ESI-MS is a valuable technique for accurate determination of complex stoichiometric ratios, and for the study of the gas-phase chemistry of metal complexes with organic ligands. This dissertation presents two broad areas where ESI-MS has been used to study such complexes. In the first area, I investigated the analytical importance of transition metal interactions with phosphorothioate and phosphorodithioate pesticides. These pesticides are important subclasses of organophosphorus pesticides commonly used in agriculture to control pests in fruits and vegetables. Using ESI-MS, I examined how the interactions of three phosphorothioate pesticides (fenitrothion, parathion, and diazinon) and one phosphorodithioate pesticide (malathion) with silver and copper ions affects the mass spectral detection of the resulting complexes. My results show that each pesticide forms silver and copper complexes that significantly improve their detection using ESI-MS. I also found that these metal-pesticide complexes do not undergo the thiono-thiolo rearrangement reaction during collision-induced dissociation, unlike protonated phosphorothioate ions. In the second part of the dissertation I explore the use of ESI-MS for characterization of gas-phase complexes that arise from uranyl(VI), vanadium(V) and iron(III) interactions with 2,6-dihydroxyiminopiperidine (DHIP) and N1, N5-dihydroxypentanediimidamide (DHPD) in aqueous solutions. I also investigated uranyl(VI) interactions with N1, N5-dihydroxyethanediimidamide (DHED). Uranium is an important fuel for nuclear power generation, and there is much interest in the possibility of its extraction from seawater using amidoxime-functionalized sorbents. Vanadium and iron can compete with uranium for binding sites on these sorbents. My results show that DHIP binds uranyl(VI) more effectively that DHPD or DHED, forming ions having uranyl(VI):DHIP stoichiometric ratios of 1:1, 1:2, and 2:3. Vanadium(V) forms 1:1 and 1:2 vanadium(V):DHIP complexes, while iron(III) forms only a 1:2 iron(III):DHIP complex. With DHPD, vanadium(V) forms only a 1:2 vanadium(V):DHPD complex, while iron(III) forms both 1:2 and 1:3 complexes with DHPD. I also observed that gas-phase uranyl(VI)-DHIP complexes are less likely to form in the presence of either vanadium(V) or iron(III).

Author: Whitney Parrish
Publisher:
ISBN:
Category : Electrospray ionization mass spectrometry
Languages : en
Pages : 75

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Electrospray Ionization Mass Spectrometry (ESI-MS) has become a powerful technique for analyzing protein- and peptide-ligand interactions and quantifying their binding constants (K[subscript]b). However, ESI-MS as an analytical method has several drawbacks, including one particular problem with the analysis of zinc (II)-containing complexes. During sample infusion through a stainless steel ESI emitter, zinc (II) can be deposited onto the emitter. Therefore, what is being detected is not indicative of what is really present in solution and K[subscript]b will be falsely low. Additionally, ligands present in solution may nonspecifically bind to the species of interest during ESI. This nonspecific binding causes K[subscript]b values to be falsely high. Lastly, in-source (gas-phase) dissociation can also occur, meaning the peptide-ligand complex can partially or completely dissociate during ESI. This dissociation causes K[subscript]b values to be incorrectly low. Each of these problems has been addressed individually, but the goal of this project is to address all three problems in one set of experiments to obtain a more reliable binding constant for a model system. For this work, the model system that was chosen to study was the [beta]-amyloid peptide with zinc (II), in particular the 1-16 and 1-28 fragments. Reference methods have been developed by the Klassen group to correct for nonspecific binding and in-source dissociation. The reference peptide method adds a reference peptide that does not bind the peptide or ligand of interest to solution to account for any nonspecific binding. In our experiments, neurotensin was used as the reference peptide. The reference ligand method adds a reference ligand that does bind the peptide of interest to solution to account for any in-source dissociation that may be occurring. Copper (II) was used as the reference ligand because it binds the [beta]-amyloid peptide with a high affinity that has been previously measured and reported by many researchers. The emitter material was changed from stainless steel to glass, and we have shown that this material change prevents zinc (II) deposition from occurring. Initial data was obtained showing appropriate binding percentages in a 1:1 [beta]-amyloid-zinc (II) solution based on equilibrium calculations. Optimized source conditions were determined based on the binding percentages obtained. A titration style experiment was designed to determine the binding constant for both model systems. The K[subscript]b value obtained for [beta]-amyloid (1-16):Zn2 complex was 1.8 (± 0.2) x 108 M−1. Two K[subscript]b values were determined for the [beta]-amyloid (1-28):Zn2 complex. These two values are 6.7 (± 0.4) x 104 M−1 and 3.2 (± 0.2) x 108 M−1. Even though this work was successful in determining a binding constant for a peptide-zinc (II) system using ESI-MS, there is variability in the results obtained. The common feature of MS and other techniques that are used to determine K[subscript]b values is reproducibility. This illustrates the need to combine complementary techniques when studying peptide-ligand systems and quantifying their binding constants.

Author: Atta-ur Rahman
Publisher: Bentham Science Publishers
ISBN: 1608052044
Category : Medical
Languages : en
Pages : 680

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Book Description
""Frontiers in Medicinal Chemistry" is an Ebook series devoted to the review of areas of important topical interest to medicinal chemists and others in allied disciplines. "Frontiers in Medicinal Chemistry" covers all the areas of medicinal chemistry, incl"

Author: Leonardo S. Santos
Publisher: John Wiley & Sons
ISBN: 9783527628735
Category : Science
Languages : en
Pages : 341

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Book Description
During the last two decades there has been considerable growth in the development of electrospray ionization mass spectrometry (ESI-MS) as a practical method in the study of reaction mechanisms. This method allows the interception and characterization of key intermediates, either as transient species or as protonated/deprotonated forms of neutral species by API-MS. The outstanding features and advantages of ESI-MS make it one of the most suitable tools for the fast screening of intermediates directly from solution, providing hitherto unavailable chemical information to organic chemists. This monograph provides an overview of the mechanisms involved in ESI-MS, the historical perspectives before looking further in-depth at specific reactions and intermediates. Written by researchers in the field, this book is an unique resource for the understanding of this cutting-edge technique.

Author: Klaus Wanner
Publisher: John Wiley & Sons
ISBN: 3527314563
Category : Science
Languages : en
Pages : 463

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This first overview of mass spectrometry-based pharmaceutical analysis is the key to improved high-throughput drug screening, rational drug design and analysis of multiple ligand-target interactions. The ready reference opens with a general introduction to the use of mass spectrometry in pharmaceutical screening, followed by a detailed description of recently developed analytical systems for use in the pharmaceutical laboratory. Applications range from simple binding assays to complex screens of biological activity and systems containing multiple targets or ligands -- all highly relevant techniques in the early stages in drug discovery, from target characterization to hit and lead finding.

Author:
Publisher: Academic Press
ISBN: 9780120342501
Category : Science
Languages : en
Pages : 282

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The role that primary amino acid sequences plays in influencing the partitioning of polypeptides between productive folding and irreversible aggregation pathways has introduced a whole new dimension to the folding problem. The volume deals with the structures of the products of protein misassembly and the role of amino acid sequences in favoring these structures.

Author: Zhiming M. Wang
Publisher: Springer Science & Business Media
ISBN: 1461494729
Category : Technology & Engineering
Languages : en
Pages : 392

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Nanodroplets, the basis of complex and advanced nanostructures such as quantum rings, quantum dots and quantum dot clusters for future electronic and optoelectronic materials and devices, have attracted the interdisciplinary interest of chemists, physicists and engineers. This book combines experimental and theoretical analyses of nanosized droplets which reveal many attractive properties. Coverage includes nanodroplet synthesis, structure, unique behaviors and their nanofabrication, including chapters on focused ion beam, atomic force microscopy, molecular beam epitaxy and the "vapor-liquid- solid" route. Particular emphasis is given to the behavior of metallic nanodroplets, water nanodroplets and nanodroplets in polymer and metamaterial nanocomposites. The contributions of leading scientists and their research groups will provide readers with deeper insight into the chemical and physical mechanisms, properties, and potential applications of various nanodroplets.

Author: Richard B. Cole
Publisher: John Wiley & Sons
ISBN: 1118211553
Category : Science
Languages : en
Pages : 900

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Book Description
Discover how advances in mass spectrometry are fueling new discoveries across a broad range of research areas Electrospray and MALDI Mass Spectrometry brings both veteran practitioners and beginning scientists up to date with the most recent trends and findings in electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In particular, this Second Edition highlights how advances in electrospray and MALDI mass spectrometry are supporting important discoveries in new and emerging fields such as proteomics and metabolomics as well as in traditional areas of chemistry and physics research. Electrospray AND MALDI Mass Spectrometry, SECOND EDITION is divided into five parts: Part A, Fundamentals of ES, explains the fundamental phenomena underlying the electrospray process, including selectivity in ionization and inherent electrochemistry, and concludes with a chapter offering a comparative inventory of source hardware Part B, Fundamentals of MALDI, confronts ionization mechanisms, instrument development, and matrix selection, and includes a final chapter that explores the special application of MALDI to obtain two-dimensional images of spatial distributions of compounds on surfaces Part C, ES and MALDI Coupling to Mass Spectrometry Instrumentation, examines the coupling of these ionization techniques to various mass analyzers, including quadrupole ion trap, time-of-flight, Fourier transform ion cyclotron resonance, and ion mobility mass spectrometers Part D, Practical Aspects of ES and MALDI, investigates analytical issues including quantification, charge-state distributions, noncovalent interactions in solution that are preserved as gas-phase ions, and various means of ion excitation in preparation for tandem mass spectrometry, and offers a guide to the interpretation of even-electron mass spectra Part E, Biological Applications of ES and MALDI, examines the role of mass spectrometry in such areas as peptide and protein characterization, carbohydrate analysis, lipid analysis, and drug discovery Written by a team of leading experts, the book not only provides a critical review of the literature, but also presents key concepts in tutorial fashion to help readers take full advantage of the latest technological breakthroughs and applications. As a result, Electrospray and MALDI Mass Spectrometry will help researchers fully leverage the power of electrospray and MALDI mass spectrometry. The judicious compartmentalization of chapters, and the pedagogic presentation style throughout, render the book highly suitable for use as a text for graduate-level courses in advanced mass spectrometry.