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Leopold J, Prabutzki P, Nimptsch A, Schiller J. Mass spectrometric investigations of the action of hypochlorous acid on monomeric and oligomeric components of glycosaminoglycans. Biochem Biophys Rep 2023; 34:101448. [PMID: 36915825 PMCID: PMC10006533 DOI: 10.1016/j.bbrep.2023.101448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Hypochlorous acid (HOCl) is a strong non-radical oxidant, which is generated during inflammatory processes under the catalysis of the enzyme myeloperoxidase (MPO). HOCl reacts particularly with sulfhydryl and amino acid residues but affects also many other biomolecules. For instance, the glycosaminoglycans of articular cartilage and synovial fluids (such as hyaluronan) undergo degradation in the presence of HOCl at which the native polysaccharide is fragmented into oligosaccharides in a complex reaction. This is an initial mass spectrometry (MS)-based investigation dealing with the HOCl-induced degradation of glycosaminoglycans and the conversion of the related monosaccharides into chlorinated products. In particular, it will be shown that the reaction between HOCl and hyaluronan is slower than originally assumed and results in the generation of different products (particularly the hyaluronan monosaccharides) by the cleavage of the β-1,3/1,4-glycosidic linkages. The MS detection of chlorinated products is, however, only possible in the case of the monosaccharides. Potential reasons will be discussed.
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Affiliation(s)
- Jenny Leopold
- Institute for Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany
| | - Patricia Prabutzki
- Institute for Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany
| | - Ariane Nimptsch
- Institute for Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany
| | - Jürgen Schiller
- Institute for Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany
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2
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Blaj DA, Kowalczuk M, Peptu C. Mass Spectrometry of Esterified Cyclodextrins. Molecules 2023; 28. [PMID: 36903247 DOI: 10.3390/molecules28052001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023] Open
Abstract
Cyclodextrins are cyclic oligosaccharides that have received special attention due to their cavity-based structural architecture that imbues them with outstanding properties, primarily related to their capacity to host various guest molecules, from low-molecular-mass compounds to polymers. Cyclodextrin derivatization has been always accompanied by the development of characterization methods, able to unfold complicated structures with increasing precision. One of the important leaps forward is represented by mass spectrometry techniques with soft ionization, mainly matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). In this context, esterified cyclodextrins (ECDs) benefited also from the formidable input of structural knowledge, thus allowing the understanding of the structural impact of reaction parameters on the obtained products, especially for the ring-opening oligomerization of cyclic esters. The current review envisages the common mass spectrometry approaches such as direct MALDI MS or ESI MS analysis, hyphenated liquid chromatography-mass spectrometry, and tandem mass spectrometry, employed for unraveling the structural features and particular processes associated with ECDs. Thus, the accurate description of complex architectures, advances in the gas phase fragmentation processes, assessment of secondary reactions, and reaction kinetics are discussed in addition to typical molecular mass measurements.
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Fasih Ramandi N, Faranoush M, Ghassempour A, Aboul-Enein HY. Mass Spectrometry: A Powerful Method for Monitoring Various Type of Leukemia, Especially MALDI-TOF in Leukemia's Proteomics Studies Review. Crit Rev Anal Chem 2021; 52:1259-1286. [PMID: 33499652 DOI: 10.1080/10408347.2021.1871844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Recent success in studying the proteome, as a source of biomarkers, has completely changed our understanding of leukemia (blood cancer). The identification of differentially expressed proteins, such as relapse and drug resistance proteins involved in leukemia by using various ionization sources and mass analyzers of mass spectrometry techniques, has helped scientists find better diagnosis, prognosis, and treatment strategies. With the aid of this powerful analytical technique, we can investigate the qualification/quantification of proteins, protein-protein interactions, post-translational modifications, and find the correlation between proteins and their genes with the hope of finding the missing parts of the successful therapy puzzle. In this review, we followed different MS sources and analyzers which used for monitoring various type of leukemia, then focused on MALDI-TOF MS as a quick and reliable method for studying proteins. Due to several review published for other techniques, the present review is the first work in this field. Also, by classifying more than 400 proteins, we have found 42 proteins are involved in two or three different stages of leukemia. Finally, we have suggested six specific biomarkers for AML, one for ALL, three biomarkers with a role in the etiology of leukemia and 13 markers with the potential for further studies.
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Affiliation(s)
- Negin Fasih Ramandi
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Faranoush
- Pediatric Growth and Development Research Center, Institute of Endocrinology, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Hassan Y Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Center, Cairo, Egypt
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Sarbu M, Ica R, Zamfir AD. Developments and applications of separation and microfluidics methods coupled to electrospray mass spectrometry in glycomics of nervous system gangliosides. Electrophoresis 2021; 42:429-449. [PMID: 33314304 DOI: 10.1002/elps.202000236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 01/19/2023]
Abstract
Gangliosides are particularly abundant in the nervous system (NS) where their pattern and structure in a certain milieu or a defined region exhibit a pronounced specificity. Since gangliosides are useful biomarkers for diagnosis of NS ailments, a clear-cut mapping of individual components represents a prerequisite for designing ganglioside-based diagnostic procedures, treatments, or vaccines. These bioclinical aspects and the high diversity of ganglioside species claim for development of specific analytical strategies. This review summarizes the state-of-the-art in the implementation of separation techniques and microfluidics coupled to MS, which have contributed significantly to the advancement of the field. In the first part, the review discusses relevant approaches based on HPLC MS and CE coupled to ESI MS and their applications in the characterization of gangliosides expressed in healthy and diseased NS. A considerable section is dedicated to microfluidics MS and ion mobility separation MS, developed for the study of brain gangliosidome and its changes triggered by various factors, as well as for ganglioside biomarker discovery in neurodegenerative diseases and brain cancer. In the last part of the review, the benefits and perspectives in ganglioside research of these high-performance techniques are presented.
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Affiliation(s)
- Mirela Sarbu
- National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Romania
| | - Raluca Ica
- National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Romania.,Department of Physics, West University of Timisoara, Timisoara, Romania
| | - Alina D Zamfir
- National Institute for Research and Development in Electrochemistry and Condensed Matter, Timisoara, Romania.,Department of Technical and Natural Sciences, "Aurel Vlaicu" University of Arad, Arad, Romania
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Prabutzki P, Leopold J, Schubert S, Schiller J, Nimptsch A. De novo synthesis of phospholipids and sphingomyelin in multipotent stromal cells - Monitoring studies by mass spectrometry. Chem Phys Lipids 2020; 232:104965. [PMID: 32888915 DOI: 10.1016/j.chemphyslip.2020.104965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/16/2020] [Accepted: 08/23/2020] [Indexed: 02/07/2023]
Abstract
Musculoskeletal diseases are extremely widespread and a significant burden on the health systems of the industrialized countries. The use of mesenchymal stromal cells is a promising approach to cure cartilage and tendon injuries, which often also occur in younger people as consequences of sport accidents. Although particular interest is on the collagen and the glycosaminoglycan composition of the tendon and potential alterations compared to healthy tissue, there is nowadays also increasing evidence that some selected phospholipids (PL) are potential mediators of tissue regeneration. Therefore, PL (and potential changes thereof) attract increasing interest in this field. We have used positive and negative ion matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to elucidate the lipid compositions of human mesenchymal stromal cells in dependence on the composition of the cell culture medium and the cultivation time. The de novo biosynthesis of PL was monitored by adding 13C labeled glucose or deuterated palmitic acid (d31-PA) to the cells and the incorporation of 13C or 2H into the different PL classes was investigated by electrospray ionization (ESI) mass spectrometry (MS). It is remarkable that all PL classes (for instance, phosphatidylcholine and -inositol) exhibited 13C incorporation - but not the sphingomyelin (SM) which is the most abundant sphingolipid in the majority of human tissues and body fluids. Using suitable internal standards it could be shown, that only 12C-containing SM is de novo generated while no 13C-labeled SM could be monitored - independent of the cultivation time, which was varied between 7 and 28 days. SM impurities stemming from the cell culture medium and the used MALDI matrix compounds (2,5-dihydroxybenzoic acid (DHB) or 9-aminoacridine (9-AA)) could be ruled out. However, incorporation of deuterated palmitic acid (d31-PA) could be observed for multiple PL, including SM. Therefore, it is suggested that there must exist another, so far unknown SM biosynthesis pathway. This pathway does not make use of glucose but relies on the use of other molecules as energy sources. Potential pathways to explain the experimental observations are discussed.
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Affiliation(s)
- Patricia Prabutzki
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Jenny Leopold
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Susanna Schubert
- Leipzig University, Saxonian Incubator for Clinical Translation, Philipp-Rosenthal-Straße 55, D-04103, Leipzig, Germany
| | - Jürgen Schiller
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Ariane Nimptsch
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Leipzig, Germany.
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Moracci L, Traldi P, Agostini M. MASS SPECTROMETRY FOR A HOLISTIC VIEW OF NATURAL EXTRACTS OF PHYTOTHERAPEUTIC INTEREST. Mass Spectrom Rev 2020; 39:553-573. [PMID: 31930557 DOI: 10.1002/mas.21619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
In the study of natural products new strategies which favor a holistic approach, integrating the traditional reductionist methods usually employed, have been proposed. In this frame, the studies carried out by us in the last decade show that fingerprints, mainly obtained by electrospray ionization mass spectrometry (ESI-MS), lead to the characterization of natural extracts from different botanical species but also of phytotherapeutic products constituted by mixtures of extracts from different plants. Laser desorption ionization and matrix-assisted laser desorption ionization techniques were also employed and by the use of different matrices some complementary results were achieved. Results obtained by standard spectrophotometric and liquid chromatography methods were compared with those achieved by direct infusion of the extract in ESI-MS conditions, indicating an excellent agreement between the two approaches. The findings of these researches were considered in the frame of complex systems theory, investigating how relationships between a system's parts can give rise to its collective behaviors and how the system interacts and forms relationships with its environment. In this view, the peculiar pharmacological behavior of biologically active natural compounds can be justified by the occurrence of molecular interactions due to the high complexity of the natural matrix. Some of these interactions have been widely studied in the case of green tea extracts (GTEs) proving unequivocally the presence of caffeine/catechin complexes in GTE samples. The presence of bimolecular complexes has been observed also in the case of Ceylon tea and Mate extracts. These data indicate that the formation of complexes in natural extracts is a common behavior and their presence must be considered in the description of natural extracts and, consequently, in their biological activity. ©2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Laura Moracci
- Nano-Inspired Biomedicine Lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, I35127, Padova, Italy
- Department of Surgical, Surgical Clinic, Oncological and Gastroenterological Sciences, University of Padova, I35122, Padova, Italy
| | - Pietro Traldi
- Nano-Inspired Biomedicine Lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, I35127, Padova, Italy
| | - Marco Agostini
- Nano-Inspired Biomedicine Lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, I35127, Padova, Italy
- Department of Surgical, Surgical Clinic, Oncological and Gastroenterological Sciences, University of Padova, I35122, Padova, Italy
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Alchoubassi G, Kińska K, Bierla K, Lobinski R, Szpunar J. Speciation of essential nutrient trace elements in coconut water. Food Chem 2020; 339:127680. [PMID: 32860999 DOI: 10.1016/j.foodchem.2020.127680] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022]
Abstract
Coconut water (Cocos Nucifera) is shown to be a source of essential elements present in the form of low-molecular weight stable complexes known for their bio-availability. The total element concentrations were in the range of 0.2-2.7, 0.3-1, 3-14 and 0.5-2 ppm for Fe, Cu, Mn, and Zn, respectively, and varied as a function of the origin of the nut and its maturity. Speciation was investigated by size-exclusion chromatography - inductively coupled plasma mass spectrometry (ICPMS), and hydrophilic interaction liquid chromatography (HILIC) - electrospray-OrbitrapMS. The metal species identified included: iron complexes with citrate and malate: FeIII(Cit)3(Mal), FeIII(Cit)2(Mal)2, FeIII(Mal)2, glutamine: FeIII(Glu)2 and nicotianamine: FeII(NA); copper complexes with phenylanine: CuII(Phe)2 and CuII(Phe)3 and nicotianamine: CuII(NA); zinc complexes with citrate: ZnII(Cit)2 and nicotianamine ZnII(NA) and manganese complex with asparagine MnII(Asp)2. The contributions of the individual species to the total elements concentrations could be estimated by HILIC - ICP MS.
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Affiliation(s)
- Ghaya Alchoubassi
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Hélioparc, 64053 Pau, France
| | - Katarzyna Kińska
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Hélioparc, 64053 Pau, France.
| | - Katarzyna Bierla
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Hélioparc, 64053 Pau, France.
| | - Ryszard Lobinski
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Hélioparc, 64053 Pau, France; IM Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia.
| | - Joanna Szpunar
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Hélioparc, 64053 Pau, France.
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8
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Abstract
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) to regulate gene expression. The heterodimer recognizes the genome via a large and diverse repertoire of DNA response elements. Assessing the binding mode of RAR and RXR with various DNA response elements is important for understanding how they select their binding site and how DNA sequence and topology allosterically regulate RAR function. A number of complementary assays are often employed for analysis of the binding mode. To biochemically and structurally characterize RAR and RXR-DNA complexes, we describe how to express and purify RAR and RXR-DNA binding domains (DBDs) and multidomain constructs. We also describe the use of electrospray ionization mass spectrometry (ESI MS) and isothermal titration calorimetry (ITC) that give information about stoichiometry and binding affinity, as well as our approaches for co-crystallization of RAR and RXR DBDs with DNA.
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Affiliation(s)
- Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France.
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9
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Roussis SG, Cedillo I, Rentel C. Automated determination of early eluting oligonucleotide impurities using ion-pair reversed-phase liquid chromatography high resolution-mass spectrometry. Anal Biochem 2020; 595:113623. [PMID: 32067983 DOI: 10.1016/j.ab.2020.113623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 10/25/2022]
Abstract
A new method is presented for the automated determination of early eluting (E.E.) oligonucleotide impurities analyzed by IP-RP HPLC HRMS. E.E. are impurities shorter than the main drug component and are primarily formed by the mechanisms of coupling failure, and depurination. The method is based on the detection of the theoretically derived most abundant mass of an impurity in the experimental data. An exhaustive list of candidate impurities and their formulas is automatically generated using the parent sequence and the known mechanisms of impurity formation. The approach accounts for possible modifications in the individual oligonucleotide sequence moieties (e.g., linkage, sugar, and base, 3', and 5' ends). The detected ion signal is summed to provide four nested levels of impurity breakdown information. The approach allows for the rapid determination of relationships and trends of impurities in samples generated by different manufacturing processes and conditions. Representative examples are given to illustrate the capabilities and utility of the approach in synthesis and purification process optimization applications.
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Kageyama Kaneshima A, Motoyama A, Takayama M. Influence of Solvent Composition and Surface Tension on the Signal Intensity of Amino Acids in Electrospray Ionization Mass Spectrometry. ACTA ACUST UNITED AC 2019; 8:A0077. [PMID: 32010543 PMCID: PMC6920628 DOI: 10.5702/massspectrometry.a0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/24/2019] [Indexed: 11/23/2022]
Abstract
The influence of solvent composition and surface tension on the signal intensity of deprotonated molecules [M−H]− in electrospray ionization mass spectrometry (ESI MS) was evaluated using alanine (Ala), threonine (Thr) and phenylalanine (Phe), which have differing levels of hydrophobicity. The surface tension of the ESI solution was varied by changing the ratio of the organic solvents methanol (MeOH) and acetonitrile (MeCN) in water (H2O). In ESI MS, the signal intensity of all the amino acids was increased with decreasing surface tension for the two solutions, H2O/MeOH and H2O/MeCN. The use of H2O/MeCN was more favorable for achieving a strong signal for the analytes compared to H2O/MeOH. The smaller vaporization enthalpy of MeCN compared to MeOH was proposed as one of the most plausible explanation for this. The order of the signal intensity of amino acids was Phe>Thr>Ala, the same order as their hydrophobicity. It can be practically concluded that the use of solutions with lower surface tensions and lower vaporization enthalpies would result in higher signal intensities in ESI MS.
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Affiliation(s)
- Ami Kageyama Kaneshima
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Akira Motoyama
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Mitsuo Takayama
- Mass Spectrometry Laboratory, Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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Roussis SG, Cedillo I, Rentel C. Semi-quantitative determination of co-eluting impurities in oligonucleotide drugs using ion-pair reversed-phase liquid chromatography mass spectrometry. J Chromatogr A 2018; 1584:106-114. [PMID: 30473112 DOI: 10.1016/j.chroma.2018.11.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/24/2018] [Accepted: 11/18/2018] [Indexed: 01/13/2023]
Abstract
Continued improvements in understanding RNA biology have led to significant success in the development of antisense oligonucleotide therapeutics, and several oligonucleotide drugs have now been approved. Manufacturing of oligonucleotides may be associated with the production of impurities. Current methods for quantification of impurities that co-elute with the main drug component rely on manual ion extraction and integration of the characteristic mass signal of each impurity. For certain applications however, especially those involving large sets of samples such as those generated in the optimization of oligonucleotide manufacturing processes, a rapid method that provides semi-quantitative determination of impurity levels would be sufficient. In this work, an automated approach has been developed to rapidly determine the relative amounts of co-eluting impurities in oligonucleotide samples. The most abundant mass in the isotopic distribution is automatically calculated from the impurity formula and used to detect the presence of the impurities. The principles of the approach are described, and representative examples are given. Impurities determined in different manufacturing lots are compared directly, and by principal component analysis. The ability of the method to determine impurity levels across large sample sets is illustrated for an oligonucleotide drug purification study.
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Affiliation(s)
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
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12
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De Freitas KCB. Resolving the Discrepancies Between Empirical and Rayleigh Charge Limiting Models for Globular Proteins. J Am Soc Mass Spectrom 2018; 29:2059-2066. [PMID: 30043359 DOI: 10.1007/s13361-018-2025-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/19/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
Starting with the Rayleigh charge limiting model, a slightly different approach is used to account for the well-known discrepancy that exists between the said model and experimental ESI MS data for globular proteins. It is shown using published datasets that for globular proteins, the mass density ρ exhibits a weak second-order dependence on its mass M, according to ρ(M)∝ M-α, α ~ 0.14. A direct equivalence established between ESI MS and x-ray techniques suggests a minimum but critical surface tension of 15.6 ± 5.2 mN/m for the droplet at the liquid-to-gas phase transition point. The packing density factor η for globular proteins is believed to lie between 1 (very tightly packed) and 4.6 (less tight, natively packed). While the Rayleigh charge limiting model has been linked historically to the CRM (J. Chem. Phys. 49:2240-2249, 1968; Anal. Chim. Acta 406:93-104, 2000), this paper does not expressly seek to justify the CRM, but rather uses empirical data and existing knowledge across subfields to help build a consistent picture of ESI MS phenomena that might be difficult to explain otherwise. These results would be useful in molecular dynamics (MD) simulations, understanding liquid-to-gas phase transitions and in opening up new routes for cross-calibration between ESI MS, IM MS, NMR and x-ray crystallography studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Karen C B De Freitas
- Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.
- The Doctors Laboratory, The Halo Building, 1 Mabledon Place, London, WC1H 9AX, UK.
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13
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Roussis SG, Cedillo I, Rentel C. Two-dimensional liquid chromatography-mass spectrometry for the characterization of modified oligonucleotide impurities. Anal Biochem 2018; 556:45-52. [PMID: 29936097 DOI: 10.1016/j.ab.2018.06.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
A 2D-LC system coupled with a TOF mass spectrometer has been evaluated for its capabilities to provide enhanced characterization of oligonucleotide impurities. To address loop limitations in the total volume (40 μL) sampled across 1D peaks, a column trap was incorporated between the 1D and 2D columns. The main advantages of the column trap include reduction of the total number of sequential 2D runs required to fully sample broad 1D peaks, and most importantly, reduction of the error in quantitative determination of the components in broad 1D peaks by avoiding the numerical stitching of data from several 2D runs. Comprehensive RP x IP provided orthogonal separation despite its lower 1D resolution. In contrast, IP x IP did not provide orthogonal separation. RP x IP using the direct on-line extended heart-cutting system with the column trap showed additional benefits, in the elimination of off-line fractionation and sample handling errors and was successfully applied in a pH stability study of a crude oligonucleotide. SAX x IP successfully separated the isobaric "n+16" doublet of the "n + O" and "[n + S-O]" impurity species, a feat not currently possible by mass spectrometry alone or 1D-LC, demonstrating the importance of the added capabilities of the 2D-LC approach.
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Abstract
Conserved across vertebrates, the habenular nuclei are a pair of small symmetrical structures in the epithalamus. The nuclei functionally link the forebrain and midbrain by receiving input from and projecting to several brain regions. Each habenular nucleus comprises two major asymmetrical subnuclei, the medial and lateral habenula. These subnuclei are associated with different physiological processes and disorders, such as depression, nicotine addiction, and encoding aversive stimuli or omitting expected rewarding stimuli. Elucidating the functions of the habenular nuclei at the molecular level requires knowledge of their neuropeptide complement. In this work, three mass spectrometry (MS) techniques-liquid chromatography (LC) coupled to Orbitrap tandem MS (MS/MS), LC coupled to Fourier transform (FT)-ion cyclotron resonance (ICR) MS/MS, and matrix-assisted laser desorption/ionization (MALDI) FT-ICR MS-were used to uncover the neuropeptide profiles of the rodent medial and lateral habenula. With the assistance of tissue stabilization and bioinformatics, a total of 262 and 177 neuropeptides produced from 27 and 20 prohormones were detected and identified from the medial and lateral habenula regions, respectively. Among these neuropeptides, 136 were exclusively found in the medial habenula, and 51 were exclusively expressed in the lateral habenula. Additionally, novel sites of sulfation, a rare post-translational modification, on the secretogranin I prohormone are identified. The results demonstrate that these two small brain nuclei have a rich and differentiated peptide repertoire, with this information enabling a range of follow-up studies.
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Affiliation(s)
- Ning Yang
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Pingli Wei
- Chemistry Department , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Qing Yu
- School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Lingjun Li
- Chemistry Department , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,School of Pharmacy , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Paul J Kenny
- Department of Pharmacology & Systems Therapeutics , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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15
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Giesen JA, Diament BJ, Grayson SM. Iodine-Containing Mass-Defect-Tuned Dendrimers for Use as Internal Mass Spectrometry Calibrants. J Am Soc Mass Spectrom 2018; 29:490-500. [PMID: 29260455 DOI: 10.1007/s13361-017-1849-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 10/18/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
Calibrants based on synthetic dendrimers have been recently proposed as a versatile alternative to peptides and proteins for both MALDI and ESI mass spectrometry calibration. Because of their modular synthetic platform, dendrimer calibrants are particularly amenable to tailoring for specific applications. Utilizing this versatility, a set of dendrimers has been designed as an internal calibrant with a tailored mass defect to differentiate them from the majority of natural peptide analytes. This was achieved by incorporating a tris-iodinated aromatic core as an initiator for the dendrimer synthesis, thereby affording multiple calibration points (m/z range 600-2300) with an optimized mass-defect offset relative to all peptides composed of the 20 most common proteinogenic amino acids. Graphical abstract ᅟ.
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Affiliation(s)
- Joseph A Giesen
- Department of Chemistry, 2015 Stern Hall, Tulane University, New Orleans, LA, 70118-5636, USA
| | - Benjamin J Diament
- Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA, 98195-2350, USA
| | - Scott M Grayson
- Department of Chemistry, 2015 Stern Hall, Tulane University, New Orleans, LA, 70118-5636, USA.
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16
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Marzo T, Navas F, Cirri D, Merlino A, Ferraro G, Messori L, Quiroga AG. Reactions of a tetranuclear Pt-thiosemicarbazone complex with model proteins. J Inorg Biochem 2018; 181:11-17. [PMID: 29353085 DOI: 10.1016/j.jinorgbio.2018.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/30/2017] [Accepted: 01/07/2018] [Indexed: 01/21/2023]
Abstract
The tetranuclear Pt complex (PtL)4 (where L2- is the anion derived from para-isopropyl thiosemicarbazone) was first described in A.G. Quiroga et al., J. Med. Chem. 41, 1998, 1399-1408. (PtL)4 manifests antiproliferative properties toward various cancer cell lines being a promising anticancer drug candidate. Yet, details of its reactivity with biomolecules have not been elucidated. To this end, we investigated the reactions of (PtL)4 with a few model proteins, i.e. bovine pancreatic ribonuclease (RNase A), cytochrome c (Cyt c) and hen egg white lysozyme (Lysozyme), through electrospray ionization mass spectrometry and other biophysical methods. A rich reactivity of (PtL)4 with the above-mentioned model proteins is observed, leading to the formation of numerous metallodrug-protein adducts. The tetranuclear complex breaks down and various fragments bind proteins up to high metal/protein ratios; this typically results into very complicated mass spectral patterns. However, some of the main mass peaks could be assigned in the case of the Lysozyme adduct. In addition, crystallographic data were obtained for the (PtL)4/Lysozyme and (PtL)4/RNase A adducts pointing at His side chains as the primary binding sites for monometallic Pt fragments. Notably, a few selected features of the interactions observed in the (PtL)4/protein adducts were reproduced by reacting (PtL)4 with a small molecule, i.e. N-methylimidazole. In conclusion, the present study confirms the prodrug nature of the tetraplatinum complex, clarifies one possible pathway for its activation through cluster disassembly and allows initial identification of adducts formed with a representative protein.
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Affiliation(s)
- Tiziano Marzo
- Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi, 13, 56124 Pisa, Italy; Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Francisco Navas
- IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain
| | - Damiano Cirri
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy
| | - Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Adoracion G Quiroga
- IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain.
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17
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Abstract
This chapter describes protocols for mass spectrometry (MS) applied to the characterization of ganglioside structures and the determination of ganglioside contents. Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) are often used to ionize biological materials and this chapter covers three protocols for atmospheric pressure MALDI MS (AP-MALDI MS), liquid chromatography-ESI MS (LC-ESI MS), and LC-ESI MS with multiple reaction monitoring (MRM). Purified gangliosides were used in AP-MALDI MS analyses while crude preparations of gangliosides were subjected to LC-ESI MS and LC-ESI MS with MRM. The LC protocol includes conditions for both reversed-phase and normal-phase column chromatography.
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Affiliation(s)
- Akemi Suzuki
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan.
| | - Minoru Suzuki
- School of Integrative and Global Majors, Tsukuba University, Tsukuba, Ibaraki, Japan
| | - Emi Ito
- Brain Research Center, RIKEN, Wakō, Saitama, Japan
| | - Takahiro Nitta
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Jin-Ichi Inokuchi
- Division of Glycopathology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
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18
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Jankowski W, Kurek J, Barczyński P, Hoffmann M. Quantum-chemical, NMR, FT IR, and ESI MS studies of complexes of colchicine with Zn(II). J Mol Model 2017; 23:127. [PMID: 28321655 PMCID: PMC5393104 DOI: 10.1007/s00894-017-3306-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/06/2017] [Indexed: 11/16/2022]
Abstract
Colchicine is a tropolone alkaloid from Colchicinum autumnale. It shows antifibrotic, antimitotic, and anti-inflammatory activities, and is used to treat gout and Mediterranean fever. In this work, complexes of colchicine with zinc(II) nitrate were synthesized and investigated using DFT, 1H and 13C NMR, FT IR, and ESI MS. The counterpoise-corrected and uncorrected interaction energies of these complexes were calculated. We also calculated their 1H, 13C NMR, and IR spectra and compared them with the corresponding experimentally obtained data. According to the ESI MS mass spectra, colchicine forms stable complexes with zinc(II) nitrate that have various stoichiometries: 2:1, 1:1:1, and 2:1:1 with respect to colchichine, Zn(II), and nitrate ion. All of the complexes were investigated using the quantum theory of atoms in molecules (QTAIM). The calculated and the measured spectra showed differences before and after the complexation process. Calculated electron densities and bond critical points indicated the presence of bonds between the ligands and the central cation in the investigated complexes that satisfied the quantum theory of atoms in molecules. DFT, NMR, FT IR, ESI MS, QTAIM and puckering studies of complexes of colchicine with Zn(II). ![]()
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Affiliation(s)
- Wojciech Jankowski
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, ul. Umultowska 89b, 61-614, Poznań, Poland.
| | - Joanna Kurek
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, ul. Umultowska 89b, 61-614, Poznań, Poland
| | - Piotr Barczyński
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, ul. Umultowska 89b, 61-614, Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, ul. Umultowska 89b, 61-614, Poznań, Poland
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19
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Vater J, Herfort S, Doellinger J, Weydmann M, Dietel K, Faetke S, Lasch P. Fusaricidins from Paenibacillus polymyxa M-1, a family of lipohexapeptides of unusual complexity-a mass spectrometric study. J Mass Spectrom 2017; 52:7-15. [PMID: 27714901 DOI: 10.1002/jms.3891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Paenibacillus polymyxa are rhizobacteria with a high potential to produce natural compounds of biotechnological and medical interest. Main products of P. polymyxa are fusaricidins, a large family of antifungal lipopeptides with a 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid side chain. We use the P. polymyxa strain M-1 as a model organism for the exploration of the biosynthetic potential of these rhizobacteria. Using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) about 40 new fusaricidins were detected which were fractionated by reversed-phase (rp) HPLC. Their structure was determined by MALDI-LIFT-TOF/TOF fragment analysis. The dominant fragment in the product ion spectra of fusaricidins appeared at m/z 256.3, 284.3 and 312.4, respectively, indicating variations in their fatty acid part. Two new subfamilies of fusaricidins were introduced which contain guanidino-3-hydroxyhepta- and nonadecanoic acid as fatty acid constituents. Apparently, the end-standing guanidine group is not modified as shown by direct infusion nano-electrospray ionization mass spectrometry (nano-ESI MS). The results of this study suggest that advanced mass spectrometry is the method of choice for investigating natural compounds of unusual diversity, like fusaricidins. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Joachim Vater
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Stefanie Herfort
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Joerg Doellinger
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Max Weydmann
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Kristin Dietel
- Abitep GmbH Berlin, Glienicker Weg 185, 12489, Berlin, Germany
| | | | - Peter Lasch
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
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20
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Sarkar S, Chakraborty I, Panwar MK, Pradeep T. Isolation and Tandem Mass Spectrometric Identification of a Stable Monolayer Protected Silver-Palladium Alloy Cluster. J Phys Chem Lett 2014; 5:3757-3762. [PMID: 26278746 DOI: 10.1021/jz5019509] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A selenolate-protected Ag-Pd alloy cluster was synthesized using a one-pot solution-phase route. The crude product upon chromatographic analyses under optimized conditions gave three distinct clusters with unique optical features. One of these exhibits a molecular peak centered at m/z 2839, in its negative ion mass spectrum assigned to Ag5Pd4(SePh)12(-), having an exact match with the corresponding calculated spectrum. Tandem mass spectrometry of the molecular ion peak up to MS(9) was performed. Complex isotope distributions in each of the mass peaks confirmed the alloy composition. We find the Ag3Pd3(-) core to be highly stable. The composition was further supported by scanning electron microscopy, energy-dispersive spectroscopy, and X-ray photoelectron spectroscopy.
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Affiliation(s)
- Sreya Sarkar
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Indranath Chakraborty
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Manoj Kumar Panwar
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | - T Pradeep
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
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21
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Chechetkin IR, Blufard AS, Khairutdinov BI, Mukhitova FK, Gorina SS, Yarin AY, Antsygina LL, Grechkin AN. Isolation and structure elucidation of linolipins C and D, complex oxylipins from flax leaves. Phytochemistry 2013; 96:110-6. [PMID: 24042063 DOI: 10.1016/j.phytochem.2013.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/05/2013] [Accepted: 08/17/2013] [Indexed: 05/08/2023]
Abstract
Two complex oxylipins (linolipins C and D) were isolated from the leaves of flax plants inoculated with phytopathogenic bacteria Pectobacterium atrosepticum. Their structures were elucidated based on UV, MS and NMR spectroscopic data. Both oxylipins were identified as digalactosyldiacylglycerol (DGDG) molecular species. Linolipin C contains one residue of divinyl ether (ω5Z)-etherolenic acid and one α-linolenate residue at sn-1 and sn-2 positions, respectively. Linolipin D possesses two (ω5Z)-etherolenic acid residues at both sn-1 and sn-2 positions. The rapid formation (2-30min) of linolipins C and D alongside with linolipins A and B occurred in the flax leaves upon their damage by freezing-thawing.
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Key Words
- (13S)-HPOT
- (13S)-hydroperoxy-MGDG
- (9Z,11E,13S,15Z)-13-hydroperoxy-9,11,15-octadecatrienoic acid
- 1,2-Di-O-[(9Z,11E,13S,15Z)-13-hydroperoxy-9,11,15-octadecatrienoyl]-3-O-β-d-galactopyranosyl-sn-glycerol
- DES
- Divinyl ether synthase
- ESI MS
- Etherolenic acid
- Flax
- Galactolipid
- LOX
- Linaceae
- Linum usitatissimum
- Oxylipin
- Pectobacterium atrosepticum
- SBOCFWSPOCJDHY-NXTVNIMXSA-N
- SSSOQCOUWWCQSF-MNNDCQRZSA-N
- divinyl ether synthase
- electrospray ionization mass spectrometry
- lipoxygenase
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Affiliation(s)
- Ivan R Chechetkin
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, P.O. Box 30, 420111 Kazan, Russia.
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22
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Chakraborty I, Kurashige W, Kanehira K, Gell L, Häkkinen H, Negishi Y, Pradeep T. Ag44(SeR)30: A Hollow Cage Silver Cluster with Selenolate Protection. J Phys Chem Lett 2013; 4:3351-3355. [PMID: 26706648 DOI: 10.1021/jz401879c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Selenolate protected, stable and atomically precise, hollow silver cluster was synthesized using solid state as well as solution state routes. The optical absorption spectrum shows multiple and sharp features similar to the thiolated Ag44 cluster, Ag44(SR)30 whose experimental structure was reported recently. High-resolution electrospray ionization mass spectrometry (HRESI MS) shows well-defined molecular ion features with two, three, and four ions with isotopic resolution, due to Ag44(SePh)30. Additional characterization with diverse tools confirmed the composition. The closed-shell 18 electron superatom electronic structure, analogous to Ag44(SR)30 stabilizes the dodecahedral cage with a large HOMO-LUMO gap of 0.71 eV. The time-dependent density functional theory (TDDFT) prediction of the optical absorption spectrum, assuming the Ag44(SR)30 structure, matches the experimental data, confirming the structure.
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Affiliation(s)
- Indranath Chakraborty
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Wataru Kurashige
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science , 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Keita Kanehira
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science , 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Lars Gell
- Departments of Chemistry and Physics, Nanoscience Center, University of Jyväskylä , Box 35, FI-40014 Jyväskylä, Finland
| | - Hannu Häkkinen
- Departments of Chemistry and Physics, Nanoscience Center, University of Jyväskylä , Box 35, FI-40014 Jyväskylä, Finland
| | - Yuichi Negishi
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science , 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Thalappil Pradeep
- DST Unit of Nanoscience (DST UNS) and Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
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23
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Alleti R, Vagner J, Dehigaspitiya DC, Moberg VE, Elshan NGRD, Tafreshi NK, Brabez N, Weber CS, Lynch RM, Hruby VJ, Gillies RJ, Morse DL, Mash EA. Synthesis and characterization of time-resolved fluorescence probes for evaluation of competitive binding to melanocortin receptors. Bioorg Med Chem 2013; 21:5029-38. [PMID: 23890524 DOI: 10.1016/j.bmc.2013.06.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/14/2013] [Accepted: 06/22/2013] [Indexed: 11/28/2022]
Abstract
Probes for use in time-resolved fluorescence competitive binding assays at melanocortin receptors based on the parental ligands MSH(4), MSH(7), and NDP-α-MSH were prepared by solid phase synthesis methods, purified, and characterized. The saturation binding of these probes was studied using HEK-293 cells engineered to overexpress the human melanocortin 4 receptor (hMC4R) as well as the human cholecystokinin 2 receptor (hCCK2R). The ratios of non-specific binding to total binding approached unity at high concentrations for each probe. At low probe concentrations, receptor-mediated binding and uptake was discernable, and so probe concentrations were kept as low as possible in determining Kd values. The Eu-DTPA-PEGO-MSH(4) probe exhibited low specific binding relative to non-specific binding, even at low nanomolar concentrations, and was deemed unsuitable for use in competition binding assays. The Eu-DTPA-PEGO probes based on MSH(7) and NDP-α-MSH exhibited Kd values of 27±3.9nM and 4.2±0.48nM, respectively, for binding with hMC4R. These probes were employed in competitive binding assays to characterize the interactions of hMC4R with monovalent and divalent MSH(4), MSH(7), and NDP-α-MSH constructs derived from squalene. Results from assays with both probes reflected only statistical enhancements, suggesting improper ligand spacing on the squalene scaffold for the divalent constructs. The Ki values from competitive binding assays that employed the MSH(7)-based probe were generally lower than the Ki values obtained when the probe based on NDP-α-MSH was employed, which is consistent with the greater potency of the latter probe. The probe based on MSH(7) was also competed with monovalent, divalent, and trivalent MSH(4) constructs that previously demonstrated multivalent binding in competitive binding assays against a variant of the probe based on NDP-α-MSH. Results from these assays confirm multivalent binding, but suggest a more modest increase in avidity for these MSH(4) constructs than was previously reported.
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Key Words
- 1-(9H-fluoren-9-yl)-3,19-dioxo-2,8,11,14,21-pentaoxa-4,18-diazatricosan-23-oic acid
- 1-hydroxybenzotriazole
- 19-amino-5-oxo-3,10,13,16-tetraoxa-6-azanonadecan-1-oic acid
- 6-chloro-1-hydroxybenzotriazole
- 9-fluorenylmethyoxycarbonyl
- Ac-Ser-Tyr-Ser-Nle-Glu-His-DPhe-Arg-Trp-Gly-Lys-Pro-Val-NH(2)
- BSA
- Cl-HOBt
- Competition binding assays
- CuAAC
- DCM
- DIC
- DIEA
- DMEM
- DMF
- DMSO
- DTPA
- Dulbecco’s Modified Eagle Medium
- ESI MS
- FT-ICR MS
- Fluorescent probes
- Fmoc
- Fmoc-PEGO
- Fourier transform ion cyclotron resonance mass spectrometry
- HOBt
- HRMS
- His-DPhe-Arg-Trp
- IC(50)
- MEM
- MSH(4)
- MSH(7)
- Melanocortin 4 receptor
- Minimum Essential Medium
- N,N-dimethylformamide
- NDP-α-MSH
- PEGO
- Saturation binding assays
- Ser-Nle-Glu-His-DPhe-Arg-Trp
- TBTA
- TEAA
- TFA
- THF
- TLC
- TRF
- Time-resolved fluorescence
- bovine serum albumin
- copper(I)-catalyzed azide-alkyne cycloaddition
- dichloromethane
- diethylenetriaminepentaacetic acid
- diisopropyl carbodiimide
- diisopropylethylamine
- dimethyl sulfoxide
- electrospray ionization mass spectrometry
- hMC4R
- half maximal inhibitory concentration
- high resolution mass spectroscopy
- human melanocortin 4 receptor
- tetrahydrofuran
- thin-layer chromatography
- time-resolved fluorescence
- triethylammonium acetate
- trifluoroacetic acid
- tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine
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Affiliation(s)
- Ramesh Alleti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0041, USA
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