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Jiang Y, Indrajith S, Perez Mellor AF, Bürgi T, Lecouvey M, Clavaguéra C, Bodo E, Houée-Levin C, Loire E, Berden G, Oomens J, Scuderi D. Final Products of One-Electron Oxidation of Cyclic Dipeptides Containing Methionine Investigated by IRMPD Spectroscopy: Does the Free Radical Choose the Final Compound? J Phys Chem B 2022; 126:10055-10068. [PMID: 36417492 DOI: 10.1021/acs.jpcb.2c06541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and the hydroxyl radical (•OH) have specific functions in biological processes, while their uncontrolled production and reactivity are known to be determining factors in pathophysiology. Methionine (Met) residues act as endogenous antioxidants, when they are oxidized into methionine sulfoxide (MetSO), thus depleting ROS and protecting the protein. We employed tandem mass spectrometry combined with IR multiple photon dissociation spectroscopy to study the oxidation induced by OH radicals produced by γ radiolysis on model cyclic dipeptides c(LMetLMet), c(LMetDMet), and c(GlyMet). Our aim was to characterize the geometries of the oxidized peptides in the gas phase and to understand the relationship between the structure of the 2-center 3-electron (2c-3e) free radical formed in the first step of the oxidation process and the final compound. Density functional theory calculations were performed to characterize the lowest energy structures of the final product of oxidation and to interpret the IR spectra. Collision-induced dissociation tandem mass spectrometry (CID-MS2) experiments of oxidized c(LMetLMet)H+ and c(LMetDMet)H+ led to the loss of one or two oxidized sulfenic acid molecules, indicating that the addition of one or two oxygen atoms occurs on the sulfur atom of both methionine side chains and no sulfone formation was observed. The CID-MS2 fragmentation mass spectrum of oxidized c(GlyMet)H+ showed only the loss of one oxidized sulfenic acid molecule. Thus, the final products of oxidation are the same regardless of the structure of the precursor sulfur-centered free radical.
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Affiliation(s)
- Yining Jiang
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Suvasthika Indrajith
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France.,Stockholm University, Roslagstullsbacken 21 C, plan 4, Albano, Fysikum, 106 91 Stockholm, Sweden
| | - Ariel Francis Perez Mellor
- Faculté des Sciences, Section de Chimie et Biologie, Département de Chimie Physique, Université de Genève, 30 Quai Ernest-Ansermet, CH-1211 Genève, Switzerland
| | - Thomas Bürgi
- Faculté des Sciences, Section de Chimie et Biologie, Département de Chimie Physique, Université de Genève, 30 Quai Ernest-Ansermet, CH-1211 Genève, Switzerland
| | - Marc Lecouvey
- Department of Chemistry, Université Sorbonne Paris Nord, CSPBAT, CNRS, UMR 7244, 1 rue de Chablis, F-93000 Bobigny, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Enrico Bodo
- Departement of Chemistry, Università di Roma La Sapienza, P. Aldo Moro 5, 00185 Rome, Italy
| | - Chantal Houée-Levin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Estelle Loire
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Debora Scuderi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
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Corinti D, Paciotti R, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations. J Inorg Biochem 2022; 237:112017. [PMID: 36209532 DOI: 10.1016/j.jinorgbio.2022.112017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl2(NH3)2, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH3)2(Cys)]+ and the intercepted cis-[PtCl(NH3)2(H2O)(Cys)]+ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH3)2(Cys)]+, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH3)2(H2O)(Cys)]+ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH3)2(H2O)]+ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH3)2(Cys)]+ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy.
| | - Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy.
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
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Ligation Motifs in Zinc-Bound Sulfonamide Drugs Assayed by IR Ion Spectroscopy. Molecules 2022; 27:molecules27103144. [PMID: 35630621 PMCID: PMC9146759 DOI: 10.3390/molecules27103144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/06/2023] Open
Abstract
The sulfonamide–zinc ion interaction, performing a key role in various biological contexts, is the focus of the present study, with the aim of elucidating ligation motifs in zinc complexes of sulfa drugs, namely sulfadiazine (SDZ) and sulfathiazole (STZ), in a perturbation-free environment. To this end, an approach is exploited based on mass spectrometry coupled with infrared multiple photon dissociation (IRMPD) spectroscopy backed by quantum chemical calculations. IR spectra of Zn(H2O+SDZ−H)+ and Zn(H2O+STZ−H)+ ions are consistent with a three-coordinate zinc complex, where ZnOH+ binds to the uncharged sulfonamide via N(heterocycle) and O(sulfonyl) donor atoms. Alternative prototropic isomers Zn(OH2)(SDZ−H)+ and Zn(OH2)(STZ−H)+ lie 63 and 26 kJ mol−1 higher in free energy, respectively, relative to the ground state Zn(OH)(SDZ)+ and Zn(OH)(STZ)+ species and do not contribute to any significant extent in the sampled population.
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Carlo MJ, Patrick AL. Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory. J Mass Spectrom Adv Clin Lab 2022; 23:14-25. [PMID: 34993503 PMCID: PMC8713122 DOI: 10.1016/j.jmsacl.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.
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Key Words
- 2-AEP, 2-aminoethylphosphonic acid
- 2P1EA, 2-phenyl-1-ethanolamine
- CIVP, cryogenic ion vibrational predissociation spectroscopy
- CLIO, Centre Laser Infrarouge d’Orsay
- DFT, density functional theory
- FA, fluoroamphetamine
- FEL, free electron laser
- FELIX, Free Electron Laser for Infrared eXperiments
- FMA, fluoromethamphetamine
- FTICR, Fourier transform ion cyclotron resonance
- GC–MS, gas chromatography-mass spectrometry
- GSNO, S- nitro glutathione
- GlcNAc, n-Acetylglucosamine
- IR, infrared
- IR2MS3, infrared-infrared double-resonance multi-stage mass spectrometry
- IRMPD, infrared multiple photon dissociation (IRMPD)
- IRMPD-MS, infrared multiple photon dissociation spectroscopy mass spectrometry
- IRPD, infrared predissociation spectroscopy
- IVR, intramolecular vibrational redistribution
- Infrared multiple photon dissociation spectroscopy
- LC, liquid chromatography
- LC-MS, liquid chromatography-mass spectrometry
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MDA, methylenedioxyamphetamine
- MDMA, methylenedioxymethamphetamine
- MMC, methylmethcathinone
- MS/MS, tandem mass spectrometry
- MSn, multi-stage mass spectrometry
- Mass spectrometry
- Metabolites
- NANT, N-acetyl-N-nitrosotryptophan
- OPO/A, optical parametric oscillator/amplifier
- PTM, post-translational modification
- Pharmaceuticals
- Post-translational modifications
- SNOCys, S-nitrosocysteine
- UV, ultraviolet
- UV-IR, ultraviolet-infrared
- Vibrational spectroscopy
- cw, continuous wave
- α-PVP, alpha-pyrrolidinovalerophenone
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Affiliation(s)
- Matthew J. Carlo
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Amanda L. Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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Chiavarino B, Sinha RK, Crestoni ME, Corinti D, Filippi A, Fraschetti C, Scuderi D, Maitre P, Fornarini S. Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay. Chemistry 2021; 27:2348-2360. [PMID: 33175428 DOI: 10.1002/chem.202003555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Indexed: 11/06/2022]
Abstract
The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]+ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]+ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Rajeev K Sinha
- Department of Atomic and Molecular Physics, Manipal University, Manipal, 576104, Karnataka, India
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Debora Scuderi
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Philippe Maitre
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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Corinti D, Chiavarino B, Scuderi D, Fraschetti C, Filippi A, Fornarini S, Crestoni ME. Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes. Int J Mol Sci 2021; 22:E692. [PMID: 33445631 PMCID: PMC7826572 DOI: 10.3390/ijms22020692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]-, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Debora Scuderi
- Institut de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France;
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
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7
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Acharya B, Kaushalya WKDN, Martens J, Berden G, Oomens J, Patrick AL. A Combined Infrared Ion Spectroscopy and Computational Chemistry Study of Hydroxyproline Isomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1205-1211. [PMID: 32383378 DOI: 10.1021/jasms.0c00061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydroxyproline is a common variation of proline, with diverse biological roles. The hydroxylation of proline gives rise to several (natural and/or synthetic) isomeric forms, including both positional isomers and stereoisomers. While mass spectrometry is widely touted as a very selective analytical technique, the identification of closely related isomers often poses a challenge. In these cases, allied technologies become helpful in providing full characterization. Here, infrared multiple photon dissociation (IRMPD) spectroscopy is used to differentiate between three isomers, namely cis-3-hydroxyproline, cis-4-hydroxyproline, and trans-4-hydroxyproline. In contrast to the protonated species which show only minor variations in their IRMPD spectra, lithiated species were found to display significant spectral differences, making their differentiation more straightforward. The conformational origin of these spectral differences was investigated by complementary quantum-chemical calculations.
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Affiliation(s)
- Baku Acharya
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States
| | - W K D N Kaushalya
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Amanda L Patrick
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States
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Corinti D, Crestoni ME, Fornarini S, Dabbish E, Sicilia E, Gabano E, Perin E, Osella D. A multi-methodological inquiry of the behavior of cisplatin-based Pt(IV) derivatives in the presence of bioreductants with a focus on the isolated encounter complexes. J Biol Inorg Chem 2020; 25:655-670. [PMID: 32296997 DOI: 10.1007/s00775-020-01789-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/31/2020] [Indexed: 01/14/2023]
Abstract
The study of Pt(IV) antitumor prodrugs able to circumvent some drawbacks of the conventional Pt(II) chemotherapeutics is the focus of a lot of attention. This paper reports a thorough study based on experimental methods (reduction kinetics, electrochemistry, tandem mass spectrometry and IR ion spectroscopy) and quantum-mechanical DFT calculations on the reduction mechanism of cisplatin-based Pt(IV) derivatives having two hydroxido (1), one hydroxido and one acetato (2), or two acetato ligands (3) in axial position. The biological reductants glutathione and ascorbic acid were taken into consideration. The presence of a hydroxido ligand resulted to play an important role in the chemical reduction with ascorbic acid, as verified by 15N-NMR kinetic analysis using 15N-enriched complexes. The reactivity trend (1 > 2 > 3) does not reflect the respective reduction peak potentials (1 < 2 < 3), an inverse relationship already documented in similar systems. Turning to a simplified environment, the Pt(IV) complexes associated with a single reductant molecule (corresponding to the encounter complex occurring along the reaction coordinate in bimolecular reactions in solution) were characterized by IR ion spectroscopy and sampled for their reactivity under collision-induced dissociation (CID) conditions. The complexes display a comparable reduction reactivity ordering as that observed in solution. DFT calculations of the free energy pathways for the observed fragmentation reactions provide theoretical support for the CID patterns and the mechanistic hypotheses on the reduction process are corroborated by the observed reaction paths. The bulk of these data offers a clue of the intricate pathways occurring in solution.Graphic abstract.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Rome, Italy.
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Rome, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, 00185, Rome, Italy
| | - Eslam Dabbish
- Department of Chemistry and Chemical Technologies, Università della Calabria, Ponte P. Bucci Cubo 14c, 87035, Arcavacata di Rende (CS), Italy.
| | - Emilia Sicilia
- Department of Chemistry and Chemical Technologies, Università della Calabria, Ponte P. Bucci Cubo 14c, 87035, Arcavacata di Rende (CS), Italy
| | - Elisabetta Gabano
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Elena Perin
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Domenico Osella
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121, Alessandria, Italy
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9
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Maitre P, Scuderi D, Corinti D, Chiavarino B, Crestoni ME, Fornarini S. Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications. Chem Rev 2019; 120:3261-3295. [PMID: 31809038 DOI: 10.1021/acs.chemrev.9b00395] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.
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Affiliation(s)
- Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), Université Paris-Sud, CNRS, Université Paris Saclay, 91405, Orsay, France
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", I-00185 Roma, Italy
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10
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Ben Nasr F, Alata I, Scuderi D, Lepère V, Brenner V, Jaïdane NE, Zehnacker A. Effects of complexation with sulfuric acid on the photodissociation of protonated Cinchona alkaloids in the gas phase. Phys Chem Chem Phys 2019; 21:15439-15451. [PMID: 31257399 DOI: 10.1039/c9cp01518c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.
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Affiliation(s)
- Feriel Ben Nasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA) Université de Tunis El Manar, LSAMA, Tunis 1060, Tunisia
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Debora Scuderi
- Univ. Paris-Sud, Laboratoire de Chimie Physique, UMR 8000, and CNRS, Orsay, F-91405, France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | | | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA) Université de Tunis El Manar, LSAMA, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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11
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Asakawa D, Takahashi H, Sekiya S, Iwamoto S, Tanaka K. Sequencing of Sulfopeptides Using Negative-Ion Tandem Mass Spectrometry with Hydrogen Attachment/Abstraction Dissociation. Anal Chem 2019; 91:10549-10556. [DOI: 10.1021/acs.analchem.9b01568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hidenori Takahashi
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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12
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Macaluso V, Scuderi D, Crestoni ME, Fornarini S, Corinti D, Dalloz E, Martinez-Nunez E, Hase WL, Spezia R. l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations. J Phys Chem A 2019; 123:3685-3696. [DOI: 10.1021/acs.jpca.9b01779] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
| | - Debora Scuderi
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Enzo Dalloz
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Emilio Martinez-Nunez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, 4, Place Jussieu, 75252 Paris Cedex 05, France
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13
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Michelini LJ, Vaz WF, D'Oliveira GDC, Pérez CN, Napolitano HB. Analysis of two novel 1-4 quinolinone structures with bromine and nitrobenzyl ligands. J Mol Model 2019; 25:55. [PMID: 30734868 DOI: 10.1007/s00894-019-3937-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 01/21/2019] [Indexed: 01/18/2023]
Abstract
The scientific community has shown particular interest in the study of quinolinones-a class of bicyclic organic compounds. An example of these compounds are the 4-quinolinones, considered to be very useful building blocks, since they can adapt their molecular structures with different ligands for applications in various fields such as pharmacy, medicine, physics and engineering. The compounds (E)-3-(benzylidene)-2-(3-nitrophenyl)-2,3-dihydro-1-(phenylsulfonyl)-quinolin-4-(1H)-one (NFQ) and (E)-3-(benzylidene)-2-(4-bromophenyl)-2,3-dihydro-1-(phenylsulfonyl) quinolin-4-(1H)-one (BFQ) were synthesized and characterized by infrared spectroscopy, 1H and 13C NMR, and melting point. NFQ crystallized in the orthorhombic Pbca space group while BFQ appears in the monoclinic P21/n space group. X-ray diffraction was used to evaluate their crystallographic structures, and Hirshfeld surface evaluates the intermolecular interactions, supramolecular arrangement and packaging. Theoretical vibrational assignments and calculated electronic properties also demonstrate acceptable agreement between experimental and theoretical results.
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Affiliation(s)
- Lidiane J Michelini
- Instituto de Química, Universidade Federal de Goiás, Goiânia, GO, Brazil.,Instituto Federal de Ciência, Educação e Tecnologia Goiano, Iporá, GO, Brazil
| | - Wesley F Vaz
- Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | | | - Caridad N Pérez
- Instituto de Química, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Hamilton B Napolitano
- Ciências Exatas e Tecnológicas, Universidade Estadual de Goiás, Anápolis, GO, Brazil.
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14
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Exploration of variations in proteome and metabolome for predictive diagnostics and personalized treatment algorithms: Innovative approach and examples for potential clinical application. J Proteomics 2018; 188:30-40. [DOI: 10.1016/j.jprot.2017.08.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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15
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Nieuwjaer N, Desfrançois C, Lecomte F, Manil B, Soorkia S, Broquier M, Grégoire G. Photodissociation Spectroscopy of Cold Protonated Synephrine: Surprising Differences between IR–UV Hole-Burning and IR Photodissociation Spectroscopy of the O–H and N–H Modes. J Phys Chem A 2018; 122:3798-3804. [DOI: 10.1021/acs.jpca.8b01422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Nieuwjaer
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - C. Desfrançois
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - F. Lecomte
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - B. Manil
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - S. Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de l’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - M. Broquier
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de l’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - G. Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de l’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
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16
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Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
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17
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Custodio JMF, Michelini LJ, de Castro MRC, Vaz WF, Neves BJ, Cravo PVL, Barreto FS, Filho MOM, Perez CN, Napolitano HB. Structural insights into a novel anticancer sulfonamide chalcone. NEW J CHEM 2018. [DOI: 10.1039/c7nj03523c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural products have stood out due to their wide range of biological activities.
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Affiliation(s)
- Jean M. F. Custodio
- Instituto de Química
- Universidade Federal de Goiás
- Goiânia
- Brazil
- Ciências Exatas e Tecnológicas
| | | | | | - Wesley F. Vaz
- Ciências Exatas e Tecnológicas
- Universidade Estadual de Goiás
- Anápolis
- Brazil
| | - Bruno J. Neves
- Programa de Pós-Graduação em Sociedade
- Tecnologia e Meio Ambiente
- Centro Universitário de Anápolis
- Anápolis
- Brazil
| | - Pedro V. L. Cravo
- Programa de Pós-Graduação em Sociedade
- Tecnologia e Meio Ambiente
- Centro Universitário de Anápolis
- Anápolis
- Brazil
| | | | | | | | - Hamilton B. Napolitano
- Ciências Exatas e Tecnológicas
- Universidade Estadual de Goiás
- Anápolis
- Brazil
- Programa de Pós-Graduação em Sociedade
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18
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Heiles S, Berden G, Oomens J, Williams ER. Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers. Phys Chem Chem Phys 2018; 20:15641-15652. [DOI: 10.1039/c8cp01458b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm−1 and theory.
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Affiliation(s)
- Sven Heiles
- Department of Chemistry
- University of California
- Berkeley
- USA
- Institute of Inorganic and Analytical Chemistry
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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19
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Borotto NB, McClory PJ, Martin BR, Håkansson K. Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry. Anal Chem 2017; 89:8304-8310. [PMID: 28708386 DOI: 10.1021/acs.analchem.7b01461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein S-sulfinylation (R-SO2-) and S-sulfonylation (R-SO3-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Phillip J McClory
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brent R Martin
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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20
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Chiavarino B, Crestoni ME, Fornarini S, Scuderi D, Salpin JY. Undervalued N3 Coordination Revealed in the Cisplatin Complex with 2'-Deoxyadenosine-5'-monophosphate by a Combined IRMPD and Theoretical Study. Inorg Chem 2017; 56:8793-8801. [PMID: 28718635 DOI: 10.1021/acs.inorgchem.7b00570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex obtained by the reaction of cisplatin and 2'-deoxyadenosine-5'-monophosphate (5'-dAMP) in water has been isolated and detected by electrospray ionization mass spectrometry. The so-formed cis-[PtCl(NH3)2(5'-dAMP)]+ complex has been studied in detail by infrared multiple photon dissociation (IRMPD) spectroscopy in two spectral ranges, namely, 700-1900 and 2800-3800 cm-1, backed by quantum-chemical calculations at the B3LYP/LACV3P/6-311G** level of theory. In agreement with the computational results, the vibrational spectroscopic characterization of cis-[PtCl(NH3)2(5'-dAMP)]+ shows that the sampled ionic population comprises two major isomers, differentiated in the X-H stretching region by their distinct fragmentation patterns. One of these species presents coordination of the platinum moiety at the N3 position of adenine, whereas in the second one, platinum is bound at the N1 position of adenine. IRMPD kinetics have allowed an estimation of their relative proportions. Surprisingly, the most abundant component of cis-[PtCl(NH3)2(5'-dAMP)]+ is the N3 isomer, although it is slightly less stable than the other potential isomers in the gas phase. In contrast, the lowest-energy species, namely, the one showing cisplatin binding to the N7 position of adenine, seems to be the one less represented in the sampled ionic population. These findings suggest that the reaction of cisplatin with 5'-dAMP is governed by the kinetics of the process occurring in solution rather than by the thermodynamic factors.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza" , Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Debora Scuderi
- LCP, Université Paris Sud Orsay, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Jean-Yves Salpin
- LAMBE, Université d'Evry Val d'Essonne, CEA, CNRS, Université Paris-Saclay , F-91025 Evry, France.,LAMBE, Université Cergy-Pontoise, Université Paris-Seine , F-91025 Evry, France
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21
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Schindler B, Barnes L, Gray CJ, Chambert S, Flitsch SL, Oomens J, Daniel R, Allouche AR, Compagnon I. IRMPD Spectroscopy Sheds New (Infrared) Light on the Sulfate Pattern of Carbohydrates. J Phys Chem A 2017; 121:2114-2120. [PMID: 28198185 DOI: 10.1021/acs.jpca.6b11642] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
IR spectroscopy of gas-phase ions is proposed to resolve positional isomers of sulfated carbohydrates. Mass spectrometric fingerprints and gas-phase vibrational spectra in the near and mid-IR regions were obtained for sulfated monosaccharides, yielding unambiguous signatures of sulfated isomers. We report the first systematic exploration of the biologically relevant but notoriously challenging deprotonated state in the near IR region. Remarkably, anions displayed very atypical vibrational profiles, which challenge the well-established DFT (Density Functionnal Theory) modeling. The proposed approach was used to elucidate the sulfate patterns in glycosaminoglycans, a ubiquitous class of mammalian carbohydrates, which is regarded as a major challenge in carbohydrate structural analysis. Isomeric glycosaminoglycan disaccharides from heparin and chondroitin sources were resolved, highlighting the potential of infrared multiple photon dissociation spectroscopy as a novel structural tool for carbohydrates.
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Affiliation(s)
- B Schindler
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France
| | - L Barnes
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France
| | - C J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - S Chambert
- Univ Lyon, INSA-Lyon, Université Lyon 1, CPE Lyon, ICBMS, UMR 5246 , Bâtiment Jules Verne, 20 avenue Albert Einstein, F-69621 Villeurbanne, France
| | - S L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, Nijmegen 6525ED, The Netherlands.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098XH, The Netherlands
| | - R Daniel
- CNRS, UMR 8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université Evry-Val-d'Essonne , Evry 91025, France
| | - A R Allouche
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France
| | - I Compagnon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 VILLEURBANNE, France.,Institut Universitaire de France IUF , 103 Boulevard St Michel, Paris 75005, France
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22
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Gregori B, Guidoni L, Crestoni ME, de Oliveira P, Houée-Levin C, Scuderi D. One-Electron Oxidation of Methionine-Containing Dipeptides of Reverse Sequence: Sulfur versus Sulfoxide Characterized by IRMPD Spectroscopy and Static and Dynamics DFT Simulations. J Phys Chem B 2017; 121:2083-2094. [DOI: 10.1021/acs.jpcb.6b12638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Leonardo Guidoni
- Dipartimento
di Scienza Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio 2, Coppito, L’Aquila I-64100, Italy
| | | | - Pedro de Oliveira
- Laboratoire
de Chimie Physique, Université Paris Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, Orsay Cedex 91405, France
| | - Chantal Houée-Levin
- Laboratoire
de Chimie Physique, Université Paris Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, Orsay Cedex 91405, France
| | - Debora Scuderi
- Laboratoire
de Chimie Physique, Université Paris Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, Orsay Cedex 91405, France
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23
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Corinti D, De Petris A, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Cisplatin Primary Complex with l-Histidine Target Revealed by IR Multiple Photon Dissociation (IRMPD) Spectroscopy. Chemphyschem 2016; 18:318-325. [PMID: 27935248 DOI: 10.1002/cphc.201601172] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/07/2016] [Indexed: 11/08/2022]
Abstract
The primary complex obtained from cisplatin and l-histidine in water has been detected and isolated by electrospray ionization. The so-obtained cis-[PtCl(NH3 )2 (histidine)]+ complex has been characterized in detail by high-resolution mass spectrometry (MS), tandem MS, IR multiple photon dissociation (IRMPD) spectroscopy, and by quantum chemical calculations. The structural features revealed by IRMPD spectroscopy indicate that platinum binds to the imidazole group, which presents tautomeric forms. Thus, depending on the position of the amino acid pendant on the imidazole ring, isomeric complexes are formed that are remarkably different with respect to the ease with which they undergo fragmentation when activated either by energetic collisions or by multiple IR photon absorption. It is shown here how IRMPD kinetics can allow their relative proportions to be estimated.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Alberto De Petris
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, 66100, Chieti, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio, Via dei Vestini 31, 66100, Chieti, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Maria E Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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24
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Jami-Alahmadi Y, Linford BD, Fridgen TD. Distinguishing Isomeric Peptides: The Unimolecular Reactivity and Structures of (LeuPro)M+ and (ProLeu)M+ (M = Alkali Metal). J Phys Chem B 2016; 120:13039-13046. [DOI: 10.1021/acs.jpcb.6b09588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yasaman Jami-Alahmadi
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| | - Bryan D. Linford
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University, St. John’s, Newfoundland A1N 4T8, Canada
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25
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Corinti D, Mannina L, Chiavarino B, Steinmetz V, Fornarini S, Crestoni ME. IRMPD signature of protonated pantothenic acid, an ubiquitous nutrient. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Barnes L, Schindler B, Allouche AR, Simon D, Chambert S, Oomens J, Compagnon I. Anharmonic simulations of the vibrational spectrum of sulfated compounds: application to the glycosaminoglycan fragment glucosamine 6-sulfate. Phys Chem Chem Phys 2015; 17:25705-13. [DOI: 10.1039/c5cp02079d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anharmonic behavior of sulfated glucosamine resolved by hybrid GVPT2 approach.
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Affiliation(s)
- Loïc Barnes
- Université de Lyon
- Lyon
- France
- Université Lyon 1
- Villeurbanne
| | | | | | - Daniel Simon
- Université de Lyon
- Lyon
- France
- Université Lyon 1
- Villeurbanne
| | | | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
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