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van Outersterp RE, Kooijman PC, Merx J, Engelke UFH, Omidikia N, Tonneijck MLH, Houthuijs KJ, Berden G, Peters TMA, Lefeber DJ, Willemsen MAAP, Mecinovic J, Jansen JJ, Coene KLM, Wevers RA, Boltje TJ, Oomens J, Martens J. Distinguishing Oligosaccharide Isomers Using Far-Infrared Ion Spectroscopy: Identification of Biomarkers for Inborn Errors of Metabolism. Anal Chem 2023. [PMID: 37341384 DOI: 10.1021/acs.analchem.3c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Distinguishing isomeric saccharides poses a major challenge for analytical workflows based on (liquid chromatography) mass spectrometry (LC-MS). In recent years, many studies have proposed infrared ion spectroscopy as a possible solution as the orthogonal, spectroscopic characterization of mass-selected ions can often distinguish isomeric species that remain unresolved using conventional MS. However, the high conformational flexibility and extensive hydrogen bonding in saccharides cause their room-temperature fingerprint infrared spectra to have broad features that often lack diagnostic value. Here, we show that room-temperature infrared spectra of ion-complexed saccharides recorded in the previously unexplored far-infrared wavelength range (300-1000 cm-1) provide well-resolved and highly diagnostic features. We show that this enables distinction of isomeric saccharides that differ either by their composition of monosaccharide units and/or the orientation of their glycosidic linkages. We demonstrate the utility of this approach from single monosaccharides up to isomeric tetrasaccharides differing only by the configuration of a single glycosidic linkage. Furthermore, through hyphenation with hydrophilic interaction liquid chromatography, we identify oligosaccharide biomarkers in patient body fluid samples, demonstrating a generalized and highly sensitive MS-based method for the identification of saccharides found in complex sample matrices.
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Affiliation(s)
- Rianne E van Outersterp
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Pieter C Kooijman
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Jona Merx
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Nematollah Omidikia
- Department of Analytical Chemistry and Chemometrics, Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Mei-Lan H Tonneijck
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Kas J Houthuijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Tessa M A Peters
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Michel A A P Willemsen
- Amalia Children's Hospital, Department of Pediatric Neurology & Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Jasmin Mecinovic
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Jeroen J Jansen
- Department of Analytical Chemistry and Chemometrics, Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Chemistry and Hematology, Elisabeth-TweeSteden Hospital, 5042 AD Tilburg, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, 6525 ED Nijmegen, The Netherlands
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Jian J, Hammink R, Tinnemans P, Bickelhaupt FM, Poater J, Mecinovic J. Probing Polar-π Interactions Between Tetrazoles and Aromatic Rings. Chem Asian J 2023; 18:e202300192. [PMID: 37015878 DOI: 10.1002/asia.202300192] [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: 03/05/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/06/2023]
Abstract
The heterocyclic tetrazole, a well-established bioisosteric replacement of carboxylic acid, plays an important role in medicinal chemistry. To deepen the functional understanding of tetrazoles in chemical sciences, it is essential to investigate the noncovalent interactions between the tetrazole ring and aromatic rings. Here, we report synthetic, spectroscopic, structural and quantum chemical analyses on specially designed 2-arylphenyl-1H-tetrazoles to study the underlying noncovalent interactions between the tetrazole ring and the neighboring aromatic ring possessing substituents at para/meta position. pKa values and proton affinities of 2-arylphenyl-1H-tetrazoles correlate well with Hammett sigma values of para-substituents at the flanking aromatic ring. Molecular orbital and energy decomposition analyses revealed that through-space NH-π interactions and π-π interactions contribute to the trend of pKa values and proton affinities of 2-arylphenyl-1Htetrazoles. The electrostatic interaction between tetrazole/tetrazolide interacting with the aromatic rings appears responsible for the observed acidity trends. These results will be helpful for the rational design of tetrazole-based drugs and materials.
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Affiliation(s)
- Jie Jian
- University of Southern Denmark: Syddansk Universitet, Department of Physics, Chemistry and Pharmacy, DENMARK
| | - Roel Hammink
- University Medical Center Nijmegen: Radboudumc, Department of Medical BioSciences, NETHERLANDS
| | - Paul Tinnemans
- Radboud University: Radboud Universiteit, Institute for Molecules and Materials, NETHERLANDS
| | - F Matthias Bickelhaupt
- VU Amsterdam: Vrije Universiteit Amsterdam, Department of Theoretical Chemistry, NETHERLANDS
| | - Jordi Poater
- Universidad de Barcelona: Universitat de Barcelona, Departament de Quimica Inorganica i Organica, SPAIN
| | - Jasmin Mecinovic
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230, Odense, DENMARK
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Jian J, Hammink R, McKenzie CJ, Bickelhaupt FM, Poater J, Mecinovic J. Probing the Lewis Acidity of Boronic Acids through Interactions with Arene Substituents. Chemistry 2021; 28:e202104044. [PMID: 34958482 PMCID: PMC9306523 DOI: 10.1002/chem.202104044] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/23/2022]
Abstract
Boronic acids are Lewis acids that exist in equilibrium with boronate forms in aqueous solution. Here we experimentally and computationally investigated the Lewis acidity of 2,6‐diarylphenylboronic acids; specially designed phenylboronic acids that possess two flanking aromatic rings with tunable aromatic character. Hammett analysis of 2,6‐diarylphenylboronic acids reveals that their Lewis acidity remains unchanged upon the introduction of EWG/EDG at the distant para position of the flanking aromatic rings. Structural and computational studies demonstrate that polar‐π interactions and solvation effects contribute to the stabilization of boronic acids and boronate forms by aromatic rings. Our physical‐organic chemistry work highlights that boronic acids and boronates can be stabilized by aromatic systems, leading to an important molecular knowledge for rational design and development of boronic acid‐based catalysts and inhibitors of biomedically important proteins.
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Affiliation(s)
- Jie Jian
- University of Southern Denmark: Syddansk Universitet, Department of Physics, Chemistry and Pharmacy, DENMARK
| | - Roel Hammink
- Radboud University Nijmegen: Radboud Universiteit, Radboud Institute for Molecular Life Sciences, NETHERLANDS
| | - Christine J McKenzie
- University of Southern Denmark: Syddansk Universitet, Department of Physics, Chemistry and Pharmacy, DENMARK
| | - F Matthias Bickelhaupt
- Free University: Vrije Universiteit Amsterdam, Department of Theoretical Chemistry, NETHERLANDS
| | - Jordi Poater
- University of Barcelona: Universitat de Barcelona, Departament de Quimica Inorganica & Organica, SPAIN
| | - Jasmin Mecinovic
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230, Odense, DENMARK
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Coleman ML, McDonough MA, Hewitson KS, Coles C, Mecinovic J, Edelmann M, Cook KM, Cockman ME, Lancaster DE, Kessler BM, Oldham NJ, Ratcliffe PJ, Schofield CJ. Asparaginyl Hydroxylation of the Notch Ankyrin Repeat Domain by Factor Inhibiting Hypoxia-inducible Factor. J Biol Chem 2007; 282:24027-38. [PMID: 17573339 DOI: 10.1074/jbc.m704102200] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The stability and activity of hypoxia-inducible factor (HIF) are regulated by the post-translational hydroxylation of specific prolyl and asparaginyl residues. We show that the HIF asparaginyl hydroxylase, factor inhibiting HIF (FIH), also catalyzes hydroxylation of highly conserved asparaginyl residues within ankyrin repeat (AR) domains (ARDs) of endogenous Notch receptors. AR hydroxylation decreases the extent of ARD binding to FIH while not affecting signaling through the canonical Notch pathway. ARD proteins were found to efficiently compete with HIF for FIH-dependent hydroxylation. Crystallographic analyses of the hydroxylated Notch ARD (2.35A) and of Notch peptides bound to FIH (2.4-2.6A) reveal the stereochemistry of hydroxylation on the AR and imply that significant conformational changes are required in the ARD fold in order to enable hydroxylation at the FIH active site. We propose that ARD proteins function as natural inhibitors of FIH and that the hydroxylation status of these proteins provides another oxygen-dependent interface that modulates HIF signaling.
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Affiliation(s)
- Mathew L Coleman
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, United Kingdom
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