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Abstract
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Fluorinated
carbohydrates have found many applications in the glycosciences.
Typically, these contain fluorination at a single position. There
are not many applications involving polyfluorinated carbohydrates,
here defined as monosaccharides in which more than one carbon has
at least one fluorine substituent directly attached to it, with the
notable exception of their use as mechanism-based inhibitors. The
increasing attention to carbohydrate physical properties, especially
around lipophilicity, has resulted in a surge of interest for this
class of compounds. This review covers the considerable body of work
toward the synthesis of polyfluorinated hexoses, pentoses, ketosugars,
and aminosugars including sialic acids and nucleosides. An overview
of the current state of the art of their glycosidation is also provided.
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Affiliation(s)
- Kler Huonnic
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, Krijgslaan 281-S4, Ghent, 9000, Belgium
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2
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Baranowski MR, Warminski M, Jemielity J, Kowalska J. 5'-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR. Nucleic Acids Res 2020; 48:8209-8224. [PMID: 32514551 PMCID: PMC7470941 DOI: 10.1093/nar/gkaa470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023] Open
Abstract
The high sensitivity of 19F nucleus to changes in the chemical environment has promoted the use of fluorine-labeled molecular probes to study structure and interactions of nucleic acids by 19F NMR. So far, most efforts have focused on incorporating the fluorine atom into nucleobase and ribose moieties using either monomer building blocks for solid-phase synthesis, or nucleoside triphosphates for enzymatic synthesis. Here, we report a simple and efficient synthesis of 5'-fluoromonophosphorylated and 5'-fluorodiphosphorylated oligodeoxyribonucleotides, which combines solid-phase and in-solution synthesis methods and requires only commercially available nucleoside phosphoramidites, followed by their evaluation as 19F NMR probes. We confirmed that the fluorine atom at the oligonucleotide 5' end did not alter the secondary structure of DNA fragments. Moreover, at the same time, it enabled real-time 19F NMR monitoring of various DNA-related biophysical processes, such as oligonucleotide hybridization (including mismatch identification), G-quadruplex folding/unfolding and its interactions with thrombin, as well as formation of an i-motif structure and its interaction with small-molecule ligands.
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Affiliation(s)
- Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
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3
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Vaugenot J, El Harras A, Tasseau O, Marchal R, Legentil L, Le Guennic B, Benvegnu T, Ferrières V. 6-Deoxy-6-fluoro galactofuranosides: regioselective glycosylation, unexpected reactivity, and anti-leishmanial activity. Org Biomol Chem 2020; 18:1462-1475. [PMID: 32025679 DOI: 10.1039/c9ob02596k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Selective glycosylation of the C-6 fluorinated galactofuranosyl acceptor 2 was studied with four galactofuranosyl donors. It was highlighted that this electron-withdrawing atom strongly impacted the behavior of the acceptor, thus leading to unprecedented glycosylation pathways. Competition between expected glycosylation of 2, ring expansion of this acceptor and furanosylation, and intermolecular aglycon transfer was observed. Further investigation of the fluorinated synthetic compounds showed that the presence of fluorine atom contributed to increase the inhibition of the growth of Leishmania tarentolae, a non-pathogenic strain of Leishmania.
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Affiliation(s)
- Jeane Vaugenot
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Abderrafek El Harras
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Olivier Tasseau
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Rémi Marchal
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Laurent Legentil
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Boris Le Guennic
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Thierry Benvegnu
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Vincent Ferrières
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
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4
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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5
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Guo F, Li Q, Zhou C. Synthesis and biological applications of fluoro-modified nucleic acids. Org Biomol Chem 2018; 15:9552-9565. [PMID: 29086791 DOI: 10.1039/c7ob02094e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Owing to the unique physical properties of a fluorine atom, incorporating fluoro-modifications into nucleic acids offers striking biophysical and biochemical features, and thus significantly extends the breadth and depth of biological applications of nucleic acids. In this review, fluoro-modified nucleic acids that have been synthesized through either solid phase synthesis or the enzymatic approach are briefly summarised, followed by a section describing their biomedical applications in nucleic acid-based therapeutics, 18F PET imaging and mechanistic studies of DNA modifying enzymes. In the last part, the utility of 19F NMR and MRI for probing the structure, dynamics and molecular interactions of fluorinated nucleic acids is reviewed.
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Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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6
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Vengut-Climent E, Peñalver P, Lucas R, Gómez-Pinto I, Aviñó A, Muro-Pastor AM, Galbis E, de Paz MV, Fonseca Guerra C, Bickelhaupt FM, Eritja R, González C, Morales JC. Glucose-nucleobase pairs within DNA: impact of hydrophobicity, alternative linking unit and DNA polymerase nucleotide insertion studies. Chem Sci 2018; 9:3544-3554. [PMID: 29780486 PMCID: PMC5934746 DOI: 10.1039/c7sc04850e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/04/2018] [Indexed: 11/21/2022] Open
Abstract
Glucose-nucleobase pairs were designed, synthesized and incorporated into duplex DNA. Their stability, structure and polymerase replication was investigated.
Recently, we studied glucose-nucleobase pairs, a binding motif found in aminoglycoside–RNA recognition. DNA duplexes with glucose as a nucleobase were able to hybridize and were selective for purines. They were less stable than natural DNA but still fit well on regular B-DNA. These results opened up the possible use of glucose as a non-aromatic DNA base mimic. Here, we have studied the incorporation and thermal stability of glucose with different types of anchoring units and alternative apolar sugar-nucleobase pairs. When we explored butanetriol instead of glycerol as a wider anchoring unit, we did not gain duplex thermal stability. This result confirmed the necessity of a more conformationally restricted linker to increase the overall duplex stability. Permethylated glucose-nucleobase pairs showed similar stability to glucoside-nucleobase pairs but no selectivity for a specific nucleobase, possibly due to the absence of hydrogen bonds between them. The three-dimensional structure of the duplex solved by NMR located both, the hydrophobic permethylated glucose and the nucleobase, inside the DNA helix as in the case of glucose-nucleobase pairs. Quantum chemical calculations on glucose-nucleobase pairs indicate that the attachment of the sugar to the DNA skeleton through the OH1 or OH4 positions yields the highest binding energies. Moreover, glucose was very selective for guanine when attached through OH1 or OH4 to the DNA. Finally, we examined DNA polymerase insertion of nucleotides in front of the saccharide unit. KF– polymerase from E. coli inserted A and G opposite glc and 6dglc with low efficiency but notable selectivity. It is even capable of extending the new pair although its efficiency depended on the DNA sequence. In contrast, Bst 2.0, SIII and BIOTAQ™ DNA polymerases seem to display a loop-out mechanism possibly due to the flexible glycerol linker used instead of deoxyribose.
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Affiliation(s)
- Empar Vengut-Climent
- Department of Biochemistry and Molecular Pharmacology , Instituto de Parasitología y Biomedicina López Neyra , CSIC , PTS Granada , Avda. del Conocimiento, 17, 18016 Armilla , Granada , Spain .
| | - Pablo Peñalver
- Department of Biochemistry and Molecular Pharmacology , Instituto de Parasitología y Biomedicina López Neyra , CSIC , PTS Granada , Avda. del Conocimiento, 17, 18016 Armilla , Granada , Spain .
| | - Ricardo Lucas
- Department of Biochemistry and Molecular Pharmacology , Instituto de Parasitología y Biomedicina López Neyra , CSIC , PTS Granada , Avda. del Conocimiento, 17, 18016 Armilla , Granada , Spain . .,Departamento de Química Orgánica y Farmacéutica , Facultad de Farmacia , Universidad de Sevilla , C/Prof. García González 2 , 41012-Sevilla , Spain
| | - Irene Gómez-Pinto
- Instituto de Química Física 'Rocasolano' , CSIC , C/. Serrano 119 , 28006 Madrid , Spain
| | - Anna Aviñó
- Instituto de Química Avanzada de Cataluña (IQAC) , CSIC , CIBER - BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis , CSIC - Universidad de Sevilla , Américo Vespucio 49 , 41092 , Sevilla , Spain
| | - Elsa Galbis
- Departamento de Química Orgánica y Farmacéutica , Facultad de Farmacia , Universidad de Sevilla , C/Prof. García González 2 , 41012-Sevilla , Spain
| | - M Violante de Paz
- Departamento de Química Orgánica y Farmacéutica , Facultad de Farmacia , Universidad de Sevilla , C/Prof. García González 2 , 41012-Sevilla , Spain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry , Amsterdam Center for Multiscale Modeling , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands.,Leiden Institute of Chemistry , Leiden University , PO Box 9502 , 2300 RA Leiden , The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry , Amsterdam Center for Multiscale Modeling , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands.,Institute of Molecules and Materials (IMM) , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Ramón Eritja
- Instituto de Química Avanzada de Cataluña (IQAC) , CSIC , CIBER - BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano' , CSIC , C/. Serrano 119 , 28006 Madrid , Spain
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology , Instituto de Parasitología y Biomedicina López Neyra , CSIC , PTS Granada , Avda. del Conocimiento, 17, 18016 Armilla , Granada , Spain .
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7
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Xu S, Feng L, Yuan J, Zhang ZG, Li Y, Peng H, Zou Y. Hexafluoroquinoxaline Based Polymer for Nonfullerene Solar Cells Reaching 9.4% Efficiency. ACS APPLIED MATERIALS & INTERFACES 2017; 9:18816-18825. [PMID: 28530392 DOI: 10.1021/acsami.7b03947] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Through introducing six fluorine atoms onto quinoxaline (Qx), a new electron acceptor unit-hexafluoroquinoxaline (HFQx) is first synthesized. On the basis of this unit, we synthesize a new donor-acceptor (D-A) copolymer (HFQx-T), which is composed of a benzodithiophene (BDT) derivative donor block and an HFQx accepting block. The strong electron-withdrawing properties of fluorine atoms increase significantly the open-circuit voltage (Voc) by tuning the highest occupied molecular orbital (HOMO) energy level. In addition, fluorine atoms enhance the absorption coefficient of the conjugated copolymer and change the film morphology, which implies an increase of the short-circuit current density (Jsc) and fill factor (FF). Indeed, the HFQx-T:ITIC blended film achieves an impressive power conversion efficiency (PCE) of 9.4% with large short-current density (Jsc) of 15.60 mA/cm2, high Voc of 0.92 V, and FF of 65% via two step annealing (thermal annealing (TA) and solvent vapor annealing (SVA) treatments). The excellent results obtained show that the new copolymer HFQx-T synthesized could be a promising candidate for organic photovoltaics.
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Affiliation(s)
- Shutao Xu
- College of Chemistry and Chemical Engineering, Central South University , Changsha 410083, China
| | - Liuliu Feng
- College of Chemistry and Chemical Engineering, Central South University , Changsha 410083, China
| | - Jun Yuan
- College of Chemistry and Chemical Engineering, Central South University , Changsha 410083, China
| | - Zhi-Guo Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Yongfang Li
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Hongjian Peng
- College of Chemistry and Chemical Engineering, Central South University , Changsha 410083, China
| | - Yingping Zou
- College of Chemistry and Chemical Engineering, Central South University , Changsha 410083, China
- State Key Laboratory for Powder Metallurgy, Central South University , Changsha 410083, China
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8
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Street STG, Chin DN, Hollingworth GJ, Berry M, Morales JC, Galan MC. Divalent Naphthalene Diimide Ligands Display High Selectivity for the Human Telomeric G-quadruplex in K + Buffer. Chemistry 2017; 23:6953-6958. [PMID: 28257554 PMCID: PMC5485019 DOI: 10.1002/chem.201700140] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 01/09/2023]
Abstract
Selective G‐quadruplex ligands offer great promise for the development of anti‐cancer therapies. A novel series of divalent cationic naphthalene diimide ligands that selectively bind to the hybrid form of the human telomeric G‐quadruplex in K+ buffer are described herein. We demonstrate that an imidazolium‐bearing mannoside‐conjugate is the most selective ligand to date for this quadruplex against several other quadruplex and duplex structures. We also show that a similarly selective methylpiperazine‐bearing ligand was more toxic to HeLa cancer cells than doxorubicin, whilst exhibiting three times less toxicity towards fetal lung fibroblasts WI‐38.
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Affiliation(s)
- Steven T G Street
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Donovan N Chin
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts, 02139, USA
| | | | - Monica Berry
- School of Physics, University of Bristol, HH Wills Physics Laboratory, Bristol, BS8 1TL, UK
| | - Juan C Morales
- Instituto de Parasitología y Biomedicina, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - M Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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9
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Oh J, Kranthiraja K, Lee C, Gunasekar K, Kim S, Ma B, Kim BJ, Jin SH. Side-Chain Fluorination: An Effective Approach to Achieving High-Performance All-Polymer Solar Cells with Efficiency Exceeding 7. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:10016-10023. [PMID: 27717212 DOI: 10.1002/adma.201602298] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/08/2016] [Indexed: 06/06/2023]
Abstract
Side-chain fluorination of polymers is demonstrated as a highly effective strategy to improve the efficiency of all-polymer solar cells from 2.93% (nonfluorinated P1) to 7.13% (fluorinated P2). This significant enhancement is achieved by synergistic improvements in open-circuit voltage, charge generation, and charge transport, as fluorination of the donor polymer optimizes the band alignment and the film morphology.
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Affiliation(s)
- Jiho Oh
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Kakaraparthi Kranthiraja
- Department of Chemistry Education, Graduate Department of Chemical Materials, Institute for Plastic Information and Energy Materials, Pusan National University, Busan, 609-735, Republic of Korea
| | - Changyeon Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Kumarasamy Gunasekar
- Department of Chemistry Education, Graduate Department of Chemical Materials, Institute for Plastic Information and Energy Materials, Pusan National University, Busan, 609-735, Republic of Korea
| | - Seonha Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Biwu Ma
- Department of Chemical and Biomedical Engineering, Florida State University, Tallahassee, FL, 32310, USA
| | - Bumjoon J Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Sung-Ho Jin
- Department of Chemistry Education, Graduate Department of Chemical Materials, Institute for Plastic Information and Energy Materials, Pusan National University, Busan, 609-735, Republic of Korea
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10
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Vengut-Climent E, Gómez-Pinto I, Lucas R, Peñalver P, Aviñó A, Fonseca Guerra C, Bickelhaupt FM, Eritja R, González C, Morales JC. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Empar Vengut-Climent
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
| | | | - Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Pablo Peñalver
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Anna Aviñó
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
- Institute of Molecules and Materials (IMM); Radboud University; 6525 AJ Nijmegen The Netherlands
| | - Ramón Eritja
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”, CSIC, 28006; Madrid Spain
| | - Juan C. Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
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11
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Vengut-Climent E, Gómez-Pinto I, Lucas R, Peñalver P, Aviñó A, Fonseca Guerra C, Bickelhaupt FM, Eritja R, González C, Morales JC. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA. Angew Chem Int Ed Engl 2016; 55:8643-7. [DOI: 10.1002/anie.201603510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/19/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Empar Vengut-Climent
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
| | | | - Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Pablo Peñalver
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
| | - Anna Aviñó
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; 1081 HV Amsterdam The Netherlands
- Institute of Molecules and Materials (IMM); Radboud University; 6525 AJ Nijmegen The Netherlands
| | - Ramón Eritja
- Instituto de Química Avanzada de Cataluña (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine; 08034 Barcelona Spain
| | - Carlos González
- Instituto de Química Física “Rocasolano”, CSIC, 28006; Madrid Spain
| | - Juan C. Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas; CSIC-Universidad de Sevilla; Américo Vespucio 49 41092 Sevilla Spain
- Department of Biochemistry and Molecular Pharmacology; Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud; 18016 Armilla Granada Spain
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12
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Hudson KL, Bartlett GJ, Diehl RC, Agirre J, Gallagher T, Kiessling LL, Woolfson DN. Carbohydrate-Aromatic Interactions in Proteins. J Am Chem Soc 2015; 137:15152-60. [PMID: 26561965 PMCID: PMC4676033 DOI: 10.1021/jacs.5b08424] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protein-carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C-H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C-H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C-H bonds engage more often in CH-π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate-aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C-H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein-carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein-carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites.
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Affiliation(s)
- Kieran L Hudson
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Gail J Bartlett
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Roger C Diehl
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York , Heslington YO10 5DD, United Kingdom
| | - Timothy Gallagher
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Laura L Kiessling
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.,Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Derek N Woolfson
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom.,School of Biochemistry, University of Bristol , Bristol BS8 1TD, United Kingdom.,BrisSynBio, University of Bristol , Life Sciences Building, Bristol BS8 1TQ, United Kingdom
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Hanessian S, Saavedra OM, Vilchis-Reyes MA, Maianti JP, Kanazawa H, Dozzo P, Matias RD, Serio A, Kondo J. Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4′-deoxy-4′-fluoro neomycin analogs. Chem Sci 2014. [DOI: 10.1039/c4sc01626b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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