1
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Jiang T, Zhou Q, Yu KK, Chen SY, Li K. Identification and quantification of N6-methyladenosine by chemical derivatization coupled with 19F NMR spectroscopy. Org Biomol Chem 2024; 22:2566-2573. [PMID: 38465392 DOI: 10.1039/d4ob00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
N 6-Methyladenosine (6mA) is a well-known prokaryotic DNA modification that has been shown to play epigenetic roles in eukaryotic DNA. Accurate detection and quantification of 6mA are prerequisites for molecular understanding of the impact of 6mA modification on DNA. However, the existing methods have several problems, such as high false-positive rate, time-consuming and complex operating procedures. Chemical sensors for the selective detection of 6mA modification are rarely reported in the literature. Fluorinated phenylboronic acid combined with 19F NMR analysis is an effective method for determining DNA or RNA modification. In this study, we presented a simple and fast chemical method for labelling the 6th imino group of 6mA using a boric-acid-derived probe. Besides, the trifluoromethyl group of trifluoromethyl phenylboronic acid (2a) could detect 6mA modification through 19F NMR. Combined with this sensor system, 6mA modification could be detected well and quickly in 6 types of deoxynucleoside mixtures and DNA samples. Taken together, the method developed in the current study has potential for specific detection of 6mA in biological samples.
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Affiliation(s)
- Ting Jiang
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Qian Zhou
- Department of Chemistry, Xihua University, Chengdu 610039, P. R. China
| | - Kang-Kang Yu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Shan-Yong Chen
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
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2
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Quintana JI, Atxabal U, Unione L, Ardá A, Jiménez-Barbero J. Exploring multivalent carbohydrate-protein interactions by NMR. Chem Soc Rev 2023; 52:1591-1613. [PMID: 36753338 PMCID: PMC9987413 DOI: 10.1039/d2cs00983h] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 02/09/2023]
Abstract
Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan-protein molecular recognition events. Different types of qualitative and quantitative information at different degrees of resolution and complexity can be extracted from the proper application of the available NMR-techniques. In fact, affinity, structural, kinetic, conformational, and dynamic characteristics of the binding process are available. Nevertheless, except in particular cases, the affinity of lectin-sugar interactions is weak, mostly at the low mM range. This feature is overcome in biological processes by using multivalency, thus augmenting the strength of the binding. However, the application of NMR methods to monitor multivalent lectin-glycan interactions is intrinsically challenging. It is well known that when large macromolecular complexes are formed, the NMR signals disappear from the NMR spectrum, due to the existence of fast transverse relaxation, related to the large size and exchange features. Indeed, at the heart of the molecular recognition event, the associated free-bound chemical exchange process for both partners takes place in a particular timescale. Thus, these factors have to be considered and overcome. In this review article, we have distinguished, in a subjective manner, the existence of multivalent presentations in the glycan or in the lectin. From the glycan perspective, we have also considered whether multiple epitopes of a given ligand are presented in the same linear chain of a saccharide (i.e., poly-LacNAc oligosaccharides) or decorating different arms of a multiantennae scaffold, either natural (as in multiantennae N-glycans) or synthetic (of dendrimer or polymer nature). From the lectin perspective, the presence of an individual binding site at every monomer of a multimeric lectin may also have key consequences for the binding event at different levels of complexity.
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Affiliation(s)
- Jon I Quintana
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Unai Atxabal
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry, II Faculty of Science and Technology, EHU-UPV, 48940 Leioa, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
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3
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F-labeled molecular probes for NMR-based detection. J Fluor Chem 2023. [DOI: 10.1016/j.jfluchem.2023.110089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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4
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Díaz-Casado L, Santana AG, Gómez-Pinto I, Villacampa A, Corzana F, Jiménez-Barbero J, González C, Asensio JL. Binding-driven reactivity attenuation enables NMR identification of selective drug candidates for nucleic acid targets. Commun Chem 2022; 5:137. [PMID: 36697799 PMCID: PMC9814457 DOI: 10.1038/s42004-022-00755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 01/28/2023] Open
Abstract
NMR methods, and in particular ligand-based approaches, are among the most robust and reliable alternatives for binding detection and consequently, they have become highly popular in the context of hit identification and drug discovery. However, when dealing with DNA/RNA targets, these techniques face limitations that have precluded widespread application in medicinal chemistry. In order to expand the arsenal of spectroscopic tools for binding detection and to overcome the existing difficulties, herein we explore the scope and limitations of a strategy that makes use of a binding indicator previously unexploited by NMR: the perturbation of the ligand reactivity caused by complex formation. The obtained results indicate that ligand reactivity can be utilised to reveal association processes and identify the best binders within mixtures of significant complexity, providing a conceptually different reactivity-based alternative within NMR screening methods.
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Affiliation(s)
- Laura Díaz-Casado
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Andrés G. Santana
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Irene Gómez-Pinto
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Alejandro Villacampa
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Francisco Corzana
- grid.119021.a0000 0001 2174 6969Dept. Química and Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26005 La Rioja, Spain
| | - Jesús Jiménez-Barbero
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC-bioGUNE). Derio, 48160 Bizkaia, Spain
| | - Carlos González
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Juan Luis Asensio
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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5
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Xu Z, Gu S, Li Y, Wu J, Zhao Y. Recognition-Enabled Automated Analyte Identification via 19F NMR. Anal Chem 2022; 94:8285-8292. [PMID: 35622989 DOI: 10.1021/acs.analchem.2c00642] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nuclear magnetic resonance (NMR) is an indispensable tool for structural elucidation and noninvasive analysis. Automated identification of analytes with NMR is highly pursued in metabolism research and disease diagnosis; however, this process is often complicated by the signal overlap and the sample matrix. We herein report a detection scheme based on 19F NMR spectroscopy and dynamic recognition, which effectively simplifies the detection signal and mitigates the influence of the matrix on the detection. It is demonstrated that this approach can not only detect and differentiate capsaicin and dihydrocapsaicin in complex real-world samples but also quantify the ibuprofen content in sustained-release capsules. Based on the 19F signals obtained in the detection using a set of three 19F probes, automated analyte identification is achieved, effectively reducing the odds of misrecognition caused by structural similarity.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Siyi Gu
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yipeng Li
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Jian Wu
- Instrumental Analysis Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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6
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Novoa-Carballal R, Martin-Pastor M, Fernandez-Megia E. Unveiling an NMR-Invisible Fraction of Polymers in Solution by Saturation Transfer Difference. ACS Macro Lett 2021; 10:1474-1479. [PMID: 35549130 PMCID: PMC8697556 DOI: 10.1021/acsmacrolett.1c00628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The observation of
signals in solution NMR requires nuclei with
sufficiently large transverse relaxation times (T2). Otherwise, broad signals embedded in the baseline
afford an invisible fraction of nuclei (IF). Based on the STD (saturation
transfer difference) sequence, IF-STD is presented as a quick tool
to unveil IF in the 1H NMR spectra of polymers. The saturation
of a polymer in a region of the NMR spectrum with IF (very short 1H T2) results in an efficient
propagation of the magnetization by spin diffusion through the network
of protons to a visible–invisible interphase with larger 1H T2 (STDon). Subtracting
this spectrum from one recorded without saturation (STDoff) produces a difference spectrum (STDoff-on), with
the nuclei at the visible–invisible interphase, that confirms
the presence of an IF. Analysis of a wide collection of polymers by
IF-STD reveals IF more common than previously thought, with relevant
IF figures when STD > 0.4% at 750 MHz. A fundamental property of
the
IF-STD experiment is that the signal is generated within a single
state comprising polymer domains with different dynamics, as opposed
to several states in exchange with different degrees of aggregation.
Contrary to a reductionist visible–invisible dichotomy, our
results confirm a continuous distribution of nuclei with diverse dynamics.
Since nuclei observed (edited) by IF-STD at the visible–invisible
interphase are in close spatial proximity to the IF (tunable with
the saturation time), they emerge as a privileged platform from which
gaining an insight into the IF itself.
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Affiliation(s)
- Ramon Novoa-Carballal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Manuel Martin-Pastor
- Unidade de Resonancia Magnética, Área de Infraestructuras de Investigación, CACTUS, Universidade of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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7
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Palmioli A, Sperandeo P, Bertuzzi S, Polissi A, Airoldi C. On-cell saturation transfer difference NMR for the identification of FimH ligands and inhibitors. Bioorg Chem 2021; 112:104876. [PMID: 33845337 DOI: 10.1016/j.bioorg.2021.104876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/14/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022]
Abstract
We describe the development of an on-cell NMR method for the rapid screening of FimH ligands and the structural identification of ligand binding epitopes. FimH is a mannose-binding bacterial adhesin expressed at the apical end of type 1 pili of uropathogenic bacterial strains and responsible for their d-mannose sensitive adhesion to host mammalian epithelial cells. Because of these properties, FimH is a key virulence factor and an attractive therapeutic target for urinary tract infection. We prepared synthetic d-mannose decorated dendrimers, we tested their ability to prevent the FimH-mediated yeast agglutination, and thus we used the compounds showing the best inhibitory activity as models of FimH multivalent ligands to set up our NMR methodology. Our experimental protocol, based on on-cell STD NMR techniques, is a suitable tool for the screening and the epitope mapping of FimH ligands aimed at the development of new antiadhesive and diagnostic tools against urinary tract infection pathogens. Notably, the study is carried out in a physiological environment, i.e. at the surface of living pathogen cells expressing FimH.
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Affiliation(s)
- Alessandro Palmioli
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Sara Bertuzzi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy; Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Spain
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Cristina Airoldi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
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8
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Monaco S, Walpole S, Doukani H, Nepravishta R, Martínez‐Bailén M, Carmona AT, Ramos‐Soriano J, Bergström M, Robina I, Angulo J. Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B. Chemistry 2020; 26:10024-10034. [PMID: 32449563 PMCID: PMC7496166 DOI: 10.1002/chem.202001723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/08/2020] [Indexed: 11/30/2022]
Abstract
Ligand-based NMR techniques to study protein-ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.
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Affiliation(s)
- Serena Monaco
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Samuel Walpole
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Hassan Doukani
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Ridvan Nepravishta
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Biochemistry & Molecular BiologySealy Center for Structural Biology & Molecular BiophysicsUniversity of Texas Medical Branch301 University BlvdGalvestonTX77555-1068USA
| | | | - Ana T. Carmona
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Javier Ramos‐Soriano
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Maria Bergström
- Department of Chemistry and Biomedical SciencesLinnaeus University391 82KalmarSweden
| | - Inmaculada Robina
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Jesus Angulo
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
- Instituto de Investigaciones Químicas (CSIC-US)Avda. Américo Vespucio, 4941092SevillaSpain
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9
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On-cell saturation transfer difference NMR study of Bombesin binding to GRP receptor. Bioorg Chem 2020; 99:103861. [PMID: 32339813 DOI: 10.1016/j.bioorg.2020.103861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/15/2023]
Abstract
We report the NMR characterization of the molecular interaction between Gastrin Releasing Peptide Receptor (GRP-R) and its natural ligand bombesin (BN). GRP-R is a transmembrane G-protein coupled receptor promoting the stimulation of cancer cell proliferation; in addition, being overexpressed on the surface of different human cancer cell lines, it is ideal for the development of new strategies for the selective targeted delivery of anticancer drugs and diagnostic devices to tumor cells. However, the design of new GRP-R binders requires structural information on receptor interaction with its natural ligands. The experimental protocol presented herein, based on on-cell STD NMR techniques, is a powerful tool for the screening and the epitope mapping of GRP-R ligands aimed at the development of new anticancer and diagnostic tools. Notably, the study can be carried out in a physiological environment, at the surface of tumoral cells overespressing GRP-R. Moreover, to the best of our knowledge, this is the first example of an NMR experiment able to detect and investigate the structural determinants of BN/GRP-R interaction.
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10
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Dahiya V, Anand BG, Kar K, Pal S. Analyzing organophosphate pesticide-serum albumin binding interaction: a combined STD NMR and molecular docking study. J Biomol Struct Dyn 2020; 39:1865-1878. [PMID: 32189579 DOI: 10.1080/07391102.2020.1745280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In Vitro analysis of the interaction of organophosphate pesticides (OP) with bovine serum albumin (BSA) is crucial to understand their potential effects at the molecular level. In this context, we have employed Saturation Transfer Difference (STD) NMR experiments in conjunction with molecular docking studies to unravel the binding interaction of the OP chlorpyrifos (CPF), diazinon (DZN) and parathion (PA) in solution. The relative STD (%) suggested the detailed epitope mapping of these OP with BSA while the concentration-dependent STD NMR studies were performed to obtain the complex dissociation constant (KD) of the OP-BSA complexes; KD=1.81 × 10-4 M, 1.30 × 10-3 M and 1.11 × 10-3 M for CPF, DZN and PA were extracted respectively. Similar binding modes were identified for all the three OP using STD site-marker experiment. ITC experiments were performed as a complementary method that revealed a high binding affinity of OP-BSA complexes through non-covalent interaction. Molecular docking confirmed the possible interacting chemical groups of OP-BSA complexes. These significant results furnish valuable information about the toxicity risk of OP to proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vandana Dahiya
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jheepasani, India
| | - Bibin G Anand
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jheepasani, India
| | - Karunakar Kar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jheepasani, India
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11
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Mondal A, Hazra A, Chakrabarty J, Bose K JC, Banerjee P. Tandem Detection of Sub-Nano Molar Level CN - and Hg 2+ in Aqueous Medium by a Suitable Molecular Sensor: A Viable Solution for Detection of CN - and Development of the RGB-Based Sensory Device. ACS OMEGA 2020; 5:6576-6587. [PMID: 32258893 PMCID: PMC7114731 DOI: 10.1021/acsomega.9b04311] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/09/2020] [Indexed: 05/04/2023]
Abstract
An inimitable urea-based multichannel chemosensor, DTPH [1,5-bis-(2,6-dichloro-4-(trifluoromethyl)phenyl)carbonohydrazide], was examined to be highly proficient to recognize CN- based on the H-bonding interaction between sensor -NH moiety and CN- in aqueous medium with explicit selectivity. In the absorption spectral titration of DTPH, a new peak at higher wavelength was emerged in titrimetric analytical studies of CN- with the zero-order reaction kinetics affirming the substantial sensor-analyte interaction. The isothermal titration calorimetry (ITC) experiment further affirmed that the sensing process was highly spontaneous with the Gibbs free energy of -26 × 104 cal/mol. The binding approach between DTPH and CN- was also validated by more than a few experimental studies by means of several spectroscopic tools along with the theoretical calculations. A very low detection limit of the chemosensor toward CN- (0.15 ppm) further instigated to design an RGB-based sensory device based on the colorimetric upshots of the chemosensor in order to develop a distinct perception regarding the presence of innocuous or precarious level of the CN- in a contaminated solution. Moreover, the reversibility of the sensor in the presence of CN- and Hg2+ originated a logic gate mimic ensemble. Additionally, the real-field along with the in vitro CN- detection efficiency of the photostable DTPH was also accomplished by using various biological specimens.
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Affiliation(s)
- Amita Mondal
- CSIR-Central
Mechanical Engineering Research Institute (CMERI), Mahatma Gandhi Avenue, Durgapur 713209, West Bengal, India
- Department
of Chemistry, National Institute of Technology, M. G. Avenue, Durgapur 713209, West
Bengal, India
| | - Abhijit Hazra
- CSIR-Central
Mechanical Engineering Research Institute (CMERI), Mahatma Gandhi Avenue, Durgapur 713209, West Bengal, India
- Academy
of Scientific & Innovative Research (AcSIR), AcSIR Headquarters CSIR-HRDC Campus, Postal Staff
College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, Uttar
Pradesh, India
| | - Jitamanyu Chakrabarty
- Department
of Chemistry, National Institute of Technology, M. G. Avenue, Durgapur 713209, West
Bengal, India
| | - Jagadeesh C. Bose K
- University
Institute of Biotechnology, Chandigarh University, Mohali, Punjab 140413, India
| | - Priyabrata Banerjee
- CSIR-Central
Mechanical Engineering Research Institute (CMERI), Mahatma Gandhi Avenue, Durgapur 713209, West Bengal, India
- Academy
of Scientific & Innovative Research (AcSIR), AcSIR Headquarters CSIR-HRDC Campus, Postal Staff
College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, Uttar
Pradesh, India
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12
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Balaji S, Ahsan MJ, Jadav SS, Trivedi V. Molecular modelling, synthesis, and antimalarial potentials of curcumin analogues containing heterocyclic ring. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2015.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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13
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Kellici TF, Ntountaniotis D, Liapakis G, Tzakos AG, Mavromoustakos T. The dynamic properties of angiotensin II type 1 receptor inverse agonists in solution and in the receptor site. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2016.11.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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14
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Palmioli A, Sperandeo P, Polissi A, Airoldi C. Targeting Bacterial Biofilm: A New LecA Multivalent Ligand with Inhibitory Activity. Chembiochem 2019; 20:2911-2915. [DOI: 10.1002/cbic.201900383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and BiosciencesUniversity of Milano–Bicocca Piazza della Scienza 2 20126 Milano Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular SciencesUniversity of Milano Via Balzaretti, 9/11/13 20133 Milano Italy
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular SciencesUniversity of Milano Via Balzaretti, 9/11/13 20133 Milano Italy
| | - Cristina Airoldi
- Department of Biotechnology and BiosciencesUniversity of Milano–Bicocca Piazza della Scienza 2 20126 Milano Italy
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15
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Valenti D, Neves JF, Cantrelle FX, Hristeva S, Lentini Santo D, Obšil T, Hanoulle X, Levy LM, Tzalis D, Landrieu I, Ottmann C. Set-up and screening of a fragment library targeting the 14-3-3 protein interface. MEDCHEMCOMM 2019; 10:1796-1802. [PMID: 31814953 DOI: 10.1039/c9md00215d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/20/2019] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions (PPIs) are at the core of regulation mechanisms in biological systems and consequently became an attractive target for therapeutic intervention. PPIs involving the adapter protein 14-3-3 are representative examples given the broad range of partner proteins forming a complex with one of its seven human isoforms. Given the challenges represented by the nature of these interactions, fragment-based approaches offer a valid alternative for the development of PPI modulators. After having assembled a fragment set tailored on PPIs' modulation, we started a screening campaign on the sigma isoform of 14-3-3 adapter proteins. Through the use of both mono- and bi-dimensional nuclear magnetic resonance spectroscopy measurements, coupled with differential scanning fluorimetry, three fragment hits were identified. These molecules bind the protein at two different regions distant from the usual binding groove highlighting new possibilities for selective modulation of 14-3-3 complexes.
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Affiliation(s)
- Dario Valenti
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany . .,Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands .
| | | | | | - Stanimira Hristeva
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
| | - Domenico Lentini Santo
- Department of Physical and Macromolecular Chemistry , Faculty of Science , Charles University , 12843 Prague , Czech Republic
| | - Tomáš Obšil
- Department of Physical and Macromolecular Chemistry , Faculty of Science , Charles University , 12843 Prague , Czech Republic.,Department of Structural Biology of Signaling Proteins , Division BIOCEV , Institute of Physiology of the Czech Academy of Sciences , Prumyslova 595, 252 50 Vestec , Czech Republic
| | - Xavier Hanoulle
- Univ. Lille , CNRS , UMR 8576 - UGSF , F-59000 Lille , France .
| | - Laura M Levy
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
| | - Dimitrios Tzalis
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
| | | | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands . .,Department of Chemistry , University of Duisburg-Essen , Universitätsstraße 7 , 45117 , Essen , Germany
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16
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Glycosaminoglycan-Protein Interactions by Nuclear Magnetic Resonance (NMR) Spectroscopy. Molecules 2018; 23:molecules23092314. [PMID: 30208595 PMCID: PMC6225283 DOI: 10.3390/molecules23092314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most utilized and informative analytical techniques for investigating glycosaminoglycan (GAG)-protein complexes. NMR methods that are commonly applied to GAG-protein systems include chemical shift perturbation, saturation transfer difference, and transferred nuclear Overhauser effect. Although these NMR methods have revealed valuable insight into the protein-GAG complexes, elucidating high-resolution structural and dynamic information of these often transient interactions remains challenging. In addition, preparation of structurally homogeneous and isotopically enriched GAG ligands for structural investigations continues to be laborious. As a result, understanding of the structure-activity relationship of GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed lately. Here, we review some of the commonly used techniques along with more novel methods such as waterLOGSY and experiments to examine structure and dynamic of lysine and arginine side chains to identify GAG-binding sites. We will also present the latest technology that is used to produce isotopically enriched as well as paramagnetically tagged GAG ligands. Recent results that were obtained from solid-state NMR of amyloid’s interaction with GAG are also presented together with a brief discussion on computer assisted modeling of GAG-protein complexes using sparse experimental data.
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17
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Roca C, Martinez-González L, Daniel-Mozo M, Sastre J, Infantes L, Mansilla A, Chaves-Sanjuan A, González-Rubio JM, Gil C, Cañada FJ, Martinez A, Sanchez-Barrena MJ, Campillo NE. Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor Ric8a with a Small Phenothiazine Molecule for the Rational Generation of Therapeutic Synapse Function Regulators. J Med Chem 2018; 61:5910-5921. [DOI: 10.1021/acs.jmedchem.8b00088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Roca
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Miguel Daniel-Mozo
- Instituto de Química Física Rocasolano-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Javier Sastre
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lourdes Infantes
- Instituto de Química Física Rocasolano-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Alicia Mansilla
- Fundación para la Investigación Biomédica, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, Km. 9, 28034 Madrid, Spain
| | | | | | - Carmen Gil
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Nuria E. Campillo
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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18
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Becker W, Bhattiprolu KC, Gubensäk N, Zangger K. Investigating Protein-Ligand Interactions by Solution Nuclear Magnetic Resonance Spectroscopy. Chemphyschem 2018; 19:895-906. [PMID: 29314603 PMCID: PMC5915746 DOI: 10.1002/cphc.201701253] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Protein-ligand interactions are of fundamental importance in almost all processes in living organisms. The ligands comprise small molecules, drugs or biological macromolecules and their interaction strength varies over several orders of magnitude. Solution NMR spectroscopy offers a large repertoire of techniques to study such complexes. Here, we give an overview of the different NMR approaches available. The information they provide ranges from the simple information about the presence of binding or epitope mapping to the complete 3 D structure of the complex. NMR spectroscopy is particularly useful for the study of weak interactions and for the screening of binding ligands with atomic resolution.
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Affiliation(s)
- Walter Becker
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | | | - Nina Gubensäk
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
| | - Klaus Zangger
- Institute of ChemistryUniversity of GrazHeinrichstrasse 28A-8010GrazAustria
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19
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Application of Heteronuclear NMR Spectroscopy to Bioinorganic and Medicinal Chemistry ☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2018. [PMCID: PMC7157447 DOI: 10.1016/b978-0-12-409547-2.10947-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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New insight on the structural features of the cytotoxic auristatins MMAE and MMAF revealed by combined NMR spectroscopy and quantum chemical modelling. Sci Rep 2017; 7:15920. [PMID: 29162861 PMCID: PMC5698355 DOI: 10.1038/s41598-017-15674-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/31/2017] [Indexed: 01/07/2023] Open
Abstract
Antibody-drug conjugates (ADCs) are emerging as a promising class of selective drug delivery systems in the battle against cancer and other diseases. The auristatins monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) appear as the cytotoxic drug in almost half of the state-of-the-art ADCs on the market or in late stage clinical trials. Here, we present the first complete NMR spectroscopic characterisation of these challenging molecules, and investigate their structural properties by a combined NMR and quantum chemical modelling approach. We find that in solution, half of the drug molecules are locked in an inactive conformation, severely decreasing their efficiency, and potentially increasing the risk of side-effects. Furthermore, we identify sites susceptible to future modification, in order to potentially improve the performance of these drugs.
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21
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Serena Monaco
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
| | - Louise E. Tailford
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Jesus Angulo
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
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22
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017; 56:15289-15293. [PMID: 28977722 PMCID: PMC5725711 DOI: 10.1002/anie.201707682] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/08/2017] [Indexed: 11/21/2022]
Abstract
Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP‐STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D2O/H2O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP‐STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket.
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Affiliation(s)
- Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Louise E Tailford
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
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23
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Yang H, Huang Y, Liu J, Tang P, Sun Q, Xiong X, Tang B, He J, Li H. Binding modes of environmental endocrine disruptors to human serum albumin: insights from STD-NMR, ITC, spectroscopic and molecular docking studies. Sci Rep 2017; 7:11126. [PMID: 28894220 PMCID: PMC5593971 DOI: 10.1038/s41598-017-11604-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/29/2017] [Indexed: 12/17/2022] Open
Abstract
Given that bisphenols have an endocrine-disrupting effect on human bodies, thoroughly exposing their potential effects at the molecular level is important. Saturation transfer difference (STD) NMR-based binding studies were performed to investigate the binding potential of two bisphenol representatives, namely, bisphenol B (BPB) and bisphenol E (BPE), toward human serum albumin (HSA). The relative STD (%) suggested that BPB and BPE show similar binding modes and orientations, in which the phenolic rings were spatially close to HSA binding site. ITC analysis results showed that BPB and BPE were bound to HSA with moderately strong binding affinity through electrostatic interactions and hydrogen bonds. The order of binding affinity of HSA for two test bisphenols is as follows: BPE > BPB. The results of fluorescence competitive experiments using 5-dimethylaminonaphthalene-1-sulfonamide and dansylsarcosine as competitors, combined with molecular docking indicated that both bisphenols are prone to attach to the binding site II in HSA. Spectroscopic results (FT-IR, CD, synchronous and 3D fluorescence spectra) showed that BPB/BPE induces different degrees of microenvironmental and conformational changes to HSA.
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Affiliation(s)
- Hongqin Yang
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Yanmei Huang
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiuyang Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Peixiao Tang
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Qiaomei Sun
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Xinnuo Xiong
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Bin Tang
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiawei He
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Hui Li
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
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24
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Gimeno A, Santos LM, Alemi M, Rivas J, Blasi D, Cotrina EY, Llop J, Valencia G, Cardoso I, Quintana J, Arsequell G, Jiménez-Barbero J. Insights on the Interaction between Transthyretin and Aβ in Solution. A Saturation Transfer Difference (STD) NMR Analysis of the Role of Iododiflunisal. J Med Chem 2017; 60:5749-5758. [DOI: 10.1021/acs.jmedchem.7b00428] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ana Gimeno
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
| | - Luis M. Santos
- IBMC—Instituto de Biologia Celular e Molecular, Campo Alegre 823, 4150 Porto, Portugal
- i3S—Instituto
de Investigação e Inovação em Saúde, Universidade do Porto, Alfredo Allen, 4200-135 Porto, Portugal
| | - Mobina Alemi
- IBMC—Instituto de Biologia Celular e Molecular, Campo Alegre 823, 4150 Porto, Portugal
- i3S—Instituto
de Investigação e Inovação em Saúde, Universidade do Porto, Alfredo Allen, 4200-135 Porto, Portugal
- Faculdade
de Medicina, Universidade do Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal
| | - Josep Rivas
- Plataforma
Drug
Discovery, Parc Científic de Barcelona (PCB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Daniel Blasi
- Plataforma
Drug
Discovery, Parc Científic de Barcelona (PCB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Ellen Y. Cotrina
- Institut de Química
Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Jordi Llop
- Radiochemistry
and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramon 182, 20009 Donostia-San Sebastian, Spain
| | - Gregorio Valencia
- Institut de Química
Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Isabel Cardoso
- IBMC—Instituto de Biologia Celular e Molecular, Campo Alegre 823, 4150 Porto, Portugal
- i3S—Instituto
de Investigação e Inovação em Saúde, Universidade do Porto, Alfredo Allen, 4200-135 Porto, Portugal
| | - Jordi Quintana
- Plataforma
Drug
Discovery, Parc Científic de Barcelona (PCB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Gemma Arsequell
- Institut de Química
Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology
Park, Building 801A, 48170 Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Departament
of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
- Plataforma
Drug
Discovery, Parc Científic de Barcelona (PCB), Baldiri Reixac 10, 08028 Barcelona, Spain
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25
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Protein-ligand binding affinity determination by the waterLOGSY method: An optimised approach considering ligand rebinding. Sci Rep 2017; 7:43727. [PMID: 28256624 PMCID: PMC5335602 DOI: 10.1038/srep43727] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/27/2017] [Indexed: 12/21/2022] Open
Abstract
WaterLOGSY is a popular ligand-observed NMR technique to screen for protein-ligand interactions, yet when applied to measure dissociation constants (KD) through ligand titration, the results were found to be strongly dependent on sample conditions. Herein, we show that accurate KDs can be obtained by waterLOGSY with optimised experimental setup.
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26
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Yang H, Huang Y, He J, Li S, Tang B, Li H. Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies. Arch Biochem Biophys 2016; 606:81-9. [PMID: 27457418 DOI: 10.1016/j.abb.2016.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 12/11/2022]
Abstract
In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, (1)H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA.
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Affiliation(s)
- Hongqin Yang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yanmei Huang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jiawei He
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Shanshan Li
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Bin Tang
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China
| | - Hui Li
- College of Chemical Engineering, Sichuan University, Chengdu 610065, PR China.
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27
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Boutet J, Blasco P, Guerreiro C, Thouron F, Dartevelle S, Nato F, Cañada FJ, Ardá A, Phalipon A, Jiménez-Barbero J, Mulard LA. Detailed Investigation of the Immunodominant Role of O-Antigen Stoichiometric O-Acetylation as Revealed by Chemical Synthesis, Immunochemistry, Solution Conformation and STD-NMR Spectroscopy for Shigella flexneri 3a. Chemistry 2016; 22:10892-911. [PMID: 27376496 DOI: 10.1002/chem.201600567] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 02/02/2023]
Abstract
Shigella flexneri 3a causes bacillary dysentery. Its O-antigen has the {2)-[α-d-Glcp-(1→3)]-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-[Ac→2]-α-l-Rhap-(1→3)-[Ac→6]≈40 % -β-d-GlcpNAc-(1→} ([(E)ABAc CAc D]) repeating unit, and the non-O-acetylated equivalent defines S. flexneri X. Propyl hepta-, octa-, and decasaccharides sharing the (E')A'BAc CD(E)A sequence, and their non-O-acetylated analogues were synthesized from a fully protected BAc CD(E)A allyl glycoside. The stepwise introduction of orthogonally protected mono- and disaccharide imidate donors was followed by a two-step deprotection process. Monoclonal antibody binding to twenty-six S. flexneri types 3a and X di- to decasaccharides was studied by an inhibition enzyme-linked immunosorbent assay (ELISA) and STD-NMR spectroscopy. Epitope mapping revealed that the 2C -acetate dominated the recognition by monoclonal IgG and IgM antibodies and that the BAc CD segment was essential for binding. The glucosyl side chain contributed to a lesser extent, albeit increasingly with the chain length. Moreover, tr-NOESY analysis also showed interaction but did not reveal any meaningful conformational change upon antibody binding.
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Affiliation(s)
- Julien Boutet
- Institut Pasteur, Unité de Chimie des Biomolécules, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France.,CNRS UMR 3523, Institut Pasteur, 75015, Paris, France.,Université Paris Descartes, Institut Pasteur, 75015, Paris, France.,Present address for J.B.: Adisseo (France), Present address for P.B., Dept. of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Pilar Blasco
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.,Present address for J.B.: Adisseo (France), Present address for P.B., Dept. of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Catherine Guerreiro
- Institut Pasteur, Unité de Chimie des Biomolécules, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France.,CNRS UMR 3523, Institut Pasteur, 75015, Paris, France
| | - Françoise Thouron
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr. Roux, 75015, Paris, France.,INSERM U1202, Institut Pasteur, 75015, Paris, France
| | - Sylvie Dartevelle
- Institut Pasteur, PF5, 28 rue du Dr. Roux, 75015, Paris, France.,CNRS UMR 3528, Institut Pasteur, 75015, Paris, France
| | - Farida Nato
- Institut Pasteur, PF5, 28 rue du Dr. Roux, 75015, Paris, France.,CNRS UMR 3528, Institut Pasteur, 75015, Paris, France
| | - F Javier Cañada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Ana Ardá
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.,Molecular Recognition & Host-Pathogen Interactions Program, CIC bioGUNE, Bizkaia Technological Park, Building 801A, 48160, Derio, Spain
| | - Armelle Phalipon
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr. Roux, 75015, Paris, France.,INSERM U1202, Institut Pasteur, 75015, Paris, France
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain. .,Molecular Recognition & Host-Pathogen Interactions Program, CIC bioGUNE, Bizkaia Technological Park, Building 801A, 48160, Derio, Spain. .,Ikerbasque, Basque Foundation for Science, Maria Lopez de Haro 3, 48013, Bilbao, Spain.
| | - Laurence A Mulard
- Institut Pasteur, Unité de Chimie des Biomolécules, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France. .,CNRS UMR 3523, Institut Pasteur, 75015, Paris, France.
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28
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Bini D, Marchetti R, Russo L, Molinaro A, Silipo A, Cipolla L. Multivalent ligand mimetics of LecA from P. aeruginosa: synthesis and NMR studies. Carbohydr Res 2016; 429:23-8. [DOI: 10.1016/j.carres.2016.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 01/14/2023]
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29
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Seetaha S, Yagi-Utsumi M, Yamaguchi T, Ishii K, Hannongbua S, Choowongkomon K, Kato K. Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. ChemMedChem 2016; 11:363-6. [PMID: 26804978 DOI: 10.1002/cmdc.201500554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Indexed: 11/07/2022]
Abstract
Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques can provide long-range structural information complemented with local information derived from chemical-shift perturbation and nuclear Overhauser effect data. Here, we address the application of paramagnetic relaxation enhancement (PRE) to detect inhibitor-induced conformational change of a drug target protein using human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) as a model protein. Using a site-specific spin-labeled HIV-1 RT mutant with selective (13) C labeling, conformation-dependent PREs were successfully observed reflecting the stabilization of an open conformation of this enzyme caused by inhibitor binding. This study demonstrates that the paramagnetism-assisted NMR approach offers an alternative strategy in protein-based drug screening to identify allosteric inhibitors of a target protein.
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Affiliation(s)
- Supaporn Seetaha
- Graduate Program in Bioscience, Faculty of Science, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Takumi Yamaguchi
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, 923-1292, Japan
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. .,Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Koichi Kato
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan. .,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Mhodaiji, Okazaki, 444-8787, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
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30
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Cho S, Im H, Lee KY, Chen J, Kang HJ, Yoon HJ, Min KH, Lee KR, Park HJ, Lee BJ. Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS). Eur J Med Chem 2015; 108:188-202. [PMID: 26649906 DOI: 10.1016/j.ejmech.2015.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/17/2015] [Accepted: 11/21/2015] [Indexed: 01/27/2023]
Abstract
The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDO8PS) from Helicobacter pylori (HpKDO8PS) was determined alone and within various complexes, revealing an extra helix (HE) that is absent in the structures of KDO8PS from other organisms. In contrast to the metal coordination of the KDO8PS enzyme from Aquifex aeolicus, HpKDO8PS is specifically coordinated with Cd(2+) or Zn(2+) ions, and isothermal titration calorimetry (ITC) and differential scanning fluorimetry (DSF) revealed that Cd(2+) thermally stabilizes the protein structure more efficiently than Zn(2+). In the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. Using the structures of HpKDO8PS and API [arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) bisubstrate inhibitor], we generated 21 compounds showing potential HpKDO8PS-binding properties via in silico virtual screening. The capacity of three, avicularin, hyperin, and MC181, to bind to HpKDO8PS was confirmed through saturation transfer difference (STD) experiments, and we identified their specific ligand binding modes by combining competition experiments and docking simulation analysis. Hyperin was confirmed to bind to the A5P binding site, primarily via hydrophilic interaction, whereas MC181 bound to both the PEP and A5P binding sites through hydrophilic and hydrophobic interactions. These results were consistent with the epitope mapping by STD. Our results are expected to provide clues for the development of HpKDO8PS inhibitors.
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Affiliation(s)
- Sujin Cho
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ki-Young Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jie Chen
- School of Pharmacy, Sungkyunkwan University, Gyeonggi-do 440-746, Republic of Korea
| | - Hae Ju Kang
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Kyung Hoon Min
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Kang Ro Lee
- School of Pharmacy, Sungkyunkwan University, Gyeonggi-do 440-746, Republic of Korea
| | - Hyun-Ju Park
- School of Pharmacy, Sungkyunkwan University, Gyeonggi-do 440-746, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
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31
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Bonanomi M, Visentin C, Natalello A, Spinelli M, Vanoni M, Airoldi C, Regonesi ME, Tortora P. How Epigallocatechin-3-gallate and Tetracycline Interact with the Josephin Domain of Ataxin-3 and Alter Its Aggregation Mode. Chemistry 2015; 21:18383-93. [PMID: 26538519 DOI: 10.1002/chem.201503086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/17/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) and tetracycline are two known inhibitors of amyloid aggregation able to counteract the fibrillation of most of the proteins involved in neurodegenerative diseases. We have recently investigated their effect on ataxin-3 (AT3), the polyglutamine-containing protein responsible for spinocerebellar ataxia type 3. We previously showed that EGCG and tetracycline can contrast the aggregation process and toxicity of expanded AT3, although by different mechanisms. Here, we have performed further experiments by using the sole Josephin domain (JD) to further elucidate the mechanism of action of the two compounds. By protein solubility assays and FTIR spectroscopy we have first observed that EGCG and tetracycline affect the JD aggregation essentially in the same way displayed when acting on the full-length expanded AT3. Then, by saturation transfer difference (STD) NMR experiments, we have shown that EGCG binds both the monomeric and the oligomeric JD form, whereas tetracycline can only interact with the oligomeric one. Surface plasmon resonance (SPR) analysis has confirmed the capability of the sole EGCG to bind monomeric JD, although with a KD value suggestive for a non-specific interaction. Our investigations provide new details on the JD interaction with EGCG and tetracycline, which could explain the different mechanisms by which the two compounds reduce the toxicity of AT3.
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Affiliation(s)
- Marcella Bonanomi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Cristina Visentin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy). .,SysBio Centre for Systems Biology, Milano and Rome (Italy).
| | - Maria E Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
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32
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Segarra‐Maset MD, Escuder B, Miravet JF. Selective Interaction of Dopamine with the Self‐Assembled Fibrillar Network of a Molecular Hydrogel Revealed by STD‐NMR. Chemistry 2015; 21:13925-9. [DOI: 10.1002/chem.201502018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Indexed: 11/09/2022]
Affiliation(s)
- María D. Segarra‐Maset
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Avenida Sos Baynat, s/n; 12071 Castellón (Spain)
| | - Beatriu Escuder
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Avenida Sos Baynat, s/n; 12071 Castellón (Spain)
| | - Juan F. Miravet
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, Avenida Sos Baynat, s/n; 12071 Castellón (Spain)
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33
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Calle LP, Echeverria B, Franconetti A, Serna S, Fernández‐Alonso MC, Diercks T, Cañada FJ, Ardá A, Reichardt N, Jiménez‐Barbero J. Monitoring Glycan–Protein Interactions by NMR Spectroscopic Analysis: A Simple Chemical Tag That Mimics Natural CH–π Interactions. Chemistry 2015; 21:11408-16. [DOI: 10.1002/chem.201501248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Luis P. Calle
- Department of Chemical and Physical Biology, CIB‐CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Begoña Echeverria
- Department of Glycotechnology, CICbiomaGUNE, Paseo Miramón 182, 20009 San Sebastián (Spain)
| | - Antonio Franconetti
- Department of Organic Chemistry, University of Sevilla, Profesor García González 1, 41012 Sevilla (Spain)
| | - Sonia Serna
- Department of Glycotechnology, CICbiomaGUNE, Paseo Miramón 182, 20009 San Sebastián (Spain)
| | | | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
| | - F. Javier Cañada
- Department of Chemical and Physical Biology, CIB‐CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Ana Ardá
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
| | | | - Jesús Jiménez‐Barbero
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao (Spain)
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34
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Unione L, Xu B, Díaz D, Martín-Santamaría S, Poveda A, Sardinha J, Rauter AP, Blériot Y, Zhang Y, Cañada FJ, Sollogoub M, Jiménez-Barbero J. Conformational Plasticity in Glycomimetics: Fluorocarbamethyl-L-idopyranosides Mimic the Intrinsic Dynamic Behaviour of Natural Idose Rings. Chemistry 2015; 21:10513-21. [PMID: 26096911 DOI: 10.1002/chem.201501249] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/08/2015] [Indexed: 11/06/2022]
Abstract
Sugar function, structure and dynamics are intricately correlated. Ring flexibility is intrinsically related to biological activity; actually plasticity in L-iduronic rings modulates their interactions with biological receptors. However, the access to the experimental values of the energy barriers and free-energy difference for conformer interconversion in water solution has been elusive. Here, a new generation of fluorine-containing glycomimetics is presented. We have applied a combination of organic synthesis, NMR spectroscopy and computational methods to investigate the conformational behaviour of idose- and glucose-like rings. We have used low-temperature NMR spectroscopic experiments to slow down the conformational exchange of the idose-like rings. Under these conditions, the exchange rate becomes slow in the (19) F NMR spectroscopic chemical shift timescale and allows shedding light on the thermodynamic and kinetic features of the equilibrium. Despite the minimal structural differences between these compounds, a remarkable difference in their dynamic behaviour indeed occurs. The importance of introducing fluorine atoms in these sugars mimics is also highlighted. Only the use of (19) F NMR spectroscopic experiments has permitted the unveiling of key features of the conformational equilibrium that would have otherwise remained unobserved.
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Affiliation(s)
- Luca Unione
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain).,Infectious Disease Programme, CIC bioGUNE, 48160 Derio, Bizkaia (Spain)
| | - Bixue Xu
- Sorbonne Universités, UPMC Univ Paris 06, Institut Universitaire de France, UMR CNRS 8232, IPCM, 4, place Jussieu, 75005 Paris (France).,Present address: The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, 202 Shachong South Road, Guiyang, 550002 (P. R. China)
| | - Dolores Díaz
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Sonsoles Martín-Santamaría
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Ana Poveda
- Infectious Disease Programme, CIC bioGUNE, 48160 Derio, Bizkaia (Spain)
| | - João Sardinha
- Sorbonne Universités, UPMC Univ Paris 06, Institut Universitaire de France, UMR CNRS 8232, IPCM, 4, place Jussieu, 75005 Paris (France).,Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, 1749-016 Lisboa (Portugal)
| | - Amelia Pilar Rauter
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, 1749-016 Lisboa (Portugal)
| | - Yves Blériot
- Université de Poitiers, UMR CNRS 7285, IC2MP, Equipe Synthèse organique, Groupe Glycochimie, 4, avenue Michel Brunet, 86022 Poitiers Cedex (France)
| | - Yongmin Zhang
- Sorbonne Universités, UPMC Univ Paris 06, Institut Universitaire de France, UMR CNRS 8232, IPCM, 4, place Jussieu, 75005 Paris (France)
| | - F Javier Cañada
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Matthieu Sollogoub
- Sorbonne Universités, UPMC Univ Paris 06, Institut Universitaire de France, UMR CNRS 8232, IPCM, 4, place Jussieu, 75005 Paris (France).
| | - Jesus Jiménez-Barbero
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain). .,Infectious Disease Programme, CIC bioGUNE, 48160 Derio, Bizkaia (Spain). .,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain).
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35
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Fernández-Tejada A, Cañada FJ, Jiménez-Barbero J. Glycans in Medicinal Chemistry: An Underexploited Resource. ChemMedChem 2015; 10:1291-5. [PMID: 25974358 DOI: 10.1002/cmdc.201500107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/05/2022]
Abstract
The biological relevance of glycans as mediators of key physiological processes, including disease-related mechanisms, makes them attractive targets for a wide range of medical applications. Despite their important biological roles, especially as molecular recognition elements, carbohydrates have not been fully exploited as therapeutics mainly due to the scarcity of structure-activity correlations and their non-drug-like properties. A more detailed understanding of the complex carbohydrate structures and their associated functions should contribute to the development of new glycan-based pharmaceuticals. Recent significant progress in oligosaccharide synthesis and chemical glycobiology has renewed the interest of the medicinal chemistry community in carbohydrates. This promises to increase our possibilities to harness them in drug discovery efforts for the development of new and more effective, synthetic glycan-based therapeutics and vaccines.
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Affiliation(s)
- Alberto Fernández-Tejada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid (Spain).
| | - F Javier Cañada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Jesús Jiménez-Barbero
- CIC bioGUNE: Center for Cooperative Research in Biosciences, Bizkaia Technology Park, 48160 Derio (Spain). .,Ikerbasque, Basque Foundation for Science, María López de Haro 13, 48009 Bilbao (Spain).
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36
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Marchetti R, Molinaro A, Silipo A. NMR as a Tool to Unveil the Molecular Basis of Glycan-mediated Host–Pathogen Interactions. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nature of the relationship between microbes and hosts spans the broad spectrum from beneficial (symbiosis) to pathogenic (disease); one of the key factors determining the establishment of any type of host–microbe interaction is the pattern of glycoconjugates exposed on cell surfaces, many known as virulence factors since they are pivotal for adhesion to host tissue, immunoevasion and immunosuppression, causing disease in the host. The recognition of these pathogen glycostructures by specific host receptors is an important means of immune defense. In this context, NMR represents a valuable tool to investigate the conformational properties of both host/pathogen signaling molecules and to disclose their interaction at a molecular level. This chapter provides an overview of several protein–carbohydrate interaction systems studied by NMR, and their implications in human and plant diseases.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant’Angelo Via Cintia 4 I-80126 Napoli Italy
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37
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Kim KM, Song JH, Kim MK, Chung ST, Jeong J, Yang JY, Choi AJ, Choi HJ, Oh JM. Physicochemical analysis methods for nanomaterials considering their toxicological evaluations. Mol Cell Toxicol 2015. [DOI: 10.1007/s13273-014-0039-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Tanoli SAK, Tanoli NU, Bondancia TM, Usmani S, Ul-Haq Z, Fernandes JB, Thomasi SS, Ferreira AG. Human serum albumin-specific recognition of the natural herbal extract of Stryphnodendron polyphyllum through STD NMR, hyphenations and docking simulation studies. RSC Adv 2015. [DOI: 10.1039/c5ra01457c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Over the last two decades, new and more advanced strategies that help in the rapid screening and identification of new ligands for a specific macromolecule have become an important domain.
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Affiliation(s)
- Sheraz A. K. Tanoli
- Laboratory of Nuclear Magnetic Resonance
- Department of Chemistry
- Federal University of São Carlos
- Brazil
| | - Nazish U. Tanoli
- Laboratory of Nuclear Magnetic Resonance
- Department of Chemistry
- Federal University of São Carlos
- Brazil
| | | | - Saman Usmani
- Dr. Panjwani Center for Molecular Medicine and Drug Research
- International Center for Chemical and Biological Sciences
- University of Karachi
- Karachi
- Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research
- International Center for Chemical and Biological Sciences
- University of Karachi
- Karachi
- Pakistan
| | | | - Sérgio S. Thomasi
- Laboratory of Nuclear Magnetic Resonance
- Department of Chemistry
- Federal University of São Carlos
- Brazil
| | - Antonio G. Ferreira
- Laboratory of Nuclear Magnetic Resonance
- Department of Chemistry
- Federal University of São Carlos
- Brazil
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