1
|
Toyama Y, Shimada I. Quantitative analysis of the slow exchange process by 19F NMR in the presence of scalar and dipolar couplings: applications to the ribose 2'- 19F probe in nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00446-7. [PMID: 38918317 DOI: 10.1007/s10858-024-00446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Solution NMR spectroscopy is a particularly powerful technique for characterizing the functional dynamics of biomolecules, which is typically achieved through the quantitative characterization of chemical exchange processes via the measurement of spin relaxation rates. In addition to the conventional nuclei such as 15N and 13C, which are abundant in biomolecules, fluorine-19 (19F) has recently garnered attention and is being widely used as a site-specific spin probe. While 19F offers the advantages of high sensitivity and low background, it can be susceptible to artifacts in quantitative relaxation analyses due to a multitude of dipolar and scalar coupling interactions with nearby 1H spins. In this study, we focused on the ribose 2'-19F spin probe in nucleic acids and investigated the effects of 1H-19F spin interactions on the quantitative characterization of slow exchange processes on the millisecond time scale. We demonstrated that the 1H-19F dipolar coupling can significantly affect the interpretation of 19F chemical exchange saturation transfer (CEST) experiments when 1H decoupling is applied, while the 1H-19F interactions have a lesser impact on Carr-Purcell-Meiboom-Gill relaxation dispersion applications. We also proposed a modified CEST scheme to alleviate these artifacts along with experimental verifications on self-complementary RNA systems. The theoretical framework presented in this study can be widely applied to various 19F spin systems where 1H-19F interactions are operative, further expanding the utility of 19F relaxation-based NMR experiments.
Collapse
Affiliation(s)
- Yuki Toyama
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima, 739-8528, Japan.
| |
Collapse
|
2
|
Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O. Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM. J Am Chem Soc 2023; 145:8583-8592. [PMID: 37023263 PMCID: PMC10119980 DOI: 10.1021/jacs.3c01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/08/2023]
Abstract
Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) 19F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, 19F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification.
Collapse
Affiliation(s)
- Yun Huang
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Krishna D. Reddy
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Clay Bracken
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Biao Qiu
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Wenhu Zhan
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - David Eliezer
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Olga Boudker
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| |
Collapse
|
3
|
Tang H, Wang L, Li S, Wei X, Lv M, Zhong F, Liu Y, Liu J, Fu B, Zhu Q, Wang D, Liu J, Ruan K, Gao J, Xu W. Inhibitors against Two PDZ Domains of MDA-9 Suppressed Migration of Breast Cancer Cells. Int J Mol Sci 2023; 24:ijms24043431. [PMID: 36834839 PMCID: PMC9964117 DOI: 10.3390/ijms24043431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Melanoma differentiation-associated gene 9 (MDA-9) is a small adaptor protein with tandem PDZ domains that promotes tumor progression and metastasis in various human cancers. However, it is difficult to develop drug-like small molecules with high affinity due to the narrow groove of the PDZ domains of MDA-9. Herein, we identified four novel hits targeting the PDZ1 and PDZ2 domains of MDA-9, namely PI1A, PI1B, PI2A, and PI2B, using a protein-observed nuclear magnetic resonance (NMR) fragment screening method. We also solved the crystal structure of the MDA-9 PDZ1 domain in complex with PI1B and characterized the binding poses of PDZ1-PI1A and PDZ2-PI2A, guided by transferred paramagnetic relaxation enhancement. The protein-ligand interaction modes were then cross-validated by the mutagenesis of the MDA-9 PDZ domains. Competitive fluorescence polarization experiments demonstrated that PI1A and PI2A blocked the binding of natural substrates to the PDZ1 and PDZ2 domains, respectively. Furthermore, these inhibitors exhibited low cellular toxicity, but suppressed the migration of MDA-MB-231 breast carcinoma cells, which recapitulated the phenotype of MDA-9 knockdown. Our work has paved the way for the development of potent inhibitors using structure-guided fragment ligation in the future.
Collapse
Affiliation(s)
- Heng Tang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lei Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Shuju Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaoli Wei
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Mengqi Lv
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Fumei Zhong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yaqian Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bangguo Fu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qizhi Zhu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Dan Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jiajia Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Ke Ruan
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jia Gao
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Correspondence: (J.G.); (W.X.)
| | - Weiping Xu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Correspondence: (J.G.); (W.X.)
| |
Collapse
|
4
|
Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
Collapse
Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| |
Collapse
|
5
|
Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
Collapse
Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| |
Collapse
|
6
|
Cui CY, Li B, Cheng D, Li XY, Chen JL, Chen YT, Su XC. Simultaneous Quantification of Biothiols and Deciphering Diverse GSH Stability in Different Live Cells by 19F-Tag. Anal Chem 2021; 94:901-908. [PMID: 34958555 DOI: 10.1021/acs.analchem.1c03673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
GSH, Cys, Hcy, and H2S are important biothiols and play important roles in the living systems. Quantitative and simultaneous determination of these biothiols under physiological conditions is still a challenge. Herein, we developed an effective 19F-reactive tag that readily interacts with these four biothiols for the generation of stable thioether products that have distinguishable 19F-chemical shifts. These thioester compounds encode the characteristic fingerprint profiles of each biothiols, allowing one to simultaneously quantify and determine these biothiols by 1D 19F NMR spectroscopy. The intra-/extracellular GSH in live cells was assessed by the established strategy, and remarkable variations in the GSH stability were determined between the normal mammalian cells and cancer cells. It is notable that GSH hydrolyzes efficiently in the out-membrane of the cancer cells and the lysates. In contrast, GSH remains stable in the tested normal cells.
Collapse
Affiliation(s)
- Chao-Yu Cui
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dan Cheng
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xia-Yan Li
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ya-Ting Chen
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| |
Collapse
|
7
|
Vogel R, Müntener T, Häussinger D. Intrinsic anisotropy parameters of a series of lanthanoid complexes deliver new insights into the structure-magnetism relationship. Chem 2021. [DOI: 10.1016/j.chempr.2021.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
8
|
Chen JL, Chen BG, Li B, Yang F, Su XC. Assessing multiple conformations of lanthanide binding tags for proteins using a sensitive 19F-reporter. Chem Commun (Camb) 2021; 57:4291-4294. [PMID: 33913982 DOI: 10.1039/d1cc00791b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantifying the isomeric species of metal complexes in solution is difficult. 19F NMR herein was used to determine the abundance of isomeric species and dynamic properties of lanthanide binding tags. The results suggest that 19F is an efficient reporter in assessing and screening paramagnetic tags suitable for protein NMR analysis.
Collapse
Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Ben-Guang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| |
Collapse
|
9
|
Gao J, Zhang L, Liu X, Li F, Ma R, Zhu Z, Zhang J, Wu J, Shi Y, Pan Y, Ge Y, Ruan K. Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2. J Phys Chem Lett 2020; 11:7267-7272. [PMID: 32787337 PMCID: PMC7441750 DOI: 10.1021/acs.jpclett.0c01894] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/28/2020] [Indexed: 05/11/2023]
Abstract
The coronavirus disease pandemic caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected the global healthcare system. As low-molecular-weight drugs have high potential to completely match interactions with essential SARS-CoV-2 targets, we propose a strategy to identify such drugs using the fragment-based approach. Herein, using ligand- and protein-observed fragment screening approaches, we identified niacin and hit 1 binding to the catalytic pocket of the main protease (Mpro) of SARS-CoV-2, thereby modestly inhibiting the enzymatic activity of Mpro. We further searched for low-molecular-weight drugs containing niacin or hit 1 pharmacophores with enhanced inhibiting activity, e.g., carmofur, bendamustine, triclabendazole, emedastine, and omeprazole, in which omeprazole is the only one binding to the C-terminal domain of SARS-CoV-2 Mpro. Our study demonstrates that the fragment-based approach is a feasible strategy for identifying low-molecular-weight drugs against the SARS-CoV-2 and other potential targets lacking specific drugs.
Collapse
Affiliation(s)
- Jia Gao
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Liang Zhang
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Xiaodan Liu
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Fudong Li
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Rongsheng Ma
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Zhongliang Zhu
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Jihui Wu
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Yunyu Shi
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Yueyin Pan
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Yushu Ge
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| | - Ke Ruan
- Ministry of Education Key Laboratory for Membrane-less
Organelles & Cellular Dynamics, Hefei National Laboratory for
Physical Sciences at the Microscale, Division of Life Sciences and
Medicine, University of Science and Technology of
China, Huangshan Road, Hefei, Anhui 230027,
P.R. China
| |
Collapse
|
10
|
Softley CA, Bostock MJ, Popowicz GM, Sattler M. Paramagnetic NMR in drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:287-309. [PMID: 32524233 PMCID: PMC7311382 DOI: 10.1007/s10858-020-00322-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/26/2020] [Indexed: 05/05/2023]
Abstract
The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.
Collapse
Affiliation(s)
- Charlotte A Softley
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| |
Collapse
|
11
|
Arthanari H, Takeuchi K, Dubey A, Wagner G. Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins. Curr Opin Struct Biol 2019; 58:294-304. [PMID: 31327528 PMCID: PMC6778509 DOI: 10.1016/j.sbi.2019.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
The first recognition of protein breathing was more than 50 years ago. Today, we are able to detect the multitude of interaction modes, structural polymorphisms, and binding-induced changes in protein structure that direct function. Solution-state NMR spectroscopy has proved to be a powerful technique, not only to obtain high-resolution structures of proteins, but also to provide unique insights into the functional dynamics of proteins. Here, we summarize recent technical landmarks in solution NMR that have enabled characterization of key biological macromolecular systems. These methods have been fundamental to atomic resolution structure determination and quantitative analysis of dynamics over a wide range of time scales by NMR. The ability of NMR to detect lowly populated protein conformations and transiently formed complexes plays a critical role in its ability to elucidate functionally important structural features of proteins and their dynamics.
Collapse
Affiliation(s)
- Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 135-0064 Tokyo, Japan.
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| |
Collapse
|
12
|
Joss D, Häussinger D. Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:284-312. [PMID: 31779884 DOI: 10.1016/j.pnmrs.2019.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 05/14/2023]
Abstract
In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, CB-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.
Collapse
Affiliation(s)
- Daniel Joss
- University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
| | | |
Collapse
|
13
|
Zimmermann K, Joss D, Müntener T, Nogueira ES, Schäfer M, Knörr L, Monnard FW, Häussinger D. Localization of ligands within human carbonic anhydrase II using 19F pseudocontact shift analysis. Chem Sci 2019; 10:5064-5072. [PMID: 31183057 PMCID: PMC6530540 DOI: 10.1039/c8sc05683h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/09/2019] [Indexed: 12/17/2022] Open
Abstract
Unraveling the native structure of protein-ligand complexes in solution enables rational drug design. We report here the use of 19F pseudocontact shift (PCS) NMR as a method to determine fluorine positions of high affinity ligands bound within the drug target human carbonic anhydrase II with high accuracy. Three different ligands were localized within the protein by analysis of the obtained PCS from simple one-dimensional 19F spectra with an accuracy of up to 0.8 Å. In order to validate the PCS, four to five independent magnetic susceptibility tensors induced by lanthanide chelating tags bound site-specifically to single cysteine mutants were refined. Least-squares minimization and a Monte-Carlo approach allowed the assessment of experimental errors on the intersection of the corresponding four to five PCS isosurfaces. By defining an angle score that reflects the relative isosurface orientation for different tensor combinations, it was established that the ligand can be localized accurately using only three tensors, if the isosurfaces are close to orthogonal. For two out of three ligands, the determined position closely matched the X-ray coordinates. Our results for the third ligand suggest, in accordance with previously reported ab initio calculations, a rotated position for the difluorophenyl substituent, enabling a favorable interaction with Phe-131. The lanthanide-fluorine distance varied between 22 and 38 Å and induced 19F PCS ranged from 0.078 to 0.409 ppm, averaging to 0.213 ppm. Accordingly, even longer metal-fluorine distances will lead to meaningful PCS, rendering the investigation of protein-ligand complexes significantly larger than 30 kDa feasible.
Collapse
Affiliation(s)
- Kaspar Zimmermann
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Daniel Joss
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Thomas Müntener
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Elisa S Nogueira
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Marc Schäfer
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Livia Knörr
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Fabien W Monnard
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| |
Collapse
|
14
|
Di Pietrantonio C, Pandey A, Gould J, Hasabnis A, Prosser RS. Understanding Protein Function Through an Ensemble Description: Characterization of Functional States by 19F NMR. Methods Enzymol 2019; 615:103-130. [DOI: 10.1016/bs.mie.2018.09.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
15
|
Abstract
GEST NMR provides dynamic information on host–guest systems. It allows signal amplification of low concentrated complexes, detection of intermolecular interactions and quantification of guest exchange rates.
Collapse
Affiliation(s)
- Liat Avram
- Faculty of Chemistry
- Weizmann Institute of Science
- 7610001 Rehovot
- Israel
| | - Amnon Bar-Shir
- Faculty of Chemistry
- Weizmann Institute of Science
- 7610001 Rehovot
- Israel
| |
Collapse
|
16
|
Liu XH, Wang T, Lin JP, Wu MB. Using virtual reality for drug discovery: a promising new outlet for novel leads. Expert Opin Drug Discov 2018; 13:1103-1114. [PMID: 30457399 DOI: 10.1080/17460441.2018.1546286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Introduction: Virtual reality (VR) environments are increasingly being used by researchers in various fields in addition to being increasingly integrated into various areas of human life, ranging from videogames to different industrial uses. VR can be used to create interactive and multimodal sensory stimuli and thus offers unique advantages over other computer-based approaches for scientific research and molecular-level applications. Consequently, VR is starting to be used in novel drug development, such as in drug discovery, and rational drug design. Areas covered: In this review, the authors discuss the basic development of VR technology, including the available hardware and software. The latest advances of VR technology in novel drug development are then detailed, and the VR programs that can be applied in relevant studies are highlighted. Expert opinion: VR will lead to a revolution in pharmaceutical development. However, there are still obstacles to the successful and extensive application of VR to drug development, including the demand for further improvements to the available hardware and software and the various limitations described with regard to accuracy and precision. As technology continues to improve, the barriers to the widespread adoption of VR will diminish and VR technologies will play an increasingly important role in novel drug development.
Collapse
Affiliation(s)
- Xiao-Huan Liu
- a School of Biological Science , Jining Medical University , Jining , China
| | - Tao Wang
- a School of Biological Science , Jining Medical University , Jining , China.,b Key Laboratory of Biomass Chemical Engineering of Ministry of Education , College of Chemical and Biological Engineering, Zhejiang University , Hangzhou , China
| | - Jian-Ping Lin
- b Key Laboratory of Biomass Chemical Engineering of Ministry of Education , College of Chemical and Biological Engineering, Zhejiang University , Hangzhou , China
| | - Mian-Bin Wu
- b Key Laboratory of Biomass Chemical Engineering of Ministry of Education , College of Chemical and Biological Engineering, Zhejiang University , Hangzhou , China.,c Zhejiang Key Laboratory of Antifungal Drugs , Taizhou , China
| |
Collapse
|
17
|
Xu D, Li B, Gao J, Liu Z, Niu X, Nshogoza G, Zhang J, Wu J, Su XC, He W, Ma R, Yang D, Ruan K. Ligand Proton Pseudocontact Shifts Determined from Paramagnetic Relaxation Dispersion in the Limit of NMR Intermediate Exchange. J Phys Chem Lett 2018; 9:3361-3367. [PMID: 29864276 DOI: 10.1021/acs.jpclett.8b01443] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Delineation of protein-ligand interaction modes is key for rational drug discovery. The availability of complex crystal structures is often limited by the aqueous solubility of the compounds, while lead-like compounds with micromolar affinities normally fall into the NMR intermediate exchange regime, in which severe line broadening to beyond the detection of interfacial resonances limits NMR applications. Here, we developed a new method to retrieve low-populated bound-state 1H pseudocontact shifts (PCSs) using paramagnetic relaxation dispersion (RD). We evaluated using a 1H PCS-RD approach in a BRM bromodomain lead-like inhibitor to filter molecular docking poses using multiple intermolecular structural restraints. Considering the universal presence of proton atoms in druglike compounds, our work will have wide application in structure-guided drug discovery even under an extreme condition of NMR intermediate exchange and low aqueous solubility of ligands.
Collapse
Affiliation(s)
- Difei Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Bin Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Jia Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
- Center of Medical Physics and Technology, Hefei Institute of Physical Science , Cancer Hospital Chinese Academy of Science , Hefei , Anhui 230031 , PR China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai , 201210 , PR China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , PR China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin , 300071 , PR China
| | - Wei He
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Daiwen Yang
- Department of Biological Sciences , National University of Singapore , Singapore , 117543 , Singapore
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| |
Collapse
|
18
|
Paramagnetic NMR as a new tool in structural biology. Emerg Top Life Sci 2018; 2:19-28. [DOI: 10.1042/etls20170084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022]
Abstract
NMR (nuclear magnetic resonance) investigation through the exploitation of paramagnetic effects is passing from an approach limited to few specialists in the field to a generally applicable method that must be considered, especially for the characterization of systems hardly affordable with other techniques. This is mostly due to the fact that paramagnetic data are long range in nature, thus providing information for the structural and dynamic characterization of complex biomolecular architectures in their native environment. On the other hand, this information usually needs to be complemented by data from other sources. Integration of paramagnetic NMR with other techniques, and the development of protocols for a joint analysis of all available data, is fundamental for achieving a comprehensive characterization of complex biological systems. We describe here a few examples of the new possibilities offered by paramagnetic data used in integrated structural approaches.
Collapse
|