1
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Asadollahi K, Scott DJ, Gooley PR. NMR applications to GPCR recognition by peptide ligands. Curr Opin Pharmacol 2023; 70:102366. [PMID: 37003111 DOI: 10.1016/j.coph.2023.102366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 04/03/2023]
Abstract
Peptides form the largest group of ligands that modulate the activity of more than 120 different GPCRs. Among which linear disordered peptide ligands usually undergo significant conformational changes upon binding that is essential for receptor recognition and activation. Conformational selection and induced fit are the extreme mechanisms of coupled folding and binding that can be distinguished by analysis of binding pathways by methods that include NMR. However, the large size of GPCRs in membrane-mimetic environments limits NMR applications. In this review, we highlight advances in the field that can be adopted to address coupled folding and binding of peptide ligands to their cognate receptors.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Victoria, 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
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2
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Zhu L, Zhao H, Wang Y, Yu C, Liu J, Li L, Li Z, Zhang J, Dai H, Wang J, Zhu L. Solubilization, purification, and ligand binding characterization of G protein-coupled receptor SMO in native membrane bilayer using styrene maleic acid copolymer. PeerJ 2022; 10:e13381. [PMID: 35529497 PMCID: PMC9074879 DOI: 10.7717/peerj.13381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 01/13/2023] Open
Abstract
Smoothened (SMO) protein is a member of the G protein-coupled receptor (GPCR) family that is involved in the Hedgehog (Hh) signaling pathway. It is a putative target for treating various cancers, including medulloblastoma and basal cell carcinoma (BCC). Characterizing membrane proteins such as SMO in their native state is highly beneficial for the development of effective pharmaceutical drugs, as their structures and functions are retained to the highest extent in this state. Therefore, although SMO protein is conventionally solubilized in detergent micelles, incorporating the protein in a lipid-based membrane mimic is still required. In this study, we used styrene maleic acid (SMA) copolymer that directly extracted membrane protein and surrounding lipids as well as formed the so-called polymer nanodiscs, to solubilize and purify the SMO transmembrane domain encapsulated by SMA-nanodiscs. The obtained SMA-nanodiscs showed high homogeneity and maintained the physiological activity of SMO protein, thereby enabling the measurement of the dissociation constant (Kd) for SMO ligands SMO-ligands Shh Signaling Antagonist V (SANT-1) and Smoothened Agonist (SAG) using ligand-based solution nuclear magnetic resonance spectroscopy. This work paves the way for investigating the structure, function, and drug development of SMO proteins in a native-like lipid environment.
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Affiliation(s)
- Lina Zhu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China,High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongxin Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yizhuo Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Chuandi Yu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Juanjuan Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Ling Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Zehua Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Han Dai
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Junfeng Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China,High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,University of Science and Technology of China, Hefei, China
| | - Lei Zhu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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3
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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4
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Bous J, Orcel H, Floquet N, Leyrat C, Lai-Kee-Him J, Gaibelet G, Ancelin A, Saint-Paul J, Trapani S, Louet M, Sounier R, Déméné H, Granier S, Bron P, Mouillac B. Cryo-electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex. SCIENCE ADVANCES 2021; 7:7/21/eabg5628. [PMID: 34020960 PMCID: PMC8139594 DOI: 10.1126/sciadv.abg5628] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/01/2021] [Indexed: 05/08/2023]
Abstract
The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein-coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo-electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.
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Affiliation(s)
- Julien Bous
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Hélène Orcel
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Joséphine Lai-Kee-Him
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Gérald Gaibelet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Aurélie Ancelin
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Julie Saint-Paul
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Stefano Trapani
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Rémy Sounier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Hélène Déméné
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
| | - Patrick Bron
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France.
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
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5
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Vaid TM, Chalmers DK, Scott DJ, Gooley PR. INPHARMA-Based Determination of Ligand Binding Modes at α 1 -Adrenergic Receptors Explains the Molecular Basis of Subtype Selectivity. Chemistry 2020; 26:11796-11805. [PMID: 32291801 DOI: 10.1002/chem.202000642] [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: 02/06/2020] [Revised: 04/02/2020] [Indexed: 01/06/2023]
Abstract
The structural poses of ligands that bind weakly to protein receptors are challenging to define. In this work we have studied ligand interactions with the adrenoreceptor (AR) subtypes, α1A -AR and α1B -AR, which belong to the G protein-coupled receptor (GPCR) superfamily, by employing the solution-based ligand-observed NMR method interligand NOEs for pharmacophore mapping (INPHARMA). A lack of receptor crystal structures and of subtype-selective drugs has hindered the definition of the physiological roles of each subtype and limited drug development. We determined the binding pose of the weakly binding α1A -AR-selective agonist A-61603 relative to an endogenous agonist, epinephrine, at both α1A -AR and α1B -AR. The NMR experimental data were quantitatively compared, by using SpINPHARMA, to the back-calculated spectra based on ligand poses obtained from all-atom molecular dynamics simulations. The results helped mechanistically explain the selectivity of (R)-A-61603 towards α1A -AR, thus demonstrating an approach for targeting subtype selectivity in ARs.
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Affiliation(s)
- Tasneem M Vaid
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, VIC, Australia.,Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Parkville, 3010, VIC, Australia.,The Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, 3015, VIC, Australia
| | - David K Chalmers
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, VIC, Australia.,The Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, 3015, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, VIC, Australia.,Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Parkville, 3010, VIC, Australia
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6
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Bumbak F, Thomas T, Noonan-Williams BJ, Vaid TM, Yan F, Whitehead AR, Bruell S, Kocan M, Tan X, Johnson MA, Bathgate RAD, Chalmers DK, Gooley PR, Scott DJ. Conformational Changes in Tyrosine 11 of Neurotensin Are Required to Activate the Neurotensin Receptor 1. ACS Pharmacol Transl Sci 2020; 3:690-705. [PMID: 32832871 PMCID: PMC7432660 DOI: 10.1021/acsptsci.0c00026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 12/12/2022]
Abstract
Cell-cell communication via endogenous peptides and their receptors is vital for controlling all aspects of human physiology and most peptides signal through G protein-coupled receptors (GPCRs). Disordered peptides bind GPCRs through complex modes for which there are few representative crystal structures. The disordered peptide neurotensin (NT) is a neuromodulator of classical neurotransmitters such as dopamine and glutamate, through activation of neurotensin receptor 1 (NTS1). While several experimental structures show how NT binds NTS1, details about the structural dynamics of NT during and after binding NTS1, or the role of peptide dynamics on receptor activation, remain obscure. Here saturation transfer difference (STD) NMR revealed that the binding mode of NT fragment NT10-13 is heterogeneous. Epitope maps of NT10-13 at NTS1 suggested that tyrosine 11 (Y11) samples other conformations to those observed in crystal structures of NT-bound NTS1. Molecular dynamics (MD) simulations confirmed that when NT is bound to NTS1, residue Y11 can exist in two χ1 rotameric states, gauche plus (g+) or gauche minus (g-). Since only the g+ Y11 state is observed in all the structures solved to date, we asked if the g- state is important for receptor activation. NT analogues with Y11 replaced with 7-OH-Tic were synthesized to restrain the dynamics of the side chain. P(OH-TIC)IL bound NTS1 with the same affinity as NT10-13 but did not activate NTS1, instead acted as an antagonist. This study highlights that flexibility of Y11 in NT may be required for NT activation of NTS1.
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Affiliation(s)
- Fabian Bumbak
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Trayder Thomas
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Billy J. Noonan-Williams
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Tasneem M. Vaid
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Fei Yan
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alice R. Whitehead
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shoni Bruell
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Martina Kocan
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- The School
of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xuan Tan
- Department
of Chemistry, The University of Alabama
at Birmingham, Birmingham, Alabama 35294-1240, United States
| | - Margaret A. Johnson
- Department
of Chemistry, The University of Alabama
at Birmingham, Birmingham, Alabama 35294-1240, United States
| | - Ross A. D. Bathgate
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
| | - David K. Chalmers
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Paul R. Gooley
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Daniel J. Scott
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
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7
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Structural biology of human GPCR drugs and endogenous ligands - insights from NMR spectroscopy. Methods 2020; 180:79-88. [PMID: 32911074 DOI: 10.1016/j.ymeth.2020.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest class of "druggable" proteins in the human genome. For more than a decade, crystal structures and, more recently, cryoEM structures of GPCR complexes have provided unprecedented insight into GPCR drug binding and cell signaling. Nevertheless, structure determination of receptors in complexes with weakly binding molecules or complex polypeptides remains especially challenging, including for hormones, many of which have so far eluded researchers. Nuclear magnetic resonance (NMR) spectroscopy has emerged as a promising approach to determine structures of ligands bound to their receptors and to provide insights into the dynamics of GPCR-bound drugs. The capability to investigate compounds with weak binding affinities has also been leveraged in NMR applications to identify novel lead compounds in drug screening campaigns. We review recent structural biology studies of GPCR ligands by NMR, highlighting new methodologies enabling studies of GPCRs with native sequences and in native-like membrane environments that provide insights into important drugs and endogenous ligands.
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8
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Park SH, Lee JH. Dynamic G Protein-Coupled Receptor Signaling Probed by Solution NMR Spectroscopy. Biochemistry 2020; 59:1065-1080. [PMID: 32092261 DOI: 10.1021/acs.biochem.0c00032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating various dynamic features of G protein-coupled receptor (GPCR) signaling. In this Perspective, we focus on NMR techniques to characterize ligand-dependent conformational dynamics of GPCRs as well as the interaction of GPCRs with their environment and ligands. We also describe circumstances under which each technique should be applied, their advantages and disadvantages, and how they can be combined with other strategies to deepen the understanding of GPCR signaling at the molecular level.
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Affiliation(s)
- Sho Hee Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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9
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Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
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Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
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10
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NMR investigation of protein-ligand interactions for G-protein coupled receptors. Future Med Chem 2019; 11:1811-1825. [PMID: 31287732 DOI: 10.4155/fmc-2018-0312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this review, we report NMR studies of ligand-GPCR interactions, including both ligand-observed and protein-observed NMR experiments. Published studies exemplify how NMR can be used as a powerful tool to design novel GPCR ligands and investigate the ligand-induced conformational changes of GPCRs. The strength of NMR also lies in its capability to explore the diverse signaling pathways and probe the allosteric modulation of these highly dynamic receptors. By offering unique opportunities for the identification, structural and functional characterization of GPCR ligands, NMR will likely play a major role for the generation of novel molecules both as new tools for the understanding of the GPCR function and as therapeutic compounds for a large diversity of pathologies.
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11
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Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees. Sci Rep 2019; 9:7703. [PMID: 31118426 PMCID: PMC6531441 DOI: 10.1038/s41598-019-43125-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 04/12/2019] [Indexed: 02/08/2023] Open
Abstract
Identifying potential protein-ligand interactions is central to the field of drug discovery as it facilitates the identification of potential novel drug leads, contributes to advancement from hits to leads, predicts potential off-target explanations for side effects of approved drugs or candidates, as well as de-orphans phenotypic hits. For the rapid identification of protein-ligand interactions, we here present a novel chemogenomics algorithm for the prediction of protein-ligand interactions using a new machine learning approach and novel class of descriptor. The algorithm applies Bayesian Additive Regression Trees (BART) on a newly proposed proteochemical space, termed the bow-pharmacological space. The space spans three distinctive sub-spaces that cover the protein space, the ligand space, and the interaction space. Thereby, the model extends the scope of classical target prediction or chemogenomic modelling that relies on one or two of these subspaces. Our model demonstrated excellent prediction power, reaching accuracies of up to 94.5–98.4% when evaluated on four human target datasets constituting enzymes, nuclear receptors, ion channels, and G-protein-coupled receptors . BART provided a reliable probabilistic description of the likelihood of interaction between proteins and ligands, which can be used in the prioritization of assays to be performed in both discovery and vigilance phases of small molecule development.
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12
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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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13
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Igonet S, Raingeval C, Cecon E, Pučić-Baković M, Lauc G, Cala O, Baranowski M, Perez J, Jockers R, Krimm I, Jawhari A. Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor. Sci Rep 2018; 8:8142. [PMID: 29802269 PMCID: PMC5970182 DOI: 10.1038/s41598-018-26113-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Structural studies of integral membrane proteins have been limited by the intrinsic conformational flexibility and the need to stabilize the proteins in solution. Stabilization by mutagenesis was very successful for structural biology of G protein-coupled receptors (GPCRs). However, it requires heavy protein engineering and may introduce structural deviations. Here we describe the use of specific calixarenes-based detergents for native GPCR stabilization. Wild type, full length human adenosine A2A receptor was used to exemplify the approach. We could stabilize native, glycosylated, non-aggregated and homogenous A2AR that maintained its ligand binding capacity. The benefit of the preparation for fragment screening, using the Saturation-Transfer Difference nuclear magnetic resonance (STD-NMR) experiment is reported. The binding of the agonist adenosine and the antagonist caffeine were observed and competition experiments with CGS-21680 and ZM241385 were performed, demonstrating the feasibility of the STD-based fragment screening on the native A2A receptor. Interestingly, adenosine was shown to bind a second binding site in the presence of the agonist CGS-21680 which corroborates published results obtained with molecular dynamics simulation. Fragment-like compounds identified using STD-NMR showed antagonistic effects on A2AR in the cAMP cellular assay. Taken together, our study shows that stabilization of native GPCRs represents an attractive approach for STD-based fragment screening and drug design.
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Affiliation(s)
| | - Claire Raingeval
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | - Gordan Lauc
- GENOS, Borongajska cesta 83h, 10000, Zagreb, Croatia
| | - Olivier Cala
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Maciej Baranowski
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Javier Perez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Krimm
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Anass Jawhari
- CALIXAR, 60 avenue Rockefeller, 69008, Lyon, France.
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14
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Ángeles Canales M, Félix Espinosa J. Ligand-detected NMR Methods in Drug Discovery. BIOPHYSICAL TECHNIQUES IN DRUG DISCOVERY 2017. [DOI: 10.1039/9781788010016-00023] [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
This book chapter describes the basic principles of NMR-based techniques for detecting ligand binding and uses examples of the application of these techniques in drug discovery programs for screening, hit validation and optimization to illustrate their utility in characterizing ligand–protein interactions. The binding of small molecules to biological receptors can be observed directly by detecting changes in a particular NMR parameter when the protein is added to a sample containing the ligand, or indirectly, using a “spy” molecule in competitive NMR experiments. Combinations of different NMR experiments can be used to confirm binding and also to obtain structural information that can be used to guide medicinal chemistry decisions. Ligand-observed NMR methods are able to identify weak affinity ligands that cannot be detected by other biophysical techniques, which means that NMR-based methods are extremely valuable tools for fragment-based drug discovery approaches.
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Affiliation(s)
- María Ángeles Canales
- Department of Química Orgánica I, Universidad Complutense de Madrid Avd. Complutense s/n 28040 Madrid Spain
| | - Juan Félix Espinosa
- Centro de Investigación Lilly Avda. de la Industria 30 28108, Alcobendas, Madrid Spain
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15
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Fredriksson K, Lottmann P, Hinz S, Onila I, Shymanets A, Harteneck C, Müller CE, Griesinger C, Exner TE. Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kai Fredriksson
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
- Present address: Fakultät für Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
| | - Philip Lottmann
- Max Planck Institute for Biophysical Chemistry; Am Faßberg 11 37077 Göttingen Germany
| | - Sonja Hinz
- Universität Bonn; Pharma-Zentrum Bonn; Pharmazeutisches Institut; Pharmazeutische Chemie; An der Immenburg 4 53121 Bonn Germany
| | - Iounut Onila
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
| | - Aliaksei Shymanets
- Department of Pharmacology and Experimental Therapy; Institute of Experimental and Clinical Pharmacology and Toxicology; Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA); University of Tübingen; Tübingen Germany
| | - Christian Harteneck
- Department of Pharmacology and Experimental Therapy; Institute of Experimental and Clinical Pharmacology and Toxicology; Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA); University of Tübingen; Tübingen Germany
| | - Christa E. Müller
- Universität Bonn; Pharma-Zentrum Bonn; Pharmazeutisches Institut; Pharmazeutische Chemie; An der Immenburg 4 53121 Bonn Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry; Am Faßberg 11 37077 Göttingen Germany
| | - Thomas E. Exner
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
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16
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Fredriksson K, Lottmann P, Hinz S, Onila I, Shymanets A, Harteneck C, Müller CE, Griesinger C, Exner TE. Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor. Angew Chem Int Ed Engl 2017; 56:5750-5754. [PMID: 28429411 DOI: 10.1002/anie.201612547] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/09/2017] [Indexed: 11/11/2022]
Abstract
G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A2A R with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A2A R.
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Affiliation(s)
- Kai Fredriksson
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany.,Present address: Fakultät für Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Philip Lottmann
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Sonja Hinz
- Universität Bonn, Pharma-Zentrum Bonn, Pharmazeutisches Institut, Pharmazeutische Chemie, An der Immenburg 4, 53121, Bonn, Germany
| | - Iounut Onila
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany
| | - Aliaksei Shymanets
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Christian Harteneck
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Christa E Müller
- Universität Bonn, Pharma-Zentrum Bonn, Pharmazeutisches Institut, Pharmazeutische Chemie, An der Immenburg 4, 53121, Bonn, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Thomas E Exner
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany
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17
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Milligan G, Shimpukade B, Ulven T, Hudson BD. Complex Pharmacology of Free Fatty Acid Receptors. Chem Rev 2016; 117:67-110. [PMID: 27299848 DOI: 10.1021/acs.chemrev.6b00056] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G protein-coupled receptors (GPCRs) are historically the most successful family of drug targets. In recent times it has become clear that the pharmacology of these receptors is far more complex than previously imagined. Understanding of the pharmacological regulation of GPCRs now extends beyond simple competitive agonism or antagonism by ligands interacting with the orthosteric binding site of the receptor to incorporate concepts of allosteric agonism, allosteric modulation, signaling bias, constitutive activity, and inverse agonism. Herein, we consider how evolving concepts of GPCR pharmacology have shaped understanding of the complex pharmacology of receptors that recognize and are activated by nonesterified or "free" fatty acids (FFAs). The FFA family of receptors is a recently deorphanized set of GPCRs, the members of which are now receiving substantial interest as novel targets for the treatment of metabolic and inflammatory diseases. Further understanding of the complex pharmacology of these receptors will be critical to unlocking their ultimate therapeutic potential.
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Affiliation(s)
- Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, Scotland, United Kingdom
| | - Bharat Shimpukade
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
| | - Brian D Hudson
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, Scotland, United Kingdom
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18
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Aguirre C, Cala O, Krimm I. Overview of Probing Protein‐Ligand Interactions Using NMR. ACTA ACUST UNITED AC 2015; 81:17.18.1-17.18.24. [DOI: 10.1002/0471140864.ps1718s81] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Olivier Cala
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, UMR5280 CNRS, Ecole Nationale Supérieure de Lyon Villeurbanne France
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19
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Fruth M, Plaza A, Hinsberger S, Sahner JH, Haupenthal J, Bischoff M, Jansen R, Müller R, Hartmann RW. Binding mode characterization of novel RNA polymerase inhibitors using a combined biochemical and NMR approach. ACS Chem Biol 2014; 9:2656-63. [PMID: 25207839 DOI: 10.1021/cb5005433] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial RNA polymerase (RNAP) represents a validated target for the development of broad-spectrum antibiotics. However, the medical value of RNAP inhibitors in clinical use is limited by the prevalence of resistant strains. To overcome this problem, we focused on the exploration of alternative target sites within the RNAP. Previously, we described the discovery of a novel RNAP inhibitor class containing an ureidothiophene-2-carboxylic acid core structure. Herein, we demonstrate that these compounds are potent against a set of methicillin-resistant Staphylococcus aureus (MRSA) strains (MIC 2-16 μg mL(-1)) and rifampicin-resistant Escherichia coli TolC strains (MIC 12.5-50 μg mL(-1)). Additionally, an abortive transcription assay revealed that these compounds inhibit the bacterial transcription process during the initiation phase. Furthermore, the binding mode of the ureidothiophene-2-carboxylic acids was characterized by mutagenesis studies and ligand-based NMR spectroscopy. Competition saturation transfer difference (STD) NMR experiments with the described RNAP inhibitor myxopyronin A (Myx) suggest that the ureidothiophene-2-carboxylic acids compete with Myx for the same binding site in the RNAP switch region. INPHARMA (interligand NOE for pharmacophore mapping) experiments and molecular docking simulations provided a binding model in which the ureidothiophene-2-carboxylic acids occupy the region of the Myx western chain binding site and slightly occlude that of the eastern chain. These results demonstrate that the ureidothiophene-2-carboxylic acids are a highly attractive new class of RNAP inhibitors that can avoid the problem of resistance.
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Affiliation(s)
| | | | | | | | | | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, 66421 Homburg/Saar, Germany
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | | | - Rolf W. Hartmann
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C23, 66123 Saarbrücken, Germany
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20
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Joseph-McCarthy D, Campbell AJ, Kern G, Moustakas D. Fragment-Based Lead Discovery and Design. J Chem Inf Model 2014; 54:693-704. [DOI: 10.1021/ci400731w] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Diane Joseph-McCarthy
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Arthur J. Campbell
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gunther Kern
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Demetri Moustakas
- Infection Innovative Medicines Unit, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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21
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Hudson BD, Shimpukade B, Mackenzie AE, Butcher AJ, Pediani JD, Christiansen E, Heathcote H, Tobin AB, Ulven T, Milligan G. The pharmacology of TUG-891, a potent and selective agonist of the free fatty acid receptor 4 (FFA4/GPR120), demonstrates both potential opportunity and possible challenges to therapeutic agonism. Mol Pharmacol 2013; 84:710-25. [PMID: 23979972 DOI: 10.1124/mol.113.087783] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
TUG-891 [3-(4-((4-fluoro-4'-methyl-[1,1'-biphenyl]-2-yl)methoxy)phenyl)propanoic acid] was recently described as a potent and selective agonist for the long chain free fatty acid (LCFA) receptor 4 (FFA4; previously G protein-coupled receptor 120, or GPR120). Herein, we have used TUG-891 to further define the function of FFA4 and used this compound in proof of principle studies to indicate the therapeutic potential of this receptor. TUG-891 displayed similar signaling properties to the LCFA α-linolenic acid at human FFA4 across various assay end points, including stimulation of Ca²⁺ mobilization, β-arrestin-1 and β-arrestin-2 recruitment, and extracellular signal-regulated kinase phosphorylation. Activation of human FFA4 by TUG-891 also resulted in rapid phosphorylation and internalization of the receptor. While these latter events were associated with desensitization of the FFA4 signaling response, removal of TUG-891 allowed both rapid recycling of FFA4 back to the cell surface and resensitization of the FFA4 Ca²⁺ signaling response. TUG-891 was also a potent agonist of mouse FFA4, but it showed only limited selectivity over mouse FFA1, complicating its use in vivo in this species. Pharmacologic dissection of responses to TUG-891 in model murine cell systems indicated that activation of FFA4 was able to mimic many potentially beneficial therapeutic properties previously reported for LCFAs, including stimulating glucagon-like peptide-1 secretion from enteroendocrine cells, enhancing glucose uptake in 3T3-L1 adipocytes, and inhibiting release of proinflammatory mediators from RAW264.7 macrophages, which suggests promise for FFA4 as a therapeutic target for type 2 diabetes and obesity. Together, these results demonstrate both potential but also significant challenges that still need to be overcome to therapeutically target FFA4.
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Affiliation(s)
- Brian D Hudson
- Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom (B.D.H., A.E.M., J.D.P., H.H., G.M.); Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark (B.S., E.C., T.U.); and MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom (A.J.B., A.B.T.)
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22
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NMR-based analysis of protein-ligand interactions. Anal Bioanal Chem 2013; 406:943-56. [PMID: 23591643 DOI: 10.1007/s00216-013-6931-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
Abstract
Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.
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23
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Holdgate G, Geschwindner S, Breeze A, Davies G, Colclough N, Temesi D, Ward L. Biophysical methods in drug discovery from small molecule to pharmaceutical. Methods Mol Biol 2013; 1008:327-355. [PMID: 23729258 DOI: 10.1007/978-1-62703-398-5_12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biophysical methods have become established in many areas of drug discovery. Application of these methods was once restricted to a relatively small number of scientists using specialized, low throughput technologies and methods. Now, automated high-throughput instruments are to be found in a growing number of laboratories. Many biophysical methods are capable of measuring the equilibrium binding constants between pairs of molecules crucial for molecular recognition processes, encompassing protein-protein, protein-small molecule, and protein-nucleic acid interactions, and several can be used to measure the kinetic or thermodynamic components controlling these biological processes. For a full characterization of a binding process, determinations of stoichiometry, binding mode, and any conformational changes associated with such interactions are also required. The suite of biophysical methods that are now available represents a powerful toolbox of techniques which can effectively deliver this full characterization.The aim of this chapter is to provide the reader with an overview of the drug discovery process and how biophysical methods, such as surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), nuclear magnetic resonance, mass spectrometry (MS), and thermal unfolding methods can answer specific questions in order to influence project progression and outcomes. The selection of these examples is based upon the experiences of the authors at AstraZeneca, and relevant approaches are highlighted where they have utility in a particular drug discovery scenario.
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24
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Abstract
Nuclear magnetic resonance (NMR) is well suited to probing the interactions between ligands and macromolecular receptors. It is a truly label-free technique, requiring only the presence of atoms (usually (1)H or (19)F) which give rise to observable resonances on either the ligand or the receptor. A number of parameters associated with these resonances can be used to distinguish rapidly tumbling compounds from ligands which bind to a macromolecular receptor. As such, NMR reports directly on the molecular components involved in the binding interaction whilst avoiding artifacts arising from the addition of an observable label. NMR is also unique amongst biophysical techniques in giving information on the chemical nature of almost all of the constituents present in the sample, thus allowing ready identification of sample, contaminants, degraded material and buffers. Solution phase NMR is also free of artifacts introduced by the presence of a solid support or matrix, although some interesting NMR techniques have been developed to identify ligand-receptor interactions in both solid and heterogeneous phase systems.NMR can readily report on molecular interactions across a wide range of affinities and timescales. Although NMR is not an inherently sensitive technique, the development of cryogenic probeheads over the past decade has dramatically increased the range of applicability of the technique and reduced the stringent sample requirements that used to be regarded as an "Achilles' heel" of NMR. The last, but by no means the least, NMR has the ability to determine structural information at atomic resolution; this has proved to be particularly useful when applied to those protein-ligand systems which cannot be readily crystallized.
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Affiliation(s)
- Ben Davis
- Vernalis Ltd (R&D), Great Abington, Cambridge, UK
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25
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Abstract
Drug discovery on membrane proteins is still a difficult task, despite the recognized importance of membrane proteins as drug targets. Here, we present an overview of NMR methods available for structure-based drug design on membrane proteins. NMR spectroscopy is capable of identifying potential binders in screening and defining their relative binding constants, binding stoichiometry, conformation in the binding pocket and the relative binding orientation for binders of different series. Examples are given in the review highlighting the potential of NMR spectroscopy for future progress in drug discovery on membrane proteins.
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26
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Lee Y, Zeng H, Mazur A, Wegstroth M, Carlomagno T, Reese M, Lee D, Becker S, Griesinger C, Hilty C. Hyperpolarized binding pocket nuclear Overhauser effect for determination of competitive ligand binding. Angew Chem Int Ed Engl 2012; 51:5179-82. [PMID: 22499357 DOI: 10.1002/anie.201201003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Youngbok Lee
- Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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27
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Lee Y, Zeng H, Mazur A, Wegstroth M, Carlomagno T, Reese M, Lee D, Becker S, Griesinger C, Hilty C. Hyperpolarized Binding Pocket Nuclear Overhauser Effect for Determination of Competitive Ligand Binding. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
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29
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G-protein coupled receptor and kinase targets: advances in drug discovery from molecular to clinical. Future Med Chem 2012; 3:1097-100. [PMID: 21806373 DOI: 10.4155/fmc.11.78] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The conference was organized by Visiongain and focused on a number of industrially relevant advances in G-protein coupled receptor and kinase research. Commercial stands were provided by Genscript (Bioassays), Merck Millipore (profiling services), Schrödinger (modeling) and Corning (assay development). The overall attendance was approximately 40 delegates taking part in four sessions over the two days.
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30
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Smith NJ. Low affinity GPCRs for metabolic intermediates: challenges for pharmacologists. Front Endocrinol (Lausanne) 2012; 3:1. [PMID: 22649402 PMCID: PMC3355937 DOI: 10.3389/fendo.2012.00001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/03/2012] [Indexed: 12/22/2022] Open
Abstract
The discovery that a number of metabolites and metabolic intermediates can act through G protein-coupled receptors has attracted great interest in the field and has led to new therapeutic targets for diseases such as hypertension, type 2 diabetes, inflammation, and metabolic syndrome. However, the low apparent affinity of these ligands for their cognate receptors poses a number of challenges for pharmacologists interested in investigating receptor structure, function or physiology. Furthermore, the endogenous ligands matched to their receptors have other, well established metabolic roles and thus selectivity is difficult to achieve. This review discusses some of the issues researchers face when working with these receptors and highlights the ways in which a number of these obstacles have been overcome.
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Affiliation(s)
- Nicola J Smith
- Molecular Cardiology, Victor Chang Cardiac Research Institute Darlinghurst, NSW, Australia.
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31
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Krimm I. INPHARMA-based identification of ligand binding site in fragment-based drug design. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20035j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Orts J, Bartoschek S, Griesinger C, Monecke P, Carlomagno T. An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude. JOURNAL OF BIOMOLECULAR NMR 2012; 52:23-30. [PMID: 22167466 PMCID: PMC3266494 DOI: 10.1007/s10858-011-9590-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/25/2011] [Indexed: 05/31/2023]
Abstract
Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs are efficiently used to filter and rank complex model structures that have been pre-selected by docking protocols. This approach dramatically reduces the degeneracy and inaccuracy of the chosen model in docking experiments, is robust with respect to inaccuracy of the structural model used to represent the free receptor and is suitable for high-throughput docking campaigns.
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Affiliation(s)
- Julien Orts
- EMBL, Structure and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stefan Bartoschek
- Sanofi-Aventis Deutschland GmbH, R&D LGCR/Parallel Synthesis & Natural Products, Industriepark Hoechst, Bldg. H811, 65926 Frankfurt am Main, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Peter Monecke
- Sanofi-Aventis Deutschland GmbH, R&D LGCR/Structure, Design & Informatics, Industriepark Hoechst, Bldg. G838, 65926 Frankfurt am Main, Germany
| | - Teresa Carlomagno
- EMBL, Structure and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Congreve M, Langmead CJ, Mason JS, Marshall FH. Progress in structure based drug design for G protein-coupled receptors. J Med Chem 2011; 54:4283-311. [PMID: 21615150 PMCID: PMC3308205 DOI: 10.1021/jm200371q] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 12/12/2022]
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, BioPark, Welwyn Garden City, Hertfordshire, UK.
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Holliday ND, Watson SJ, Brown AJH. Drug discovery opportunities and challenges at g protein coupled receptors for long chain free Fatty acids. Front Endocrinol (Lausanne) 2011; 2:112. [PMID: 22649399 PMCID: PMC3355945 DOI: 10.3389/fendo.2011.00112] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 12/15/2011] [Indexed: 01/13/2023] Open
Abstract
Discovery of G protein coupled receptors for long chain free fatty acids (FFAs), FFA1 (GPR40) and GPR120, has expanded our understanding of these nutrients as signaling molecules. These receptors have emerged as important sensors for FFA levels in the circulation or the gut lumen, based on evidence from in vitro and rodent models, and an increasing number of human studies. Here we consider their promise as therapeutic targets for metabolic disease, including type 2 diabetes and obesity. FFA1 directly mediates acute FFA-induced glucose-stimulated insulin secretion in pancreatic beta-cells, while GPR120 and FFA1 trigger release of incretins from intestinal endocrine cells, and so indirectly enhance insulin secretion and promote satiety. GPR120 signaling in adipocytes and macrophages also results in insulin sensitizing and beneficial anti-inflammatory effects. Drug discovery has focused on agonists to replicate acute benefits of FFA receptor signaling, with promising early results for FFA1 agonists in man. Controversy surrounding chronic effects of FFA1 on beta-cells illustrates that long term benefits of antagonists also need exploring. It has proved challenging to generate highly selective potent ligands for FFA1 or GPR120 subtypes, given that both receptors have hydrophobic orthosteric binding sites, which are not completely defined and have modest ligand affinity. Structure activity relationships are also reliant on functional read outs, in the absence of robust binding assays to provide direct affinity estimates. Nevertheless synthetic ligands have already helped dissect specific contributions of FFA1 and GPR120 signaling from the many possible cellular effects of FFAs. Approaches including use of fluorescent ligand binding assays, and targeting allosteric receptor sites, may improve further pre-clinical ligand development at these receptors, to exploit their unique potential to target multiple facets of diabetes.
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Affiliation(s)
- Nicholas D. Holliday
- Cell Signalling Research Group, School of Biomedical Sciences, The Medical School, Queen’s Medical Centre, University of NottinghamNottingham, UK
- *Correspondence: Nicholas D. Holliday, Cell Signalling Research Group, School of Biomedical Sciences, The Medical School, Queen’s Medical Centre, University of Nottingham, Floor C, Nottingham NG7 2UH, UK. e-mail:
| | - Sarah-Jane Watson
- Cell Signalling Research Group, School of Biomedical Sciences, The Medical School, Queen’s Medical Centre, University of NottinghamNottingham, UK
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Hudson B, Smith NJ, Milligan G. Experimental Challenges to Targeting Poorly Characterized GPCRs: Uncovering the Therapeutic Potential for Free Fatty Acid Receptors. PHARMACOLOGY OF G PROTEIN COUPLED RECEPTORS 2011; 62:175-218. [DOI: 10.1016/b978-0-12-385952-5.00006-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Abstract
G protein-coupled receptors (GPCRs) comprise a large class of transmembrane proteins that play critical roles in both normal physiology and pathophysiology. These critical roles offer targets for therapeutic intervention, as exemplified by the substantial fraction of current pharmaceutical agents that target members of this family. Tremendous contributions to our understanding of GPCR structure and dynamics have come from both indirect and direct structural characterization techniques. Key features of GPCR conformations derived from both types of characterization techniques are reviewed.
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Affiliation(s)
- Abby L. Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN 38152, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-901-678-2638; Fax: +1-901-678-3447
| | - Debra L. Bautista
- Christian Brothers High School, 5900 Walnut Grove Road, Memphis, TN 38120, USA; E-Mail: (D.L.B.)
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