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Vu O, Bender BJ, Pankewitz L, Huster D, Beck-Sickinger AG, Meiler J. The Structural Basis of Peptide Binding at Class A G Protein-Coupled Receptors. Molecules 2021; 27:molecules27010210. [PMID: 35011444 PMCID: PMC8746363 DOI: 10.3390/molecules27010210] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/16/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest membrane protein family and a significant target class for therapeutics. Receptors from GPCRs’ largest class, class A, influence virtually every aspect of human physiology. About 45% of the members of this family endogenously bind flexible peptides or peptides segments within larger protein ligands. While many of these peptides have been structurally characterized in their solution state, the few studies of peptides in their receptor-bound state suggest that these peptides interact with a shared set of residues and undergo significant conformational changes. For the purpose of understanding binding dynamics and the development of peptidomimetic drug compounds, further studies should investigate the peptide ligands that are complexed to their cognate receptor.
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Affiliation(s)
- Oanh Vu
- Deparment of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
| | - Brian Joseph Bender
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Lisa Pankewitz
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstr. 16–18, D-04107 Leipzig, Germany;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany;
| | - Jens Meiler
- Deparment of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Leipzig University Medical Center, Institute for Drug Discovery, Departments of Chemistry and Computer Science, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
- Correspondence:
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Bender BJ, Marlow B, Meiler J. Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs. PLoS Comput Biol 2020; 16:e1007597. [PMID: 33112852 PMCID: PMC7652349 DOI: 10.1371/journal.pcbi.1007597] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 11/09/2020] [Accepted: 08/11/2020] [Indexed: 01/16/2023] Open
Abstract
As sequencing methodologies continue to advance, the availability of protein sequences far outpaces the ability of structure determination. Homology modeling is used to bridge this gap but relies on high-identity templates for accurate model building. G-protein coupled receptors (GPCRs) represent a significant target class for pharmaceutical therapies in which homology modeling could fill the knowledge gap for structure-based drug design. To date, only about 17% of druggable GPCRs have had their structures characterized at atomic resolution. However, modeling of the remaining 83% is hindered by the low sequence identity between receptors. Here we test key inputs in the model building process using GPCRs as a focus to improve the pipeline in two critical ways: Firstly, we use a blended sequence- and structure-based alignment that accounts for structure conservation in loop regions. Secondly, by merging multiple template structures into one comparative model, the best possible template for every region of a target can be used expanding the conformational space sampled in a meaningful way. This optimization allows for accurate modeling of receptors using templates as low as 20% sequence identity, which accounts for nearly the entire druggable space of GPCRs. A model database of all non-odorant GPCRs is made available at www.rosettagpcr.org. Additionally, all protocols are made available with insights into modifications that may improve accuracy at new targets.
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Affiliation(s)
- Brian Joseph Bender
- Department of Pharmacology, Department of Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brennica Marlow
- Department of Pharmacology, Department of Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Department of Pharmacology, Department of Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC, Germany
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Bender BJ, Vortmeier G, Ernicke S, Bosse M, Kaiser A, Els-Heindl S, Krug U, Beck-Sickinger A, Meiler J, Huster D. Structural Model of Ghrelin Bound to its G Protein-Coupled Receptor. Structure 2019; 27:537-544.e4. [PMID: 30686667 DOI: 10.1016/j.str.2018.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/14/2018] [Accepted: 12/05/2018] [Indexed: 12/27/2022]
Abstract
The peptide ghrelin targets the growth hormone secretagogue receptor 1a (GHSR) to signal changes in cell metabolism and is a sought-after therapeutic target, although no structure is known to date. To investigate the structural basis of ghrelin binding to GHSR, we used solid-state nuclear magnetic resonance (NMR) spectroscopy, site-directed mutagenesis, and Rosetta modeling. The use of saturation transfer difference NMR identified key residues in the peptide for receptor binding beyond the known motif. This information combined with assignment of the secondary structure of ghrelin in its receptor-bound state was incorporated into Rosetta using an approach that accounts for flexible binding partners. The NMR data and models revealed an extended binding surface that was confirmed via mutagenesis. Our results agree with a growing evidence of peptides interacting via two sites at G protein-coupled receptors.
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Affiliation(s)
- Brian Joseph Bender
- Department of Pharmacology and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Gerrit Vortmeier
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Stefan Ernicke
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mathias Bosse
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Sylvia Els-Heindl
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Ulrike Krug
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Annette Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Jens Meiler
- Department of Pharmacology and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany.
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Sánchez-Soto M, Casadó-Anguera V, Yano H, Bender BJ, Cai NS, Moreno E, Canela EI, Cortés A, Meiler J, Casadó V, Ferré S. α 2A- and α 2C-Adrenoceptors as Potential Targets for Dopamine and Dopamine Receptor Ligands. Mol Neurobiol 2018; 55:8438-8454. [PMID: 29552726 DOI: 10.1007/s12035-018-1004-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/07/2018] [Indexed: 01/12/2023]
Abstract
The poor norepinephrine innervation and high density of Gi/o-coupled α2A- and α2C-adrenoceptors in the striatum and the dense striatal dopamine innervation have prompted the possibility that dopamine could be an effective adrenoceptor ligand. Nevertheless, the reported adrenoceptor agonistic properties of dopamine are still inconclusive. In this study, we analyzed the binding of norepinephrine, dopamine, and several compounds reported as selective dopamine D2-like receptor ligands, such as the D3 receptor agonist 7-OH-PIPAT and the D4 receptor agonist RO-105824, to α2-adrenoceptors in cortical and striatal tissue, which express α2A-adrenoceptors and both α2A- and α2C-adrenoceptors, respectively. The affinity of dopamine for α2-adrenoceptors was found to be similar to that for D1-like and D2-like receptors. Moreover, the exogenous dopamine receptor ligands also showed high affinity for α2A- and α2C-adrenoceptors. Their ability to activate Gi/o proteins through α2A- and α2C-adrenoceptors was also analyzed in transfected cells with bioluminescent resonance energy transfer techniques. The relative ligand potencies and efficacies were dependent on the Gi/o protein subtype. Furthermore, dopamine binding to α2-adrenoceptors was functional, inducing changes in dynamic mass redistribution, adenylyl cyclase activity, and ERK1/2 phosphorylation. Binding events were further studied with computer modeling of ligand docking. Docking of dopamine at α2A- and α2C-adrenoceptors was nearly identical to its binding to the crystallized D3 receptor. Therefore, we provide conclusive evidence that α2A- and α2C-adrenoceptors are functional receptors for norepinephrine, dopamine, and other previously assumed selective D2-like receptor ligands, which calls for revisiting previous studies with those ligands.
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Affiliation(s)
- Marta Sánchez-Soto
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Triad Technology Building, 333 Cassell Drive, Baltimore, MD, 21224, USA.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Verònica Casadó-Anguera
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Hideaki Yano
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Triad Technology Building, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Brian Joseph Bender
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ning-Sheng Cai
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Triad Technology Building, 333 Cassell Drive, Baltimore, MD, 21224, USA
| | - Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Enric I Canela
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Antoni Cortés
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Jens Meiler
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain. .,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Institute of Biomedicine, University of Barcelona, Barcelona, Spain.
| | - Sergi Ferré
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Triad Technology Building, 333 Cassell Drive, Baltimore, MD, 21224, USA.
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