1
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Sachdev S, Creemer BA, Gardella TJ, Cheloha RW. Highly biased agonism for GPCR ligands via nanobody tethering. Nat Commun 2024; 15:4687. [PMID: 38824166 PMCID: PMC11144202 DOI: 10.1038/s41467-024-49068-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/22/2024] [Indexed: 06/03/2024] Open
Abstract
Ligand-induced activation of G protein-coupled receptors (GPCRs) can initiate signaling through multiple distinct pathways with differing biological and physiological outcomes. There is intense interest in understanding how variation in GPCR ligand structure can be used to promote pathway selective signaling ("biased agonism") with the goal of promoting desirable responses and avoiding deleterious side effects. Here we present an approach in which a conventional peptide ligand for the type 1 parathyroid hormone receptor (PTHR1) is converted from an agonist which induces signaling through all relevant pathways to a compound that is highly selective for a single pathway. This is achieved not through variation in the core structure of the agonist, but rather by linking it to a nanobody tethering agent that binds with high affinity to a separate site on the receptor not involved in signal transduction. The resulting conjugate represents the most biased agonist of PTHR1 reported to date. This approach holds promise for facile generation of pathway selective ligands for other GPCRs.
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Affiliation(s)
- Shivani Sachdev
- Laboratory of Bioorganic Chemistry, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bathesda, MD, USA
| | - Brendan A Creemer
- Laboratory of Bioorganic Chemistry, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bathesda, MD, USA
| | - Thomas J Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ross W Cheloha
- Laboratory of Bioorganic Chemistry, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bathesda, MD, USA.
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2
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Sachdev S, Creemer BA, Gardella TJ, Cheloha RW. Highly biased agonism for GPCR ligands via nanobody tethering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561766. [PMID: 37873435 PMCID: PMC10592785 DOI: 10.1101/2023.10.10.561766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Ligand-induced activation of G protein-coupled receptors (GPCRs) can initiate signaling through multiple distinct pathways with differing biological and physiological outcomes. There is intense interest in understanding how variation in GPCR ligand structure can be used to promote pathway selective signaling ("biased agonism") with the goal of promoting desirable responses and avoiding deleterious side effects. Here we present a new approach in which a conventional peptide ligand for the type 1 parathyroid hormone receptor (PTHR1) is converted from an agonist which induces signaling through all relevant pathways to a compound that is highly selective for a single pathway. This is achieved not through variation in the core structure of the agonist, but rather by linking it to a nanobody tethering agent that binds with high affinity to a separate site on the receptor not involved in signal transduction. The resulting conjugate represents the most biased agonist of PTHR1 reported to date. This approach holds promise for facile generation of pathway selective ligands for other GPCRs.
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3
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Gross JD, Zhou Y, Barak LS, Caron MG. Ghrelin receptor signaling in health and disease: a biased view. Trends Endocrinol Metab 2023; 34:106-118. [PMID: 36567228 PMCID: PMC9852078 DOI: 10.1016/j.tem.2022.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/23/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022]
Abstract
As allosteric complexes, G-protein-coupled receptors (GPCRs) respond to extracellular stimuli and pleiotropically couple to intracellular transducers to elicit signaling pathway-dependent effects in a process known as biased signaling or functional selectivity. One such GPCR, the ghrelin receptor (GHSR1a), has a crucial role in restoring and maintaining metabolic homeostasis during disrupted energy balance. Thus, pharmacological modulation of GHSR1a bias could offer a promising strategy to treat several metabolism-based disorders. Here, we summarize current evidence supporting GHSR1a functional selectivity in vivo and highlight recent structural data. We propose that precise determinations of GHSR1a molecular pharmacology and pathway-specific physiological effects will enable discovery of GHSR1a drugs with tailored signaling profiles, thereby providing safer and more effective treatments for metabolic diseases.
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Affiliation(s)
- Joshua D Gross
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Yang Zhou
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Lawrence S Barak
- Department of Cell Biology, Duke University, Durham, NC 27710, USA.
| | - Marc G Caron
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
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4
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Moreno E, Casajuana-Martin N, Coyle M, Campos BC, Galaj E, Del Torrent CL, Seyedian A, Rea W, Cai NS, Bonifazi A, Florán B, Xi ZX, Guitart X, Casadó V, Newman AH, Bishop C, Pardo L, Ferré S. Pharmacological targeting of G protein-coupled receptor heteromers. Pharmacol Res 2022; 185:106476. [PMID: 36182040 PMCID: PMC9645299 DOI: 10.1016/j.phrs.2022.106476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022]
Abstract
A main rationale for the role of G protein-coupled receptor (GPCR) heteromers as targets for drug development is the putative ability of selective ligands for specific GPCRs to change their pharmacological properties upon GPCR heteromerization. The present study provides a proof of concept for this rationale by demonstrating that heteromerization of dopamine D1 and D3 receptors (D1R and D3R) influences the pharmacological properties of three structurally similar selective dopamine D3R ligands, the phenylpiperazine derivatives PG01042, PG01037 and VK4-116. By using D1R-D3R heteromer-disrupting peptides, it could be demonstrated that the three D3R ligands display different D1R-D3R heteromer-dependent pharmacological properties: PG01042, acting as G protein-biased agonist, counteracted D1R-mediated signaling in the D1R-D3R heteromer; PG01037, acting as a D3R antagonist cross-antagonized D1R-mediated signaling in the D1R-D3R heteromer; and VK4-116 specifically acted as a ß-arrestin-biased agonist in the D1R-D3R heteromer. Molecular dynamics simulations predicted potential molecular mechanisms mediating these qualitatively different pharmacological properties of the selective D3R ligands that are dependent on D1R-D3R heteromerization. The results of in vitro experiments were paralleled by qualitatively different pharmacological properties of the D3R ligands in vivo. The results supported the involvement of D1R-D3R heteromers in the locomotor activation by D1R agonists in reserpinized mice and L-DOPA-induced dyskinesia in rats, highlighting the D1R-D3R heteromer as a main pharmacological target for L-DOPA-induced dyskinesia in Parkinson's disease. More generally, the present study implies that when suspecting its pathogenetic role, a GPCR heteromer, and not its individual GPCR units, should be considered as main target for drug development.
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Affiliation(s)
- Estefanía Moreno
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Michael Coyle
- Behavioral Neuroscience Program, Department of Psychology, Binghamton University, 4400 Vestal Parkway East, Binghamton, NY, USA
| | - Baruc Campos Campos
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA; Center for Research and Advanced Studies, Department of Physiology, Biophysics, and Neurosciences, Mexico City, Mexico
| | - Ewa Galaj
- Addiction Biology Unit, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Arta Seyedian
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - William Rea
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Ning-Sheng Cai
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Benjamín Florán
- Center for Research and Advanced Studies, Department of Physiology, Biophysics, and Neurosciences, Mexico City, Mexico
| | - Zheng-Xiong Xi
- Addiction Biology Unit, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Xavier Guitart
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Vicent Casadó
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Amy H Newman
- Medicinal Chemistry Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Christopher Bishop
- Behavioral Neuroscience Program, Department of Psychology, Binghamton University, 4400 Vestal Parkway East, Binghamton, NY, USA.
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, Spain.
| | - Sergi Ferré
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
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5
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Wingler LM, Feld AP. Nanobodies as Probes and Modulators of Cardiovascular G Protein-Coupled Receptors. J Cardiovasc Pharmacol 2022; 80:342-353. [PMID: 34840268 DOI: 10.1097/fjc.0000000000001185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/06/2021] [Indexed: 01/31/2023]
Abstract
ABSTRACT Understanding the activation of G protein-coupled receptors (GPCRs) is of paramount importance to the field of cardiovascular medicine due to the critical physiological roles of these receptors and their prominence as drug targets. Although many cardiovascular GPCRs have been extensively studied as model receptors for decades, new complexities in their regulation continue to emerge. As a result, there is an ongoing need to develop novel approaches to monitor and to modulate GPCR activation. In less than a decade, nanobodies, or recombinant single-domain antibody fragments from camelids, have become indispensable tools for interrogating GPCRs both in purified systems and in living cells. Nanobodies have gained traction rapidly due to their biochemical tractability and their ability to recognize defined states of native proteins. Here, we review how nanobodies have been adopted to elucidate the structure, pharmacology, and signaling of cardiovascular GPCRs, resolving long-standing mysteries and revealing unexpected mechanisms. We also discuss how advancing technologies to discover nanobodies with tailored specificities may expand the impact of these tools for both basic science and therapeutic applications.
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Affiliation(s)
- Laura M Wingler
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
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6
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Egyed A, Kiss DJ, Keserű GM. The Impact of the Secondary Binding Pocket on the Pharmacology of Class A GPCRs. Front Pharmacol 2022; 13:847788. [PMID: 35355719 PMCID: PMC8959758 DOI: 10.3389/fphar.2022.847788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are considered important therapeutic targets due to their pathophysiological significance and pharmacological relevance. Class A receptors represent the largest group of GPCRs that gives the highest number of validated drug targets. Endogenous ligands bind to the orthosteric binding pocket (OBP) embedded in the intrahelical space of the receptor. During the last 10 years, however, it has been turned out that in many receptors there is secondary binding pocket (SBP) located in the extracellular vestibule that is much less conserved. In some cases, it serves as a stable allosteric site harbouring allosteric ligands that modulate the pharmacology of orthosteric binders. In other cases it is used by bitopic compounds occupying both the OBP and SBP. In these terms, SBP binding moieties might influence the pharmacology of the bitopic ligands. Together with others, our research group showed that SBP binders contribute significantly to the affinity, selectivity, functional activity, functional selectivity and binding kinetics of bitopic ligands. Based on these observations we developed a structure-based protocol for designing bitopic compounds with desired pharmacological profile.
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Affiliation(s)
- Attila Egyed
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dóra Judit Kiss
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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7
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Ippolito M, De Pascali F, Inoue A, Benovic JL. Phenylalanine 193 in Extracellular Loop 2 of the β 2-Adrenergic Receptor Coordinates β-Arrestin Interaction. Mol Pharmacol 2022; 101:87-94. [PMID: 34853152 PMCID: PMC8969133 DOI: 10.1124/molpharm.121.000332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/21/2021] [Indexed: 02/03/2023] Open
Abstract
G protein-coupled receptors (GPCRs) transduce a diverse variety of extracellular stimuli into intracellular signaling. These receptors are the most clinically productive drug targets at present. Despite decades of research on the signaling consequences of molecule-receptor interactions, conformational components of receptor-effector interactions remain incompletely described. The β 2-adrenergic receptor (β 2AR) is a prototypical and extensively studied GPCR that can provide insight into this aspect of GPCR signaling thanks to robust structural data and rich pharmacopeia. Using bioluminescence resonance energy transfer -based biosensors, second messenger assays, and biochemical techniques, we characterize the properties of β 2AR-F193A. This single point mutation in extracellular loop 2 of the β 2AR is sufficient to intrinsically bias the β 2AR away from β-arrestin interaction and demonstrates altered regulatory outcomes downstream of this functional selectivity. This study highlights the importance of extracellular control of intracellular response to stimuli and suggests a previously undescribed role for the extracellular loops of the receptor and the extracellular pocket formed by transmembrane domains 2, 3, and 7 in GPCR regulation that may contribute to biased signaling at GPCRs. SIGNIFICANCE STATEMENT: The role of extracellular G protein-coupled receptor (GPCR) domains in mediating intracellular interactions is poorly understood. We characterized the effects of extracellular loop mutations on agonist-promoted interactions of GPCRs with G protein and β-arrestin. Our studies reveal that F193 in extracellular loop 2 in the β2-adrenergic receptor mediates interactions with G protein and β-arrestin with a biased loss of β-arrestin binding. These results provide new insights on the role of the extracellular domain in differentially modulating intracellular interactions with GPCRs.
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Affiliation(s)
- Michael Ippolito
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Francesco De Pascali
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Asuka Inoue
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
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8
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Pulido D, Casadó-Anguera V, Gómez-Autet M, Llopart N, Moreno E, Casajuana-Martin N, Ferré S, Pardo L, Casadó V, Royo M. Heterobivalent Ligand for the Adenosine A 2A-Dopamine D 2 Receptor Heteromer. J Med Chem 2022; 65:616-632. [PMID: 34982555 DOI: 10.1021/acs.jmedchem.1c01763] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A G protein-coupled receptor heteromer that fulfills the established criteria for its existence in vivo is the complex between adenosine A2A (A2AR) and dopamine D2 (D2R) receptors. Here, we have designed and synthesized heterobivalent ligands for the A2AR-D2R heteromer with various spacer lengths. The indispensable simultaneous binding of these ligands to the two different orthosteric sites of the heteromer has been evaluated by radioligand competition-binding assays in the absence and presence of specific peptides that disrupt the formation of the heteromer, label-free dynamic mass redistribution assays in living cells, and molecular dynamic simulations. This combination of techniques has permitted us to identify compound 26 [KDB1 (A2AR) = 2.1 nM, KDB1 (D2R) = 0.13 nM], with a spacer length of 43-atoms, as a true bivalent ligand that simultaneously binds to the two different orthosteric sites. Moreover, bioluminescence resonance energy transfer experiments indicate that 26 favors the stabilization of the A2AR-D2R heteromer.
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Affiliation(s)
- Daniel Pulido
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08034 Barcelona, Spain.,Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
| | - Verònica Casadó-Anguera
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Marc Gómez-Autet
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Natàlia Llopart
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sergi Ferré
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Miriam Royo
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08034 Barcelona, Spain.,Department of Surfactants and Nanobiotechnology, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
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9
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Tyagi R, Singh A, Chaudhary KK, Yadav MK. Pharmacophore modeling and its applications. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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10
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Hernández-Alvarado RB, Madariaga-Mazón A, Cosme-Vela F, Marmolejo-Valencia AF, Nefzi A, Martinez-Mayorga K. Encoding mu-opioid receptor biased agonism with interaction fingerprints. J Comput Aided Mol Des 2021; 35:1081-1093. [PMID: 34713377 DOI: 10.1007/s10822-021-00422-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/07/2021] [Indexed: 10/20/2022]
Abstract
Opioids are potent painkillers, however, their therapeutic use requires close medical monitoring to diminish the risk of severe adverse effects. The G-protein biased agonists of the μ-opioid receptor (MOR) have shown safer therapeutic profiles than non-biased ligands. In this work, we performed extensive all-atom molecular dynamics simulations of two markedly biased ligands and a balanced reference molecule. From those simulations, we identified a protein-ligand interaction fingerprint that characterizes biased ligands. Then, we built and virtually screened a database containing 68,740 ligands with proven or potential GPCR agonistic activity. Exemplary molecules that fulfill the interacting pattern for biased agonism are showcased, illustrating the usefulness of this work for the search of biased MOR ligands and how this contributes to the understanding of MOR biased signaling.
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Affiliation(s)
| | | | - Fernando Cosme-Vela
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Adel Nefzi
- Center for Translational Science, Florida International University, Port St. Lucie, FL, USA.,Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, USA
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11
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Sun B, Feng D, Chu MLH, Fish I, Lovera S, Sands ZA, Kelm S, Valade A, Wood M, Ceska T, Kobilka TS, Lebon F, Kobilka BK. Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist. Nat Commun 2021; 12:3305. [PMID: 34083522 PMCID: PMC8175458 DOI: 10.1038/s41467-021-23519-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Dopamine D1 receptor (D1R) is an important drug target implicated in many psychiatric and neurological disorders. Selective agonism of D1R are sought to be the therapeutic strategy for these disorders. Most selective D1R agonists share a dopamine-like catechol moiety in their molecular structure, and their therapeutic potential is therefore limited by poor pharmacological properties in vivo. Recently, a class of non-catechol D1R selective agonists with a distinct scaffold and pharmacological properties were reported. Here, we report the crystal structure of D1R in complex with stimulatory G protein (Gs) and a non-catechol agonist Compound 1 at 3.8 Å resolution. The structure reveals the ligand bound to D1R in an extended conformation, spanning from the orthosteric site to extracellular loop 2 (ECL2). Structural analysis reveals that the unique features of D1R ligand binding pocket explains the remarkable selectivity of this scaffold for D1R over other aminergic receptors, and sheds light on the mechanism for D1R activation by the non-catechol agonist.
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Affiliation(s)
| | - Dan Feng
- ConfometRx, Inc., Santa Clara, CA, USA
| | | | | | | | - Zara A Sands
- UCB Pharma, Braine-l'Alleud, Belgium
- Confo Therapeutics, Zwijnaarde, Belgium
| | | | | | | | | | | | | | - Brian K Kobilka
- ConfometRx, Inc., Santa Clara, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Marmolejo-Valencia AF, Madariaga-Mazón A, Martinez-Mayorga K. Bias-inducing allosteric binding site in mu-opioid receptor signaling. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04505-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Abstract
G-protein-biased agonism of the mu-opioid receptor (μ-OR) is emerging as a promising strategy in analgesia. A deep understanding of how biased agonists modulate and differentiate G-protein-coupled receptors (GPCR) signaling pathways and how this is transferred into the cell are open questions. Here, using extensive all-atom molecular dynamics simulations, we analyzed the binding recognition process and signaling effects of three prototype μ-OR agonists. Our suggested structural mechanism of biased signaling in μ-OR involves an allosteric sodium ion site, water networks, conformational rearrangements in conserved motifs and collective motions of loops and transmembrane helices. These analyses led us to highlight the relevance of a bias-inducing allosteric binding site in the understanding of μ-OR’s G-protein-biased signaling. These results also suggest a competitive equilibrium between the agonists and the allosteric sodium ion, where the bias-inducing allosteric binding site can be modulated by this ion or an agonist such as herkinorin. Notably, herkinorin arises as the archetype modulator of μ-OR and its interactive pattern could be used for screening efforts via protein–ligand interaction fingerprint (PLIF) studies.
Article highlights
Agonists and a sodium ion compete for the bias-inducing allosteric binding site that modulates signaling in mu-opioid receptors.
Molecular dynamics simulations of the prototype μ-OR agonist suggest a competitive equilibrium involving the agonist and an allosteric sodium ion.
Analysis of experimental data from the literature and molecular models provides the structural bases of biased agonism on μ-OR.
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13
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Bock A, Bermudez M. Allosteric coupling and biased agonism in G protein‐coupled receptors. FEBS J 2021; 288:2513-2528. [DOI: 10.1111/febs.15783] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Andreas Bock
- Receptor Signaling Lab Max‐Delbrueck‐Center for Molecular Medicine Berlin Germany
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14
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Ippolito M, Benovic JL. Biased agonism at β-adrenergic receptors. Cell Signal 2020; 80:109905. [PMID: 33385503 DOI: 10.1016/j.cellsig.2020.109905] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/10/2020] [Accepted: 12/27/2020] [Indexed: 12/19/2022]
Abstract
The β-adrenergic receptors (βARs) include three subtypes, β1, β2 and β3. These receptors are widely expressed and regulate numerous physiological processes including cardiovascular and metabolic functions and airway tone. The βARs are also important targets in the treatment of many diseases including hypertension, heart failure and asthma. In some cases, the use of current βAR ligands to treat a disease is suboptimal and can lead to severe side effects. One strategy to potentially improve such treatments is the development of biased agonists that selectively regulate a subset of βAR signaling pathways and responses. Here we discuss the compounds identified to date that preferentially activate a Gs- or β-arrestin-mediated signaling pathway through βARs. Mechanistic insight on how these compounds bias signaling sheds light on the potential development of even more selective compounds that should have increased utility in treating disease.
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Affiliation(s)
- Michael Ippolito
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, United States of America
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, United States of America.
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15
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Biased Ligands Differentially Shape the Conformation of the Extracellular Loop Region in 5-HT 2B Receptors. Int J Mol Sci 2020; 21:ijms21249728. [PMID: 33419260 PMCID: PMC7767279 DOI: 10.3390/ijms21249728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/05/2023] Open
Abstract
G protein-coupled receptors are linked to various intracellular transducers, each pathway associated with different physiological effects. Biased ligands, capable of activating one pathway over another, are gaining attention for their therapeutic potential, as they could selectively activate beneficial pathways whilst avoiding those responsible for adverse effects. We performed molecular dynamics simulations with known β-arrestin-biased ligands like lysergic acid diethylamide and ergotamine in complex with the 5-HT2B receptor and discovered that the extent of ligand bias is directly connected with the degree of closure of the extracellular loop region. Given a loose allosteric coupling of extracellular and intracellular receptor regions, we delineate a concept for biased signaling at serotonin receptors, by which conformational interference with binding pocket closure restricts the signaling repertoire of the receptor. Molecular docking studies of biased ligands gathered from the BiasDB demonstrate that larger ligands only show plausible docking poses in the ergotamine-bound structure, highlighting the conformational constraints associated with bias. This emphasizes the importance of selecting the appropriate receptor conformation on which to base virtual screening workflows in structure-based drug design of biased ligands. As this mechanism of ligand bias has also been observed for muscarinic receptors, our studies provide a general mechanism of signaling bias transferable between aminergic receptors.
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16
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Holze J, Bermudez M, Pfeil EM, Kauk M, Bödefeld T, Irmen M, Matera C, Dallanoce C, De Amici M, Holzgrabe U, König GM, Tränkle C, Wolber G, Schrage R, Mohr K, Hoffmann C, Kostenis E, Bock A. Ligand-Specific Allosteric Coupling Controls G-Protein-Coupled Receptor Signaling. ACS Pharmacol Transl Sci 2020; 3:859-867. [PMID: 33073186 DOI: 10.1021/acsptsci.0c00069] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Indexed: 12/15/2022]
Abstract
Allosteric coupling describes a reciprocal process whereby G-protein-coupled receptors (GPCRs) relay ligand-induced conformational changes from the extracellular binding pocket to the intracellular signaling surface. Therefore, GPCR activation is sensitive to both the type of extracellular ligand and intracellular signaling protein. We hypothesized that ligand-specific allosteric coupling may result in preferential (i.e., biased) engagement of downstream effectors. However, the structural basis underlying ligand-dependent control of this essential allosteric mechanism is poorly understood. Here, we show that two sets of extended muscarinic acetylcholine receptor M1 agonists, which only differ in linker length, progressively constrain receptor signaling. We demonstrate that stepwise shortening of their chemical linker gradually hampers binding pocket closure, resulting in divergent coupling to distinct G-protein families. Our data provide an experimental strategy for the design of ligands with selective G-protein recognition and reveal a potentially general mechanism of ligand-specific allosteric coupling.
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Affiliation(s)
- Janine Holze
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Eva Marie Pfeil
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn 53121, Germany
| | - Michael Kauk
- Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena 07745, Germany
| | - Theresa Bödefeld
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany
| | - Matthias Irmen
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany
| | - Carlo Matera
- Department of Pharmaceutical Sciences, University of Milan, Milan 20133, Italy
| | - Clelia Dallanoce
- Department of Pharmaceutical Sciences, University of Milan, Milan 20133, Italy
| | - Marco De Amici
- Department of Pharmaceutical Sciences, University of Milan, Milan 20133, Italy
| | - Ulrike Holzgrabe
- Department of Pharmaceutical and Medical Chemistry, Institute of Pharmacy, University of Würzburg, Würzburg D-97074, Germany
| | | | - Christian Tränkle
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Ramona Schrage
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany
| | - Klaus Mohr
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany
| | - Carsten Hoffmann
- Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena 07745, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn 53121, Germany
| | - Andreas Bock
- Pharmacology and Toxicology Section, Institute of Pharmacy, University of Bonn, Bonn 53121, Germany.,Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
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17
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Singh G, Inoue A, Gutkind JS, Russell RB, Raimondi F. PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. Nucleic Acids Res 2020; 47:W395-W401. [PMID: 31143927 PMCID: PMC6602504 DOI: 10.1093/nar/gkz392] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/13/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.
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Affiliation(s)
- Gurdeep Singh
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert B Russell
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Francesco Raimondi
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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18
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Wingler LM, Skiba MA, McMahon C, Staus DP, Kleinhenz ALW, Suomivuori CM, Latorraca NR, Dror RO, Lefkowitz RJ, Kruse AC. Angiotensin and biased analogs induce structurally distinct active conformations within a GPCR. Science 2020; 367:888-892. [PMID: 32079768 DOI: 10.1126/science.aay9813] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
Abstract
Biased agonists of G protein-coupled receptors (GPCRs) preferentially activate a subset of downstream signaling pathways. In this work, we present crystal structures of angiotensin II type 1 receptor (AT1R) (2.7 to 2.9 angstroms) bound to three ligands with divergent bias profiles: the balanced endogenous agonist angiotensin II (AngII) and two strongly β-arrestin-biased analogs. Compared with other ligands, AngII promotes more-substantial rearrangements not only at the bottom of the ligand-binding pocket but also in a key polar network in the receptor core, which forms a sodium-binding site in most GPCRs. Divergences from the family consensus in this region, which appears to act as a biased signaling switch, may predispose the AT1R and certain other GPCRs (such as chemokine receptors) to adopt conformations that are capable of activating β-arrestin but not heterotrimeric Gq protein signaling.
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Affiliation(s)
- Laura M Wingler
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dean P Staus
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Alissa L W Kleinhenz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Robert J Lefkowitz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. .,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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19
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Schaller D, Šribar D, Noonan T, Deng L, Nguyen TN, Pach S, Machalz D, Bermudez M, Wolber G. Next generation 3D pharmacophore modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1468] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David Schaller
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Dora Šribar
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Theresa Noonan
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Lihua Deng
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Trung Ngoc Nguyen
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Szymon Pach
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - David Machalz
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Marcel Bermudez
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry Freie Universität Berlin Berlin Germany
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20
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Jakubik J, El-Fakahany EE. Current Advances in Allosteric Modulation of Muscarinic Receptors. Biomolecules 2020; 10:biom10020325. [PMID: 32085536 PMCID: PMC7072599 DOI: 10.3390/biom10020325] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023] Open
Abstract
Allosteric modulators are ligands that bind to a site on the receptor that is spatially separated from the orthosteric binding site for the endogenous neurotransmitter. Allosteric modulators modulate the binding affinity, potency, and efficacy of orthosteric ligands. Muscarinic acetylcholine receptors are prototypical allosterically-modulated G-protein-coupled receptors. They are a potential therapeutic target for the treatment of psychiatric, neurologic, and internal diseases like schizophrenia, Alzheimer’s disease, Huntington disease, type 2 diabetes, or chronic pulmonary obstruction. Here, we reviewed the progress made during the last decade in our understanding of their mechanisms of binding, allosteric modulation, and in vivo actions in order to understand the translational impact of studying this important class of pharmacological agents. We overviewed newly developed allosteric modulators of muscarinic receptors as well as new spin-off ideas like bitopic ligands combining allosteric and orthosteric moieties and photo-switchable ligands based on bitopic agents.
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Affiliation(s)
- Jan Jakubik
- Department of Neurochemistry, Institute of Physiology CAS, 142 20 Prague, Czech Republic
- Correspondence: (J.J.); (E.E.E.-F.)
| | - Esam E. El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN 55455, USA
- Correspondence: (J.J.); (E.E.E.-F.)
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21
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Bermudez M, Nguyen TN, Omieczynski C, Wolber G. Strategies for the discovery of biased GPCR ligands. Drug Discov Today 2019; 24:1031-1037. [PMID: 30831262 DOI: 10.1016/j.drudis.2019.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/13/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
Abstract
G-protein-coupled receptors (GPCRs) represent important drug targets with complex pharmacological characteristics. Biased signaling represents one important dimension, describing ligand-dependent shifts of naturally imprinted signaling profiles. Because biased GPCR modulators provide potential therapeutic benefits including higher efficiencies and reduced adverse effects, the identification of such ligands as drug candidates is highly desirable. This review aims to provide an overview of the challenges and strategies in the discovery of biased ligands. We show different approaches for biased ligand discovery in the example of G-protein-biased opioid analgesics and discuss possibilities to design biased ligands by targeting extracellular receptor regions.
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Affiliation(s)
- Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany.
| | - Trung Ngoc Nguyen
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany
| | - Christian Omieczynski
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany
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