1
|
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble and functional membrane protein analogues. Nature 2024:10.1038/s41586-024-07601-y. [PMID: 38898281 DOI: 10.1038/s41586-024-07601-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors2, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
Collapse
Affiliation(s)
- Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Goldbach
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Petra E M Balbi
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Srajan Kapoor
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Jagrity Choudhury
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Christian Schellhaas
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Simon Kozlov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Sergey Ovchinnikov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex J Vecchio
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
2
|
Krishna Kumar K, Wang H, Habrian C, Latorraca NR, Xu J, O'Brien ES, Zhang C, Montabana E, Koehl A, Marqusee S, Isacoff EY, Kobilka BK. Stepwise activation of a metabotropic glutamate receptor. Nature 2024; 629:951-956. [PMID: 38632403 DOI: 10.1038/s41586-024-07327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich domain to their 7-transmembrane domain1. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the extracellular ligand-binding domain to the G protein-coupling 7-transmembrane domain2. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging, we reveal distinct receptor conformations upon allosteric modulator and G protein binding.
Collapse
Affiliation(s)
- Kaavya Krishna Kumar
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Chris Habrian
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naomi R Latorraca
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Evan S O'Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chensong Zhang
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elizabeth Montabana
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Antoine Koehl
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- QB3 Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Ehud Y Isacoff
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
3
|
Zhang M, Chen T, Lu X, Lan X, Chen Z, Lu S. G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery. Signal Transduct Target Ther 2024; 9:88. [PMID: 38594257 PMCID: PMC11004190 DOI: 10.1038/s41392-024-01803-6] [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: 08/15/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.
Collapse
Affiliation(s)
- Mingyang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China
| | - Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
4
|
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble functional analogues of integral membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.540044. [PMID: 38496615 PMCID: PMC10942269 DOI: 10.1101/2023.05.09.540044] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
De novo design of complex protein folds using solely computational means remains a significant challenge. Here, we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from GPCRs, are not found in the soluble proteome and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses reveal high thermal stability of the designs and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, standing as a proof-of-concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
Collapse
|
5
|
Addis P, Bali U, Baron F, Campbell A, Harborne S, Jagger L, Milne G, Pearce M, Rosethorne EM, Satchell R, Swift D, Young B, Unitt JF. Key aspects of modern GPCR drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:1-22. [PMID: 37625784 DOI: 10.1016/j.slasd.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most versatile cell surface receptor family with a broad repertoire of ligands and functions. We've learned an enormous amount about discovering drugs of this receptor class since the first GPCR was cloned and expressed in 1986, such that it's now well-recognized that GPCRs are the most successful target class for approved drugs. Here we take the reader through a GPCR drug discovery journey from target to the clinic, highlighting the key learnings, best practices, challenges, trends and insights on discovering drugs that ultimately modulate GPCR function therapeutically in patients. The future of GPCR drug discovery is inspiring, with more desirable drug mechanisms and new technologies enabling the delivery of better and more successful drugs.
Collapse
Affiliation(s)
- Phil Addis
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Utsav Bali
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Frank Baron
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Adrian Campbell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Steven Harborne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Liz Jagger
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Gavin Milne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Martin Pearce
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Elizabeth M Rosethorne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Rupert Satchell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Denise Swift
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Barbara Young
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - John F Unitt
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK.
| |
Collapse
|
6
|
Du Y, Gao F, Sun H, Wu C, Zhu G, Zhu M. Novel substituted 4-(Arylethynyl)-Pyrrolo[2,3-d]pyrimidines negative allosteric modulators (NAMs) of the metabotropic glutamate receptor subtype 5 (mGlu5) Treat depressive disorder in mice. Eur J Med Chem 2023; 261:115855. [PMID: 37847955 DOI: 10.1016/j.ejmech.2023.115855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/13/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
Abstract
In view of the fact that the G-protein-coupled receptors (GPCRs) sit at the top of the signaling pathways triggering a diverse range of signaling cascades towards a cellular event, GPCRs are regarded as central drug targets. mGlu5, a type of classical GPCRs, is highly expressed in the central nervous system (CNS) and responds to the neurotransmitter glutamate. Researches show that mGlu5 is a potential drug target for the treatment of depression. Up to now, multiple mGlu5 negative allosteric modulators (NAMs) have entered clinical trials, but no small molecule mGlu5 NAM has yet to reach market. Herein, we report the structural optimization and structure-activity relationship studies of a series of novel mGlu5 NAMs. Among them, the novel compound 10b is a high-affinity mGluR5 antagonist, with an IC50 value of 11.5 nM. Besides, we evaluated the anti-depressant effect of compound 10b using the chronic unpredictable mild stress (CUMS)-induced depression model. The data showed that the mice in CUMS group were featured by decreased level of serum 5-HT and increased level of serum CORT, and the expression of synaptic proteins were reduced, including GluA1, GluA2, p-PKA, BDNF and TrkB. However, those factors for identifying sensitivity to depression-like behaviors could be improved by compound 10b treatment. The preliminary toxicology evaluations indicated that compound 10b had a good safety profile in vivo. Collectively, the compound 10b represents a promising lead compound for the treatment of depressive disorder.
Collapse
Affiliation(s)
- Yonglei Du
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui, 230601, China
| | - Feng Gao
- Key Laboratory of Xin'an Medicine, the Ministry of Education and Key Laboratory of Molecular Biology (Brain diseases), Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Hongwei Sun
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui, 230601, China
| | - Chenglin Wu
- School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
| | - Guoqi Zhu
- Key Laboratory of Xin'an Medicine, the Ministry of Education and Key Laboratory of Molecular Biology (Brain diseases), Anhui University of Chinese Medicine, Hefei, 230012, China.
| | - Manzhou Zhu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of Education, Institutes of Physical Science and Information Technology and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei, Anhui, 230601, China.
| |
Collapse
|
7
|
Maria-Solano MA, Choi S. Dynamic allosteric networks drive adenosine A 1 receptor activation and G-protein coupling. eLife 2023; 12:RP90773. [PMID: 37656635 PMCID: PMC10473838 DOI: 10.7554/elife.90773] [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] [Indexed: 09/03/2023] Open
Abstract
G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1 receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.
Collapse
Affiliation(s)
- Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
| |
Collapse
|
8
|
Kumar KK, Wang H, Habrian C, Latorraca NR, Xu J, O’Brien ES, Zhang C, Montabana E, Koehl A, Marqusee S, Isacoff EY, Kobilka BK. Step-wise activation of a Family C GPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555158. [PMID: 37693614 PMCID: PMC10491200 DOI: 10.1101/2023.08.29.555158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain (ECD) that is linked via a cysteine-rich domain (CRDs) to their 7-transmembrane (TM) domain. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the ECD to the G protein-coupling TM. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging we reveal distinct receptor conformations upon allosteric modulator and G protein binding.
Collapse
Affiliation(s)
- Kaavya Krishna Kumar
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
- Sarafin ChEM-H, 290 Jane Stanford Way, Stanford, California 94305, USA
| | - Chris Habrian
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
| | - Naomi R. Latorraca
- Department of Molecular and Cell Biology, University of California Berkeley, CA 94720, USA
| | - Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
| | - Evan S. O’Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
| | - Chensong Zhang
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Elizabeth Montabana
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
| | - Antoine Koehl
- Department of Statistics, University of California, Berkeley, CA 94720, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, CA 94720, USA; QB3 Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley CA 94720, USA
| | - Ehud Y. Isacoff
- Department of Molecular and Cell Biology, University of California Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley CA 94720, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, California 94305, USA
| |
Collapse
|
9
|
Hakami Zanjani AA, Nguyen TQT, Jacobsen L, Khandelia H. The molecular basis of the antidepressant action of the magic mushroom extract, psilocin. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140914. [PMID: 37019325 DOI: 10.1016/j.bbapap.2023.140914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Magic mushrooms, and their extract psilocybin, are well-known for their psychedelic properties and recreational use. Psilocin, the bio-active form of psilocybin, can potentially treat various psychiatric diseases. Psilocin putatively exerts its psychedelic effect as an agonist to the serotonin 2A receptor (5-HT2AR), which is also the receptor for the neurological hormone serotonin. The two key chemical differences between the two molecules are first, that the primary amine in serotonin is replaced with a tertiary amine in psilocin, and second, the hydroxyl group is substituted differently on the aromatic ring. Here, we find that psilocin can bind to 5-HT2AR with an affinity higher than serotonin, and provide the molecular logic behind the higher binding affinity of psilocin using extensive molecular dynamics simulations and free energy calculations. The binding free energy of psilocin is dependent upon the protonation states of the ligands, as well as that of the key residue in the binding site: Aspartate 155. We find that the tertiary amine of psilocin, and not the altered substitution of the hydroxyl group in the ring is responsible for the increased affinity of psilocin. We propose design rules for effective antidepressants based on molecular insights from our simulations.
Collapse
Affiliation(s)
- Ali Asghar Hakami Zanjani
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Teresa Quynh Tram Nguyen
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
| | - Luise Jacobsen
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark
| | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| |
Collapse
|
10
|
Function and structure of bradykinin receptor 2 for drug discovery. Acta Pharmacol Sin 2023; 44:489-498. [PMID: 36075965 PMCID: PMC9453710 DOI: 10.1038/s41401-022-00982-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/11/2022] [Indexed: 11/08/2022] Open
Abstract
Type 2 bradykinin receptor (B2R) is an essential G protein-coupled receptor (GPCR) that regulates the cardiovascular system as a vasodepressor. Dysfunction of B2R is also closely related to cancers and hereditary angioedema (HAE). Although several B2R agonists and antagonists have been developed, icatibant is the only B2R antagonist clinically used for treating HAE. The recently determined structures of B2R have provided molecular insights into the functions and regulation of B2R, which shed light on structure-based drug design for the treatment of B2R-related diseases. In this review, we summarize the structure and function of B2R in relation to drug discovery and discuss future research directions to elucidate the remaining unknown functions of B2R dimerization.
Collapse
|
11
|
Shen S, Zhao C, Wu C, Sun S, Li Z, Yan W, Shao Z. Allosteric modulation of G protein-coupled receptor signaling. Front Endocrinol (Lausanne) 2023; 14:1137604. [PMID: 36875468 PMCID: PMC9978769 DOI: 10.3389/fendo.2023.1137604] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of transmembrane proteins, regulate a wide array of physiological processes in response to extracellular signals. Although these receptors have proven to be the most successful class of drug targets, their complicated signal transduction pathways (including different effector G proteins and β-arrestins) and mediation by orthosteric ligands often cause difficulties for drug development, such as on- or off-target effects. Interestingly, identification of ligands that engage allosteric binding sites, which are different from classic orthosteric sites, can promote pathway-specific effects in cooperation with orthosteric ligands. Such pharmacological properties of allosteric modulators offer new strategies to design safer GPCR-targeted therapeutics for various diseases. Here, we explore recent structural studies of GPCRs bound to allosteric modulators. Our inspection of all GPCR families reveals recognition mechanisms of allosteric regulation. More importantly, this review highlights the diversity of allosteric sites and presents how allosteric modulators control specific GPCR pathways to provide opportunities for the development of new valuable agents.
Collapse
Affiliation(s)
| | | | | | | | | | - Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
12
|
Kampen S, Rodríguez D, Jørgensen M, Kruszyk-Kujawa M, Huang X, Collins M, Boyle N, Maurel D, Rudling A, Lebon G, Carlsson J. Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5. ACS Chem Biol 2022; 17:2744-2752. [PMID: 36149353 PMCID: PMC9594040 DOI: 10.1021/acschembio.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recently determined structures of class C G protein-coupled receptors (GPCRs) revealed the location of allosteric binding sites and opened new opportunities for the discovery of novel modulators. In this work, molecular docking screens for allosteric modulators targeting the metabotropic glutamate receptor 5 (mGlu5) were performed. The mGlu5 receptor is activated by the main excitatory neurotransmitter of the nervous central system, L-glutamate, and mGlu5 receptor activity can be allosterically modulated by negative or positive allosteric modulators. The mGlu5 receptor is a promising target for the treatment of psychiatric and neurodegenerative diseases, and several allosteric modulators of this GPCR have been evaluated in clinical trials. Chemical libraries containing fragment- (1.6 million molecules) and lead-like (4.6 million molecules) compounds were docked to an allosteric binding site of mGlu5 identified in X-ray crystal structures. Among the top-ranked compounds, 59 fragments and 59 lead-like compounds were selected for experimental evaluation. Of these, four fragment- and seven lead-like compounds were confirmed to bind to the allosteric site with affinities ranging from 0.43 to 8.6 μM, corresponding to a hit rate of 9%. The four compounds with the highest affinities were demonstrated to be negative allosteric modulators of mGlu5 signaling in functional assays. The results demonstrate that virtual screens of fragment- and lead-like chemical libraries have complementary advantages and illustrate how access to high-resolution structures of GPCRs in complex with allosteric modulators can accelerate lead discovery.
Collapse
Affiliation(s)
- Stefanie Kampen
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - David Rodríguez
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21 Solna, Sweden,H.
Lundbeck A/S, Ottiliavej
9, DK-2500 Valby, Denmark
| | | | | | - Xinyan Huang
- Lundbeck
Research USA, 215 College Road, Paramus, New Jersey 07652 - 1431, United States
| | - Michael Collins
- Lundbeck
Research USA, 215 College Road, Paramus, New Jersey 07652 - 1431, United States
| | - Noel Boyle
- Lundbeck
Research USA, 215 College Road, Paramus, New Jersey 07652 - 1431, United States
| | - Damien Maurel
- IGF,
Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Axel Rudling
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21 Solna, Sweden
| | - Guillaume Lebon
- IGF,
Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Jens Carlsson
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden,
| |
Collapse
|
13
|
Allosteric modulation of GPCRs: From structural insights to in silico drug discovery. Pharmacol Ther 2022; 237:108242. [DOI: 10.1016/j.pharmthera.2022.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 11/19/2022]
|
14
|
Berto L, Dumazer A, Malhaire F, Cannone G, Kutti Ragunath V, Goudet C, Lebon G. [Recent advances in the structural biology of the class C G protein-coupled receptors: The metabotropic Glutamate receptor 5]. Biol Aujourdhui 2022; 215:85-94. [PMID: 35275053 DOI: 10.1051/jbio/2021013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Class C GPCRs, that include metabotropic glutamate receptors (mGlu), taste receptors, GABAB receptor and Calcium-sensing receptor, are unusual in terms of their molecular architecture and allosteric regulation. They all form obligatory dimers, dimerization being fundamental for their function. More specifically, the mGlu are activated by the main excitatory neurotransmitter, L-glutamate. mGlu activation by glutamate binding in the venus flytrap domain (VFT) triggers conformational changes that are transmitted, through the Cystein-Rich Domain (CRD), to the conserved fold of 7 transmembrane helices (7TM), that couples to intracellular G protein. mGlu activity can also be allosterically modulated by positive (PAM) or negative (NAM) allosteric modulators binding to the 7TM. Recent progress in cryo-electron microscopy (cryoEM) has allowed unprecedented advances in deciphering the structural and molecular basis of their activation mechanism. The agonist induces a large movement between the subunits, bringing the 7TMs together and stabilizing a 7TM conformation structurally similar to the inactive state. The diversity of inactive conformations for the class C was unexpected but allows PAM stabilising a 7TM active conformation independent of the conformational changes induced by agonists, representing an alternative mode of mGlu activation. Here we present and discuss recent structural characterisation of mGlu receptors, highlighting findings that make the class C of GPCR unique. Understanding the structural basis of mGlu dimer signaling represents a landmark achievement and paves the way for structural investigation of GPCR dimer signaling in general. Structural information will open new avenues for structure-based drug design.
Collapse
Affiliation(s)
- Ludovic Berto
- IGF, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Anaëlle Dumazer
- IGF, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Fanny Malhaire
- IGF, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | | | | | - Cyril Goudet
- IGF, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Guillaume Lebon
- IGF, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| |
Collapse
|
15
|
Zhao Q, Chapman A, Huang Y, Ferguson M, McBride S, Kelly M, Weiner M, Li X. Ligand-Directed GPCR Antibody Discovery. Methods Mol Biol 2022; 2394:319-342. [PMID: 35094336 DOI: 10.1007/978-1-0716-1811-0_19] [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] [Indexed: 06/14/2023]
Abstract
Developing affinity reagents recognizing and modulating G-protein coupled receptors (GPCR) function by traditional animal immunization or in vitro screening methods is challenging. Some anti-GPCR antibodies exist on the market, but the success rate of development is still poor compared with antibodies targeting soluble or peripherally anchored proteins. More importantly, most of these antibodies do not modulate GPCR function. The current pipeline for antibody development primarily screens for overall affinity rather than functional epitope recognition. We developed a new strategy utilizing natural ligand affinity to generate a library of antibody variants with an inherent bias toward the active site of the GPCR. Instead of using phage libraries displaying antibodies with random CDR sequences at polymorphism sites observed in natural immune repertoire sequences, we generated focused antibody libraries with a natural ligand encoded within or conjugated to one of the CDRs or the N-terminus. To tailor antibody binding to the active site, we limited the sequence randomization of the antibody in regions holstering the ligand while leaving the ligand-carrying part unaltered in the first round of randomization. With hits from the successful first round, the second round of randomization of the ligand-carrying part was then performed to eliminate the bias of the ligand. Based on our results on three different GPCR targets, the proposed pipeline will enable the rapid generation of functional antibodies (both agonists and antagonists) against high-value targets with poor function epitope exposures including GPCR, channels, transporters as well as cell surface targets whose binding site is heavily masked by glycosylation.
Collapse
Affiliation(s)
- Qi Zhao
- Abcam plc, Branford, CT, USA.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Wang P, Gao X, Zhang K, Pei Q, Xu X, Yan F, Dong J, Jing C. Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:24125-24139. [PMID: 34596645 DOI: 10.1039/d1cp02157e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Positive allosteric modulators (PAMs) of human metabotropic glutamate receptor 2 (hmGlu2) are well-known in the treatment of psychiatric disorders for their higher selectivity and lower tolerance risk. A variety of PAMs have been reported over the last decade and two compounds were in Phase II clinical trials for schizophrenia and anxiety. These trials were discontinued on account of the unsatisfactory therapeutic efficacy, but PAMs were explored as novel treatments for addiction and epilepsy. Thus, it is still important to explore novel hmGlu2 PAMs in the near future. Nowadays, the challenges in optimizing drug potency and improving scaffold diversity for PAMs are the noncomprehensive character analyses of multiple scaffolds; the exploration of the binding modes of PAMs in the allosteric binding site have been proposed to reduce this difficulty. However, there has been no comprehensive research about the binding profiles of PAMs in the hmGlu2 receptor. To address this issue, this work explores the binding characters of eight PAMs representing five chemical series by multiple computational methods. As a result, the shared binding modes of the eight studied PAMs interacting with 15 residues in the allosteric binding site were defined. In addition, the reduced hydrophobicity with low electronegativity of R1, increased hydrophobicity with low negative electron density of R2 and the electronegativity of the linker were identified as indicators that regulate the affinity of PAMs. This finding agrees well with the physicochemical properties of reported multiple series PAMs. This comprehensive work sheds additional light on the binding mechanism and physicochemical regularity underlining PAMs affinity and could be further utilized as a structural and energetic blueprint for discovering and assessing novel PAMs for hmGlu2.
Collapse
Affiliation(s)
- Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Xiaonan Gao
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Ke Zhang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Qinglan Pei
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Xiaobo Xu
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Fengmei Yan
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Jianghong Dong
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Chenxi Jing
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| |
Collapse
|
17
|
Allosteric modulators enhance agonist efficacy by increasing the residence time of a GPCR in the active state. Nat Commun 2021; 12:5426. [PMID: 34521824 PMCID: PMC8440590 DOI: 10.1038/s41467-021-25620-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/20/2021] [Indexed: 01/17/2023] Open
Abstract
Much hope in drug development comes from the discovery of positive allosteric modulators (PAM) that display target subtype selectivity and act by increasing agonist potency and efficacy. How such compounds can allosterically influence agonist action remains unclear. Metabotropic glutamate receptors (mGlu) are G protein-coupled receptors that represent promising targets for brain diseases, and for which PAMs acting in the transmembrane domain have been developed. Here, we explore the effect of a PAM on the structural dynamics of mGlu2 in optimized detergent micelles using single molecule FRET at submillisecond timescales. We show that glutamate only partially stabilizes the extracellular domains in the active state. Full activation is only observed in the presence of a PAM or the Gi protein. Our results provide important insights on the role of allosteric modulators in mGlu activation, by stabilizing the active state of a receptor that is otherwise rapidly oscillating between active and inactive states. Here, the authors use smFRET to assess the structural dynamics of metabotropic glutamate receptor mGlu2 and show that a positive allosteric modulator or the Gi protein stabilize mGlu2 in the glutamate-induced active state, leading to the full activation of the receptor.
Collapse
|
18
|
Agonists and allosteric modulators promote signaling from different metabotropic glutamate receptor 5 conformations. Cell Rep 2021; 36:109648. [PMID: 34469715 PMCID: PMC8424648 DOI: 10.1016/j.celrep.2021.109648] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/08/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Metabotropic glutamate receptors (mGluRs) are dimeric G-protein-coupled receptors activated by the main excitatory neurotransmitter, L-glutamate. mGluR activation by agonists binding in the venus flytrap domain is regulated by positive (PAM) or negative (NAM) allosteric modulators binding to the 7-transmembrane domain (7TM). We report the cryo-electron microscopy structures of fully inactive and intermediate-active conformations of mGlu5 receptor bound to an antagonist and a NAM or an agonist and a PAM, respectively, as well as the crystal structure of the 7TM bound to a photoswitchable NAM. The agonist induces a large movement between the subunits, bringing the 7TMs together and stabilizing a 7TM conformation structurally similar to the inactive state. Using functional approaches, we demonstrate that the PAM stabilizes a 7TM active conformation independent of the conformational changes induced by agonists, representing an alternative mode of mGlu activation. These findings provide a structural basis for different mGluR activation modes. Cryo-EM analysis of thermostabilized mGlu5 receptor bound to inhibitors or activators X-ray structure of trans-Alloswitch-1 bound to thermostable mGlu5 7TMs Photopharmacology provides insight into allosteric regulation of mGlu5 7TMs Multiple conformations of mGlu5 receptor activate G protein
Collapse
|
19
|
Subtype-selective mechanisms of negative allosteric modulators binding to group I metabotropic glutamate receptors. Acta Pharmacol Sin 2021; 42:1354-1367. [PMID: 33122823 PMCID: PMC8285414 DOI: 10.1038/s41401-020-00541-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Group I metabotropic glutamate receptors (mGlu1 and mGlu5) are promising targets for multiple psychiatric and neurodegenerative disorders. Understanding the subtype selectivity of mGlu1 and mGlu5 allosteric sites is essential for the rational design of novel modulators with single- or dual-target mechanism of action. In this study, starting from the deposited mGlu1 and mGlu5 crystal structures, we utilized computational modeling approaches integrating docking, molecular dynamics simulation, and efficient post-trajectory analysis to reveal the subtype-selective mechanism of mGlu1 and mGlu5 to 10 diverse drug scaffolds representing known negative allosteric modulators (NAMs) in the literature. The results of modeling identified six pairs of non-conserved residues and four pairs of conserved ones as critical features to distinguish the selective NAMs binding to the corresponding receptors. In addition, nine pairs of residues are beneficial to the development of novel dual-target NAMs of group I metabotropic glutamate receptors. Furthermore, the binding modes of a reported dual-target NAM (VU0467558) in mGlu1 and mGlu5 were predicted to verify the identified residues that play key roles in the receptor selectivity and the dual-target binding. The results of this study can guide rational structure-based design of novel NAMs, and the approach can be generally applicable to characterize the features of selectivity for other G-protein-coupled receptors.
Collapse
|
20
|
Seven AB, Barros-Álvarez X, de Lapeyrière M, Papasergi-Scott MM, Robertson MJ, Zhang C, Nwokonko RM, Gao Y, Meyerowitz JG, Rocher JP, Schelshorn D, Kobilka BK, Mathiesen JM, Skiniotis G. G-protein activation by a metabotropic glutamate receptor. Nature 2021; 595:450-454. [PMID: 34194039 DOI: 10.1038/s41586-021-03680-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/01/2021] [Indexed: 01/14/2023]
Abstract
Family C G-protein-coupled receptors (GPCRs) operate as obligate dimers with extracellular domains that recognize small ligands, leading to G-protein activation on the transmembrane (TM) domains of these receptors by an unknown mechanism1. Here we show structures of homodimers of the family C metabotropic glutamate receptor 2 (mGlu2) in distinct functional states and in complex with heterotrimeric Gi. Upon activation of the extracellular domain, the two transmembrane domains undergo extensive rearrangement in relative orientation to establish an asymmetric TM6-TM6 interface that promotes conformational changes in the cytoplasmic domain of one protomer. Nucleotide-bound Gi can be observed pre-coupled to inactive mGlu2, but its transition to the nucleotide-free form seems to depend on establishing the active-state TM6-TM6 interface. In contrast to family A and B GPCRs, G-protein coupling does not involve the cytoplasmic opening of TM6 but is facilitated through the coordination of intracellular loops 2 and 3, as well as a critical contribution from the C terminus of the receptor. The findings highlight the synergy of global and local conformational transitions to facilitate a new mode of G-protein activation.
Collapse
Affiliation(s)
- Alpay B Seven
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ximena Barros-Álvarez
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Makaía M Papasergi-Scott
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chensong Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert M Nwokonko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Gao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin G Meyerowitz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Jesper M Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
21
|
Thibado JK, Tano JY, Lee J, Salas-Estrada L, Provasi D, Strauss A, Marcelo Lamim Ribeiro J, Xiang G, Broichhagen J, Filizola M, Lohse MJ, Levitz J. Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors. eLife 2021; 10:e67027. [PMID: 33880992 PMCID: PMC8102066 DOI: 10.7554/elife.67027] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
The metabotropic glutamate receptors (mGluRs) form a family of neuromodulatory G-protein-coupled receptors that contain both a seven-helix transmembrane domain (TMD) and a large extracellular ligand-binding domain (LBD) which enables stable dimerization. Although numerous studies have revealed variability across subtypes in the initial activation steps at the level of LBD dimers, an understanding of inter-TMD interaction and rearrangement remains limited. Here, we use a combination of single molecule fluorescence, molecular dynamics, functional assays, and conformational sensors to reveal that distinct TMD assembly properties drive differences between mGluR subtypes. We uncover a variable region within transmembrane helix 4 (TM4) that contributes to homo- and heterodimerization in a subtype-specific manner and tunes orthosteric, allosteric, and basal activation. We also confirm a critical role for a conserved inter-TM6 interface in stabilizing the active state during orthosteric or allosteric activation. Together this study shows that inter-TMD assembly and dynamic rearrangement drive mGluR function with distinct properties between subtypes.
Collapse
Affiliation(s)
- Jordana K Thibado
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell MedicineNew YorkUnited States
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Alexa Strauss
- Tri-Institutional PhD Program in Chemical BiologyNew YorkUnited States
| | | | - Guoqing Xiang
- Department of Biochemistry, Weill Cornell MedicineNew YorkUnited States
| | | | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Martin J Lohse
- Max Delbrück Center for Molecular MedicineBerlinGermany
- ISAR Bioscience InstitutePlanegg-MunichGermany
| | - Joshua Levitz
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Graduate School of Medical SciencesNew YorkUnited States
- Department of Biochemistry, Weill Cornell MedicineNew YorkUnited States
- Tri-Institutional PhD Program in Chemical BiologyNew YorkUnited States
| |
Collapse
|
22
|
Arsova A, Møller TC, Hellyer SD, Vedel L, Foster SR, Hansen JL, Bräuner-Osborne H, Gregory KJ. Positive Allosteric Modulators of Metabotropic Glutamate Receptor 5 as Tool Compounds to Study Signaling Bias. Mol Pharmacol 2021; 99:328-341. [PMID: 33602724 DOI: 10.1124/molpharm.120.000185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/27/2021] [Indexed: 11/22/2022] Open
Abstract
Positive allosteric modulation of metabotropic glutamate subtype 5 (mGlu5) receptor has emerged as a potential new therapeutic strategy for the treatment of schizophrenia and cognitive impairments. However, positive allosteric modulator (PAM) agonist activity has been associated with adverse side effects, and neurotoxicity has also been observed for pure PAMs. The structural and pharmacological basis of therapeutic versus adverse mGlu5 PAM in vivo effects remains unknown. Thus, gaining insights into the signaling fingerprints, as well as the binding kinetics of structurally diverse mGlu5 PAMs, may help in the rational design of compounds with desired properties. We assessed the binding and signaling profiles of N-methyl-5-(phenylethynyl)pyrimidin-2-amine (MPPA), 3-cyano-N-(2,5-diphenylpyrazol-3-yl)benzamide (CDPPB), and 1-[4-(4-chloro-2-fluoro-phenyl)piperazin-1-yl]-2-(4-pyridylmethoxy)ethenone [compound 2c, a close analog of 1-(4-(2-chloro-4-fluorophenyl)piperazin-1-yl)-2-(pyridin-4-ylmethoxy)ethanone] in human embryonic kidney 293A cells stably expressing mGlu5 using Ca2+ mobilization, inositol monophosphate (IP1) accumulation, extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation, and receptor internalization assays. Of the three allosteric ligands, only CDPPB had intrinsic agonist efficacy, and it also had the longest receptor residence time and highest affinity. MPPA was a biased PAM, showing higher positive cooperativity with orthosteric agonists in ERK1/2 phosphorylation and Ca2+ mobilization over IP1 accumulation and receptor internalization. In primary cortical neurons, all three PAMs showed stronger positive cooperativity with (S)-3,5-dihydroxyphenylglycine (DHPG) in Ca2+ mobilization over IP1 accumulation. Our characterization of three structurally diverse mGlu5 PAMs provides further molecular pharmacological insights and presents the first assessment of PAM-mediated mGlu5 internalization. SIGNIFICANCE STATEMENT: Enhancing metabotropic glutamate receptor subtype 5 (mGlu5) activity is a promising strategy to treat cognitive and positive symptoms in schizophrenia. It is increasingly evident that positive allosteric modulators (PAMs) of mGlu5 are not all equal in preclinical models; there remains a need to better understand the molecular pharmacological properties of mGlu5 PAMs. This study reports detailed characterization of the binding and functional pharmacological properties of mGlu5 PAMs and is the first study of the effects of mGlu5 PAMs on receptor internalization.
Collapse
Affiliation(s)
- Angela Arsova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Thor C Møller
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Shane D Hellyer
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Line Vedel
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Simon R Foster
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Jakob L Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| | - Karen J Gregory
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, Australia (S.D.H., K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv, Denmark (J.L.H.)
| |
Collapse
|
23
|
Orgován Z, Ferenczy GG, Keserű GM. Allosteric Molecular Switches in Metabotropic Glutamate Receptors. ChemMedChem 2021; 16:81-93. [PMID: 32686363 PMCID: PMC7818470 DOI: 10.1002/cmdc.202000444] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 12/22/2022]
Abstract
Metabotropic glutamate receptors (mGlu) are class C G protein-coupled receptors of eight subtypes that are omnipresently expressed in the central nervous system. mGlus have relevance in several psychiatric and neurological disorders, therefore they raise considerable interest as drug targets. Allosteric modulators of mGlus offer advantages over orthosteric ligands owing to their increased potential to achieve subtype selectivity, and this has prompted discovery programs that have produced a large number of reported allosteric mGlu ligands. However, the optimization of allosteric ligands into drug candidates has proved to be challenging owing to induced-fit effects, flat or steep structure-activity relationships and unexpected changes in theirpharmacology. Subtle structural changes identified as molecular switches might modulate the functional activity of allosteric ligands. Here we review these switches discovered in the metabotropic glutamate receptor family..
Collapse
Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesMagyar tudósok krt. 2Budapest1117Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesMagyar tudósok krt. 2Budapest1117Hungary
| | - György M. Keserű
- Medicinal Chemistry Research GroupResearch Centre for Natural SciencesMagyar tudósok krt. 2Budapest1117Hungary
| |
Collapse
|
24
|
Ren R, Pang B, Han Y, Li Y. A Glimpse of the Structural Biology of the Metabolism of Sphingosine-1-Phosphate. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2021; 4:2515256421995601. [PMID: 37366379 PMCID: PMC10243590 DOI: 10.1177/2515256421995601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 06/28/2023]
Abstract
As a key sphingolipid metabolite, sphingosine-1-phosphate (S1P) plays crucial roles in vascular and immune systems. It regulates angiogenesis, vascular integrity and homeostasis, allergic responses, and lymphocyte trafficking. S1P is interconverted with sphingosine, which is also derived from the deacylation of ceramide. S1P levels and the ratio to ceramide in cells are tightly regulated by its metabolic pathways. Abnormal S1P production causes the occurrence and progression of numerous severe diseases, such as metabolic syndrome, cancers, autoimmune disorders such as multiple sclerosis, and kidney and cardiovascular diseases. In recent years, huge advances on the structure of S1P metabolic pathways have been accomplished. In this review, we have got a glimpse of S1P metabolism through structural and biochemical studies of: sphingosine kinases, S1P transporters and S1P receptors, and the development of therapeutics targeting S1P signaling. The progress we summarize here could provide fresh perspectives to further the exploration of S1P functions and facilitate the development of therapeutic molecules targeting S1P signaling with improved specificity and therapeutic effects.
Collapse
Affiliation(s)
- Ruobing Ren
- Kobilka Institute of Innovative Drug
Discovery, School of Life and Health Sciences, the Chinese University
of Hong Kong, Shenzhen, China
| | - Bin Pang
- Kobilka Institute of Innovative Drug
Discovery, School of Life and Health Sciences, the Chinese University
of Hong Kong, Shenzhen, China
| | - Yufei Han
- Kobilka Institute of Innovative Drug
Discovery, School of Life and Health Sciences, the Chinese University
of Hong Kong, Shenzhen, China
| | - Yihao Li
- Kobilka Institute of Innovative Drug
Discovery, School of Life and Health Sciences, the Chinese University
of Hong Kong, Shenzhen, China
| |
Collapse
|
25
|
Gregory KJ, Goudet C. International Union of Basic and Clinical Pharmacology. CXI. Pharmacology, Signaling, and Physiology of Metabotropic Glutamate Receptors. Pharmacol Rev 2020; 73:521-569. [PMID: 33361406 DOI: 10.1124/pr.119.019133] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Metabotropic glutamate (mGlu) receptors respond to glutamate, the major excitatory neurotransmitter in the mammalian brain, mediating a modulatory role that is critical for higher-order brain functions such as learning and memory. Since the first mGlu receptor was cloned in 1992, eight subtypes have been identified along with many isoforms and splice variants. The mGlu receptors are transmembrane-spanning proteins belonging to the class C G protein-coupled receptor family and represent attractive targets for a multitude of central nervous system disorders. Concerted drug discovery efforts over the past three decades have yielded a wealth of pharmacological tools including subtype-selective agents that competitively block or mimic the actions of glutamate or act allosterically via distinct sites to enhance or inhibit receptor activity. Herein, we review the physiologic and pathophysiological roles for individual mGlu receptor subtypes including the pleiotropic nature of intracellular signal transduction arising from each. We provide a comprehensive analysis of the in vitro and in vivo pharmacological properties of prototypical and commercially available orthosteric agonists and antagonists as well as allosteric modulators, including ligands that have entered clinical trials. Finally, we highlight emerging areas of research that hold promise to facilitate rational design of highly selective mGlu receptor-targeting therapeutics in the future. SIGNIFICANCE STATEMENT: The metabotropic glutamate receptors are attractive therapeutic targets for a range of psychiatric and neurological disorders. Over the past three decades, intense discovery efforts have yielded diverse pharmacological tools acting either competitively or allosterically, which have enabled dissection of fundamental biological process modulated by metabotropic glutamate receptors and established proof of concept for many therapeutic indications. We review metabotropic glutamate receptor molecular pharmacology and highlight emerging areas that are offering new avenues to selectively modulate neurotransmission.
Collapse
Affiliation(s)
- Karen J Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.) and Institut de Génomique Fonctionnelle (IGF), University of Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Sante et de la Recherche Medicale (INSERM), Montpellier, France (C.G.)
| | - Cyril Goudet
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.) and Institut de Génomique Fonctionnelle (IGF), University of Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Sante et de la Recherche Medicale (INSERM), Montpellier, France (C.G.)
| |
Collapse
|
26
|
Ellaithy A, Gonzalez-Maeso J, Logothetis DA, Levitz J. Structural and Biophysical Mechanisms of Class C G Protein-Coupled Receptor Function. Trends Biochem Sci 2020; 45:1049-1064. [PMID: 32861513 PMCID: PMC7642020 DOI: 10.1016/j.tibs.2020.07.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Groundbreaking structural and spectroscopic studies of class A G protein-coupled receptors (GPCRs), such as rhodopsin and the β2 adrenergic receptor, have provided a picture of how structural rearrangements between transmembrane helices control ligand binding, receptor activation, and effector coupling. However, the activation mechanism of other GPCR classes remains more elusive, in large part due to complexity in their domain assembly and quaternary structure. In this review, we focus on the class C GPCRs, which include metabotropic glutamate receptors (mGluRs) and gamma-aminobutyric acid B (GABAB) receptors (GABABRs) most prominently. We discuss the unique biophysical questions raised by the presence of large extracellular ligand-binding domains (LBDs) and constitutive homo/heterodimerization. Furthermore, we discuss how recent studies have begun to unravel how these fundamental class C GPCR features impact the processes of ligand binding, receptor activation, signal transduction, regulation by accessory proteins, and crosstalk with other GPCRs.
Collapse
Affiliation(s)
- Amr Ellaithy
- Department of Neurology, University of Iowa, Iowa City, IA 52242, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Diomedes A Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, College of Science and Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA.
| |
Collapse
|
27
|
Structural Basis for Activation of the Heterodimeric GABAB Receptor. J Mol Biol 2020; 432:5966-5984. [DOI: 10.1016/j.jmb.2020.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
|
28
|
Deflorian F, Perez-Benito L, Lenselink EB, Congreve M, van Vlijmen HWT, Mason JS, Graaf CD, Tresadern G. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. J Chem Inf Model 2020; 60:5563-5579. [PMID: 32539374 DOI: 10.1021/acs.jcim.0c00449] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The computational prediction of relative binding free energies is a crucial goal for drug discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug target class. However, they present increased complexity to model compared to soluble globular proteins. Despite breakthroughs, experimental X-ray crystal and cryo-EM structures are challenging to attain, meaning computational models of the receptor and ligand binding mode are sometimes necessary. This leads to uncertainty in understanding ligand-protein binding induced changes such as, water positioning and displacement, side chain positioning, hydrogen bond networks, and the overall structure of the hydration shell around the ligand and protein. In other words, the very elements that define structure activity relationships (SARs) and are crucial for accurate binding free energy calculations are typically more uncertain for GPCRs. In this work we use free energy perturbation (FEP) to predict the relative binding free energies for ligands of two different GPCRs. We pinpoint the key aspects for success such as the important role of key water molecules, amino acid ionization states, and the benefit of equilibration with specific ligands. Initial calculations following typical FEP setup and execution protocols delivered no correlation with experiment, but we show how results are improved in a logical and systematic way. This approach gave, in the best cases, a coefficient of determination (R2) compared with experiment in the range of 0.6-0.9 and mean unsigned errors compared to experiment of 0.6-0.7 kcal/mol. We anticipate that our findings will be applicable to other difficult-to-model protein ligand data sets and be of wide interest for the community to continue improving FE binding energy predictions.
Collapse
Affiliation(s)
- Francesca Deflorian
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300, RA, The Netherlands
| | - Miles Congreve
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Herman W T van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Jonathan S Mason
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| |
Collapse
|
29
|
Leach K, Hannan FM, Josephs TM, Keller AN, Møller TC, Ward DT, Kallay E, Mason RS, Thakker RV, Riccardi D, Conigrave AD, Bräuner-Osborne H. International Union of Basic and Clinical Pharmacology. CVIII. Calcium-Sensing Receptor Nomenclature, Pharmacology, and Function. Pharmacol Rev 2020; 72:558-604. [PMID: 32467152 PMCID: PMC7116503 DOI: 10.1124/pr.119.018531] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The calcium-sensing receptor (CaSR) is a class C G protein-coupled receptor that responds to multiple endogenous agonists and allosteric modulators, including divalent and trivalent cations, L-amino acids, γ-glutamyl peptides, polyamines, polycationic peptides, and protons. The CaSR plays a critical role in extracellular calcium (Ca2+ o) homeostasis, as demonstrated by the many naturally occurring mutations in the CaSR or its signaling partners that cause Ca2+ o homeostasis disorders. However, CaSR tissue expression in mammals is broad and includes tissues unrelated to Ca2+ o homeostasis, in which it, for example, regulates the secretion of digestive hormones, airway constriction, cardiovascular effects, cellular differentiation, and proliferation. Thus, although the CaSR is targeted clinically by the positive allosteric modulators (PAMs) cinacalcet, evocalcet, and etelcalcetide in hyperparathyroidism, it is also a putative therapeutic target in diabetes, asthma, cardiovascular disease, and cancer. The CaSR is somewhat unique in possessing multiple ligand binding sites, including at least five putative sites for the "orthosteric" agonist Ca2+ o, an allosteric site for endogenous L-amino acids, two further allosteric sites for small molecules and the peptide PAM, etelcalcetide, and additional sites for other cations and anions. The CaSR is promiscuous in its G protein-coupling preferences, and signals via Gq/11, Gi/o, potentially G12/13, and even Gs in some cell types. Not surprisingly, the CaSR is subject to biased agonism, in which distinct ligands preferentially stimulate a subset of the CaSR's possible signaling responses, to the exclusion of others. The CaSR thus serves as a model receptor to study natural bias and allostery. SIGNIFICANCE STATEMENT: The calcium-sensing receptor (CaSR) is a complex G protein-coupled receptor that possesses multiple orthosteric and allosteric binding sites, is subject to biased signaling via several different G proteins, and has numerous (patho)physiological roles. Understanding the complexities of CaSR structure, function, and biology will aid future drug discovery efforts seeking to target this receptor for a diversity of diseases. This review summarizes what is known to date regarding key structural, pharmacological, and physiological features of the CaSR.
Collapse
Affiliation(s)
- Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Fadil M Hannan
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Tracy M Josephs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Andrew N Keller
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Thor C Møller
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Donald T Ward
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Enikö Kallay
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Rebecca S Mason
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Rajesh V Thakker
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Daniela Riccardi
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Arthur D Conigrave
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| | - Hans Bräuner-Osborne
- Drug Discovery Biology, Monash Institute of Pharmaceutical Science, Monash University, Parkville, Australia (K.L., T.M.J., A.N.K.); Nuffield Department of Women's & Reproductive Health (F.M.H.) and Academic Endocrine Unit, Radcliffe Department of Clinical Medicine (F.M.H., R.V.T.), University of Oxford, Oxford, United Kingdom; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (T.C.M., H.B.-O.); Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom (D.T.W.); Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria (E.K.); Physiology, School of Medical Sciences and Bosch Institute (R.S.M.) and School of Life & Environmental Sciences, Charles Perkins Centre (A.D.C.), University of Sydney, Sydney, Australia; and School of Biosciences, Cardiff University, Cardiff, United Kingdom (D.R.)
| |
Collapse
|
30
|
Sengmany K, Hellyer SD, Christopoulos A, Lapinsky DJ, Leach K, Gregory KJ. Differential contribution of metabotropic glutamate receptor 5 common allosteric binding site residues to biased allosteric agonism. Biochem Pharmacol 2020; 177:114011. [DOI: 10.1016/j.bcp.2020.114011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/29/2020] [Indexed: 01/06/2023]
|
31
|
Probe dependence and biased potentiation of metabotropic glutamate receptor 5 is mediated by differential ligand interactions in the common allosteric binding site. Biochem Pharmacol 2020; 177:114013. [DOI: 10.1016/j.bcp.2020.114013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/30/2020] [Indexed: 01/04/2023]
|
32
|
Sutkeviciute I, Vilardaga JP. Structural insights into emergent signaling modes of G protein-coupled receptors. J Biol Chem 2020; 295:11626-11642. [PMID: 32571882 DOI: 10.1074/jbc.rev120.009348] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/21/2020] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of cell membrane proteins, with >800 GPCRs in humans alone, and recognize highly diverse ligands, ranging from photons to large protein molecules. Very important to human medicine, GPCRs are targeted by about 35% of prescription drugs. GPCRs are characterized by a seven-transmembrane α-helical structure, transmitting extracellular signals into cells to regulate major physiological processes via heterotrimeric G proteins and β-arrestins. Initially viewed as receptors whose signaling via G proteins is delimited to the plasma membrane, it is now recognized that GPCRs signal also at various intracellular locations, and the mechanisms and (patho)physiological relevance of such signaling modes are actively investigated. The propensity of GPCRs to adopt different signaling modes is largely encoded in the structural plasticity of the receptors themselves and of their signaling complexes. Here, we review emerging modes of GPCR signaling via endosomal membranes and the physiological implications of such signaling modes. We further summarize recent structural insights into mechanisms of GPCR activation and signaling. We particularly emphasize the structural mechanisms governing the continued GPCR signaling from endosomes and the structural aspects of the GPCR resensitization mechanism and discuss the recently uncovered and important roles of lipids in these processes.
Collapse
Affiliation(s)
- Ieva Sutkeviciute
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jean-Pierre Vilardaga
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
33
|
Structure-based discovery and development of metabotropic glutamate receptor 5 negative allosteric modulators. ADVANCES IN PHARMACOLOGY 2020; 88:35-58. [PMID: 32416871 DOI: 10.1016/bs.apha.2020.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The metabotropic glutamate (mGlu) receptors are a family of eight class C G protein-coupled receptors (GPCRs) which modulate cell signaling and synaptic transmission to the major excitatory neurotransmitter l-glutamate (l-glutamic acid). Due to their role in modulating glutamate response, their widespread distribution in the central nervous system (CNS) and some evidence of dysregulation in disease, the mGlu receptors have become attractive pharmacological targets. As the orthosteric (glutamate) binding site is highly conserved across the eight mGlu receptors, it is difficult not only to generate ligands with subtype selectivity but, due to the nature of the binding site, with suitable drug-like properties to allow oral bioavailability and CNS penetration. Selective pharmacological targeting of a single receptor subtype can be achieved by targeting alternative (allosteric) binding sites. The nature of the allosteric binding pockets allows ligands to be developed that have good physical chemical properties as evidenced by several allosteric modulators of mGlu receptors entering clinical trials. The first negative allosteric modulators of the metabotropic glutamate 5 (mGlu5) receptor were discovered from high throughput screening activities. An alternative approach to drug discovery is to use structural knowledge to enable structure-based drug design (SBDD), which allows the design of molecules in a more rational, rather than empirical, fashion. Here we will describe the process of SBDD in the discovery of the mGlu5 negative allosteric modulator HTL0014242 and describe how knowledge of receptor structure can also be used to gain insights into the receptor activation mechanisms.
Collapse
|
34
|
Arsova A, Møller TC, Vedel L, Hansen JL, Foster SR, Gregory KJ, Bräuner-Osborne H. Detailed In Vitro Pharmacological Characterization of Clinically Tested Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5. Mol Pharmacol 2020; 98:49-60. [PMID: 32358164 DOI: 10.1124/mol.119.119032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/10/2020] [Indexed: 12/14/2022] Open
Abstract
Negative allosteric modulation of the metabotropic glutamate 5 (mGlu5) receptor has emerged as a potential strategy for the treatment of neurologic disorders. Despite the success in preclinical studies, many mGlu5 negative allosteric modulators (NAMs) that have reached clinical trials failed due to lack of efficacy. In this study, we provide a detailed in vitro pharmacological characterization of nine clinically and preclinically tested NAMs. We evaluated inhibition of l-glutamate-induced signaling with Ca2+ mobilization, inositol monophosphate (IP1) accumulation, extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation, and real-time receptor internalization assays on rat mGlu5 expressed in HEK293A cells. Moreover, we determined association rates (kon) and dissociation rates (koff), as well as NAM affinities with [3H]methoxy-PEPy binding experiments. kon and koff values varied greatly between the nine NAMs (34- and 139-fold, respectively) resulting in long receptor residence times (>400 min) for basimglurant and mavoglurant, medium residence times (10-30 min) for AZD2066, remeglurant, and (RS)-remeglurant, and low residence times (<10 mins) for dipraglurant, F169521, F1699611, and STX107. We found that all NAMs inhibited l-glutamate-induced mGlu5 receptor internalization, generally with a similar potency to IP1 accumulation and ERK1/2 phosphorylation, whereas Ca2+ mobilization was less potently inhibited. Operational model of allosterism analyses revealed that dipraglurant and (RS)-remeglurant were biased toward (affinity) receptor internalization and away (cooperativity) from the ERK1/2 phosphorylation pathway, respectively. Our study is the first to measure mGlu5 NAM binding kinetics and negative allosteric modulation of mGlu5 receptor internalization and adds significant new knowledge about the molecular pharmacology of a diverse range of clinically relevant NAMs. SIGNIFICANCE STATEMENT: The metabotropic glutamate 5 (mGlu5) receptor is important in many brain functions and implicated in several neurological pathologies. Negative allosteric modulators (NAMs) have shown promising results in preclinical models but have so far failed in human clinical trials. Here we provide the most comprehensive and comparative molecular pharmacological study to date of nine preclinically/clinically tested NAMs at the mGlu5 receptor, which is also the first study to measure ligand binding kinetics and negative allosteric modulation of mGlu5 receptor internalization.
Collapse
Affiliation(s)
- Angela Arsova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| | - Thor C Møller
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| | - Line Vedel
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| | - Jakob Lerche Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| | - Simon R Foster
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| | - Karen J Gregory
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.A., T.C.M., L.V., S.R.F., H.B.-O.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (K.J.G.); and Cardiovascular Research, Novo Nordisk A/S, Måløv, Denmark (J.L.H.)
| |
Collapse
|
35
|
Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
|
36
|
Severina HI, Georgiyants VA, Kovalenko SM, Avdeeva NV, Yarcev AI, Prohoda SN. Molecular docking studies of N-substituted 4-methoxy-6-oxo-1-aryl-pyridazine-3-carboxamide derivatives as potential modulators of glutamate receptors. RESEARCH RESULTS IN PHARMACOLOGY 2020. [DOI: 10.3897/rrpharmacology.6.52026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction: The virtual target-oriented screening is a necessary stage of modern drug-design. In the present study, the affinity of pyridazine derivatives for the most promising antiparkinsonian biotargets – I–III groups of metabotropic and ionotropic NMDA-glutamate receptors – was evaluated.
Materials and methods: Docking of the studied ligands to the active sites of biotargets – mGluR5, mGluR3, mGluR8, NMDA GluN2B – was performed using AutoDockVina. Base of the preparation of ligands and proteins – AutoDockTools-1.5.6. A Discovery Studio Visualizer 2017/R2 was used to visualize the interpretation of the results.
Results and discussion: A high degree of the affinity is predicted for group III of the metabotropic mGlu8 receptors – binding energy from -5.0 to -8.7 kcal/mol, compared to -6.1 kcal/mol of that of the reference drug (L-AP4), as well as for the ionotropic NMDA GluN2B receptors –binding energy from -8.7 to -11.6 kcal/mol, compared to -11.3 kcal/mol of that of ifenprodil.
Conclusion: The prospects of the searching for glutamate receptor modulators in a number of n-substituted 4-methoxy-6-oxo-1-aryl-pyridazine-3-carboxamide derivatives are proved. Some aspects of the structure-affinity relationship are discussed.
Collapse
|
37
|
Bruder M, Polo G, Trivella DBB. Natural allosteric modulators and their biological targets: molecular signatures and mechanisms. Nat Prod Rep 2020; 37:488-514. [PMID: 32048675 DOI: 10.1039/c9np00064j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to 2018Over the last decade more than two hundred single natural products were confirmed as natural allosteric modulators (alloNPs) of proteins. The compounds are presented and discussed with the support of a chemical space, constructed using a principal component analysis (PCA) of molecular descriptors from chemical compounds of distinct databases. This analysis showed that alloNPs are dispersed throughout the majority of the chemical space defined by natural products in general. Moreover, a cluster of alloNPs was shown to occupy a region almost devoid of allosteric modulators retrieved from a dataset composed mainly of synthetic compounds, further highlighting the importance to explore the entire natural chemical space for probing allosteric mechanisms. The protein targets which alloNPs bind to comprised 81 different proteins, which were classified into 5 major groups, with enzymes, in particular hydrolases, being the main representative group. The review also brings a critical interpretation on the mechanisms by which alloNPs display their molecular action on proteins. In the latter analysis, alloNPs were classified according to their final effect on the target protein, resulting in 3 major categories: (i) local alteration of the orthosteric site; (ii) global alteration in protein dynamics that change function; and (iii) oligomer stabilisation or protein complex destabilisation via protein-protein interaction in sites distant from the orthosteric site. G-protein coupled receptors (GPCRs), which use a combination of the three types of allosteric regulation found, were also probed by natural products. In summary, the natural allosteric modulators reviewed herein emphasise their importance for exploring alternative chemotherapeutic strategies, potentially pushing the boundaries of the druggable space of pharmacologically relevant drug targets.
Collapse
Affiliation(s)
- Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), National Centre for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil.
| | | | | |
Collapse
|
38
|
Zhao Y, Chen J, Liu Q, Li Y. Profiling the Structural Determinants of Aryl Benzamide Derivatives as Negative Allosteric Modulators of mGluR5 by In Silico Study. Molecules 2020; 25:molecules25020406. [PMID: 31963723 PMCID: PMC7024197 DOI: 10.3390/molecules25020406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 11/16/2022] Open
Abstract
Glutamate plays a crucial role in the treatment of depression by interacting with the metabotropic glutamate receptor subtype 5 (mGluR5), whose negative allosteric modulators (NAMs) are thus promising antidepressants. At present, to explore the structural features of 106 newly synthesized aryl benzamide series molecules as mGluR5 NAMs, a set of ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses were firstly carried out applying comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. In addition, receptor-based analysis, namely molecular docking and molecular dynamics (MD) simulations, were performed to further elucidate the binding modes of mGluR5 NAMs. As a result, the optimal CoMSIA model obtained shows that cross-validated correlation coefficient Q2 = 0.70, non-cross-validated correlation coefficient R2ncv = 0.89, predicted correlation coefficient R2pre = 0.87. Moreover, we found that aryl benzamide series molecules bind as mGluR5 NAMs at Site 1, which consists of amino acids Pro655, Tyr659, Ile625, Ile651, Ile944, Ser658, Ser654, Ser969, Ser965, Ala970, Ala973, Trp945, Phe948, Pro903, Asn907, Val966, Leu904, and Met962. This site is the same as that of other types of NAMs; mGluR5 NAMs are stabilized in the "linear" and "arc" configurations mainly through the H-bonds interactions, π-π stacking interaction with Trp945, and hydrophobic contacts. We hope that the models and information obtained will help understand the interaction mechanism of NAMs and design and optimize NAMs as new types of antidepressants.
Collapse
Affiliation(s)
- Yujing Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering, Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, China; (Y.Z.); (J.C.)
| | - Jiabin Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering, Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, China; (Y.Z.); (J.C.)
| | - Qilei Liu
- Institute of Chemical Process Systems Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China;
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering, Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, China; (Y.Z.); (J.C.)
- Correspondence: ; Tel.: +86-15640888728
| |
Collapse
|
39
|
Discovery of dihydropyrazino-benzimidazole derivatives as metabotropic glutamate receptor-2 (mGluR2) positive allosteric modulators (PAMs). Eur J Med Chem 2020; 186:111881. [DOI: 10.1016/j.ejmech.2019.111881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 11/17/2022]
|
40
|
Pérez-Benito L, Llinas del Torrent C, Pardo L, Tresadern G. The computational modeling of allosteric modulation of metabotropic glutamate receptors. FROM STRUCTURE TO CLINICAL DEVELOPMENT: ALLOSTERIC MODULATION OF G PROTEIN-COUPLED RECEPTORS 2020; 88:1-33. [DOI: 10.1016/bs.apha.2020.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
41
|
Jong YJI, Harmon SK, O’Malley KL. Location and Cell-Type-Specific Bias of Metabotropic Glutamate Receptor, mGlu 5, Negative Allosteric Modulators. ACS Chem Neurosci 2019; 10:4558-4570. [PMID: 31609579 DOI: 10.1021/acschemneuro.9b00415] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Emerging data indicate that G-protein coupled receptor (GPCR) signaling is determined by not only the agonist and a given receptor but also a variety of cell-type-specific factors that can influence a receptor's response. For example, the metabotropic glutamate receptor, mGlu5, which is implicated in a number of neuropsychiatric disorders such as depression, anxiety, and autism, also signals from inside the cell which leads to sustained Ca2+ mobilization versus rapid transient responses. Because mGlu5 is an important drug target, many negative allosteric modulators (NAMs) have been generated to modulate its activity. Here we show that NAMs such as AFQ056, AZD2066, and RG7090 elicit very different end points when tested in postnatal neuronal cultures expressing endogenous mGlu5 receptors. For example, AFQ056 fails to block intracellular mGlu5-mediated Ca2+ increases whereas RG7090 is very effective. These differences are not due to differential receptor levels, since about the same number of mGlu5 receptors are present on neurons from the cortex, hippocampus, and striatum based on pharmacological, biochemical, and molecular data. Moreover, biotinylation studies reveal that more than 90% of the receptor is intracellular in these neurons. Taken together, these data indicate that the tested NAMs exhibit both location-dependent and cell type specific bias for mGlu5-mediated Ca2+ mobilization which may affect clinical outcomes.
Collapse
Affiliation(s)
- Yuh-Jiin Ivy Jong
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Steven K. Harmon
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Karen L. O’Malley
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| |
Collapse
|
42
|
Ferenczy GG, Keserű GM. Thermodynamic profiling for fragment-based lead discovery and optimization. Expert Opin Drug Discov 2019; 15:117-129. [PMID: 31741402 DOI: 10.1080/17460441.2020.1691166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The enthalpic and entropic components of the ligand-protein binding free energy reflect the type and quality of the interactions and relate to the physicochemical properties of the ligands. These findings have significance in medicinal chemistry optimizations since they suggest that the thermodynamic profiling of the binding may help monitor and control the unfavorable size and hydrophobicity increase typically accompanying affinity improvements and leading to suboptimal pharmacokinetic properties.Areas covered: This review describes the ligand-protein binding event in terms of elementary steps, their associated interactions, and their enthalpic and entropic consequences. The relationships among the breaking and forming interactions, the binding thermodynamic profile, and the physicochemical properties of the ligands are also discussed.Expert opinion: Analysis of the size dependence of available affinity and favorable enthalpy highlights the limitation of the simultaneous optimization of these quantities. Indeed, moderate, rather than very high affinities can be conciliated with favorable physicochemical and pharmacokinetic profiles as it is supported by the affinity range of historical oral drugs. Although thermodynamic quantities are not suitable endpoints for medicinal chemistry optimizations owing to the complexity of the binding thermodynamics, thermodynamic profiling together with structural studies can be advantageously used to understand the details of the binding process and to optimize it.
Collapse
Affiliation(s)
- György G Ferenczy
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
| |
Collapse
|
43
|
Orgován Z, Ferenczy GG, Keserű GM. Fragment-Based Approaches for Allosteric Metabotropic Glutamate Receptor (mGluR) Modulators. Curr Top Med Chem 2019; 19:1768-1781. [PMID: 31393248 DOI: 10.2174/1568026619666190808150039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/03/2019] [Accepted: 07/29/2019] [Indexed: 12/28/2022]
Abstract
Metabotropic glutamate receptors (mGluR) are members of the class C G-Protein Coupled Receptors (GPCR-s) and have eight subtypes. These receptors are responsible for a variety of functions in the central and peripheral nervous systems and their modulation has therapeutic utility in neurological and psychiatric disorders. It was previously established that selective orthosteric modulation of these receptors is challenging, and this stimulated the search for allosteric modulators. Fragment-Based Drug Discovery (FBDD) is a viable approach to find ligands binding at allosteric sites owing to their limited size and interactions. However, it was also observed that the structure-activity relationship of allosteric modulators is often sharp and inconsistent. This can be attributed to the characteristics of the allosteric binding site of mGluRs that is a water channel where ligand binding is accompanied with induced fit and interference with the water network, both playing a role in receptor activation. In this review, we summarize fragment-based drug discovery programs on mGluR allosteric modulators and their contribution identifying of new mGluR ligands with better activity and selectivity.
Collapse
Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar Tudosok Korutja, Budapest H-1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar Tudosok Korutja, Budapest H-1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar Tudosok Korutja, Budapest H-1117, Hungary
| |
Collapse
|
44
|
Zarzycka B, Zaidi SA, Roth BL, Katritch V. Harnessing Ion-Binding Sites for GPCR Pharmacology. Pharmacol Rev 2019; 71:571-595. [PMID: 31551350 PMCID: PMC6782022 DOI: 10.1124/pr.119.017863] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Endogenous ions play important roles in the function and pharmacology of G-protein coupled receptors (GPCRs). Historically the evidence for ionic modulation of GPCR function dates to 1973 with studies of opioid receptors, where it was demonstrated that physiologic concentrations of sodium allosterically attenuated agonist binding. This Na+-selective effect was distinct from effects of other monovalent and divalent cations, with the latter usually counteracting sodium's negative allosteric modulation of binding. Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na+ site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophysical, and structural characterization of ions bound to GPCRs. Taken together, these findings provide a molecular understanding of the unique roles of Na+ and other ions as GPCR allosteric modulators. We will also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacological profiles. SIGNIFICANCE STATEMENT: The function and pharmacology of GPCRs strongly depend on the presence of mono and divalent ions in experimental assays and in living organisms. Recent insights into the molecular mechanism of this ion-dependent allosterism from structural, biophysical, biochemical, and computational studies provide quantitative understandings of the pharmacological effects of drugs in vitro and in vivo and open new avenues for the rational design of chemical probes and drug candidates with improved properties.
Collapse
Affiliation(s)
- Barbara Zarzycka
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Saheem A Zaidi
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bryan L Roth
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Vsevolod Katritch
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
45
|
Orgován Z, Ferenczy GG, Keserű GM. The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu 5 receptor case study. J Comput Aided Mol Des 2019; 33:787-797. [PMID: 31542869 PMCID: PMC6825653 DOI: 10.1007/s10822-019-00224-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/15/2019] [Indexed: 12/22/2022]
Abstract
Stabilizing unique receptor conformations, allosteric modulators of G-protein coupled receptors (GPCRs) might open novel treatment options due to their new pharmacological action, their enhanced specificity and selectivity in both binding and signaling. Ligand binding occurs at intrahelical allosteric sites and involves significant induced fit effects that include conformational changes in the local protein environment and water networks. Based on the analysis of available crystal structures of metabotropic glutamate receptor 5 (mGlu5) we investigated these effects in the binding of mGlu5 receptor negative allosteric modulators. A large set of retrospective virtual screens revealed that the use of multiple protein structures and the inclusion of selected water molecules improves virtual screening performance compared to conventional docking strategies. The role of water molecules and protein flexibility in ligand binding can be taken into account efficiently by the proposed docking protocol that provided reasonable enrichment of true positives. This protocol is expected to be useful also for identifying intrahelical allosteric modulators for other GPCR targets.
Collapse
Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary.
| |
Collapse
|
46
|
Ribeiro JML, Filizola M. Insights From Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders. Front Mol Neurosci 2019; 12:207. [PMID: 31507375 PMCID: PMC6716474 DOI: 10.3389/fnmol.2019.00207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/07/2019] [Indexed: 01/20/2023] Open
Abstract
Effective treatments for pain management remain elusive due to the dangerous side-effects of current gold-standard opioid analgesics, including the respiratory depression that has led to skyrocketing death rates from opioid overdoses over the past decade. In an attempt to address the horrific opioid crisis worldwide, the National Institute on Drug Abuse has recently proposed boosting research on specific pharmacological mechanisms mediated by a number of G protein-coupled receptors (GPCRs). This research is expected to expedite the discovery of medications for opioid overdose and opioid use disorders, leading toward a safer and more effective treatment of pain. Here, we review mechanistic insights from recent all-atom molecular dynamics simulations of a specific subset of GPCRs for which high-resolution experimental structures are available, including opioid, cannabinoid, orexin, metabotropic glutamate, and dopamine receptor subtypes.
Collapse
Affiliation(s)
- João Marcelo Lamim Ribeiro
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
47
|
Jiang QX. Structural Variability in the RLR-MAVS Pathway and Sensitive Detection of Viral RNAs. Med Chem 2019; 15:443-458. [PMID: 30569868 DOI: 10.2174/1573406415666181219101613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 12/25/2022]
Abstract
Cells need high-sensitivity detection of non-self molecules in order to fight against pathogens. These cellular sensors are thus of significant importance to medicinal purposes, especially for treating novel emerging pathogens. RIG-I-like receptors (RLRs) are intracellular sensors for viral RNAs (vRNAs). Their active forms activate mitochondrial antiviral signaling protein (MAVS) and trigger downstream immune responses against viral infection. Functional and structural studies of the RLR-MAVS signaling pathway have revealed significant supramolecular variability in the past few years, which revealed different aspects of the functional signaling pathway. Here I will discuss the molecular events of RLR-MAVS pathway from the angle of detecting single copy or a very low copy number of vRNAs in the presence of non-specific competition from cytosolic RNAs, and review key structural variability in the RLR / vRNA complexes, the MAVS helical polymers, and the adapter-mediated interactions between the active RLR / vRNA complex and the inactive MAVS in triggering the initiation of the MAVS filaments. These structural variations may not be exclusive to each other, but instead may reflect the adaptation of the signaling pathways to different conditions or reach different levels of sensitivity in its response to exogenous vRNAs.
Collapse
Affiliation(s)
- Qiu-Xing Jiang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, United States
| |
Collapse
|
48
|
Jójárt B, Orgován Z, Márki Á, Pándy-Szekeres G, Ferenczy GG, Keserű GM. Allosteric activation of metabotropic glutamate receptor 5. J Biomol Struct Dyn 2019; 38:2624-2632. [DOI: 10.1080/07391102.2019.1638302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Szeged, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Márki
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, Hungary
| | - Gáspár Pándy-Szekeres
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|
49
|
Cong X, Chéron JB, Golebiowski J, Antonczak S, Fiorucci S. Allosteric Modulation Mechanism of the mGluR 5 Transmembrane Domain. J Chem Inf Model 2019; 59:2871-2878. [PMID: 31025859 DOI: 10.1021/acs.jcim.9b00045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Positive allosteric modulators (PAMs) of metabotropic glutamate receptor type 5 (mGluR5), a prototypical class C G protein-coupled receptor (GPCR), have shown therapeutic potential for various neurological disorders. Understanding the allosteric activation mechanism is essential for the rational design of mGluR5 PAMs. We studied the actions of positive and negative allosteric modulators within the transmembrane domain of mGluR5, using enhance-sampling all-atom molecular dynamics simulations. We found dual binding modes of the PAM, associated with distinct shapes of the allosteric pocket. The negative allosteric modulators, in contrast, showed only one binding mode. The simulations revealed the mechanism by which the PAM activated the receptor, in the absence of the orthosteric agonist (the so-called allosteric agonism). The mechanism relied on dynamic communications between amino-acid motifs that are highly conserved across class C GPCRs. The findings may guide structure-based design and virtual screening of allosteric modulators for mGluR5 as well as for other class C GPCRs.
Collapse
Affiliation(s)
- Xiaojing Cong
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| | - Jean-Baptiste Chéron
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France.,Department of Brain and Cognitive Sciences , Daegu Gyeongbuk Institute of Science and Technology , Daegu 711-873 , South Korea
| | - Serge Antonczak
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS , Institut de Chimie de Nice UMR7272 , Nice 06108 , France
| |
Collapse
|
50
|
Analysis of tractable allosteric sites in G protein-coupled receptors. Sci Rep 2019; 9:6180. [PMID: 30992500 PMCID: PMC6467999 DOI: 10.1038/s41598-019-42618-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/28/2019] [Indexed: 11/21/2022] Open
Abstract
Allosteric modulation of G protein-coupled receptors represent a promising mechanism of pharmacological intervention. Dramatic developments witnessed in the structural biology of membrane proteins continue to reveal that the binding sites of allosteric modulators are widely distributed, including along protein surfaces. Here we restrict consideration to intrahelical and intracellular sites together with allosteric conformational locks, and show that the protein mapping tools FTMap and FTSite identify 83% and 88% of such experimentally confirmed allosteric sites within the three strongest sites found. The methods were also able to find partially hidden allosteric sites that were not fully formed in X-ray structures crystallized in the absence of allosteric ligands. These results confirm that the intrahelical sites capable of binding druglike allosteric modulators are among the strongest ligand recognition sites in a large fraction of GPCRs and suggest that both FTMap and FTSite are useful tools for identifying allosteric sites and to aid in the design of such compounds in a range of GPCR targets.
Collapse
|