1
|
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
|
2
|
Kapur B, Baldessari F, Lazaratos M, Nar H, Schnapp G, Giorgetti A, Bondar AN. Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68. Comput Struct Biotechnol J 2023; 21:4370-4384. [PMID: 37711190 PMCID: PMC10498176 DOI: 10.1016/j.csbj.2023.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Proton-sensing G Protein Coupled Receptors (GPCRs) sense changes in the extracellular pH to effect cell signaling for cellular homeostasis. They tend to be overexpressed in solid tumors associated with acidic extracellular pH, and are of direct interest as drug targets. How proton-sensing GPCRs sense extracellular acidification and activate upon protonation change is important to understand, because it may guide the design of therapeutics. Lack of publicly available experimental structures make it challenging to discriminate between conflicting mechanisms proposed for proton-binding, as main roles have been assigned to either an extracellular histidine cluster or to an internal carboxylic triad. Here we present a protocol to derive and evaluate structural models of the proton-sensing GPR68. This approach integrates state-of-the-art homology modeling with microsecond-timescale atomistic simulations, and with a detailed assessment of the compatibility of the structural models with known structural features of class A GPCRs. To decipher structural elements of potential interest for protonation-coupled conformational changes of GPR68, we used the best-compatible model as a starting point for independent atomistic simulations of GPR68 with different protonation states, and graph computations to characterize the response of GPR68 to changes in protonation. We found that GPR68 hosts an extended hydrogen-bond network that inter-connects the extracellular histidine cluster to the internal carboxylic triad, and which can even reach groups at the cytoplasmic G-protein binding site. Taken together, results suggest that GPR68 relies on dynamic, hydrogen-bond networks to inter-connect extracellular and internal proton-binding sites, and to elicit conformational changes at the cytoplasmic G-protein binding site.
Collapse
Affiliation(s)
- Bhav Kapur
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
- Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | | | - Michalis Lazaratos
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Herbert Nar
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Gisela Schnapp
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alejandro Giorgetti
- University of Verona, Department of Biotechnology, 37134 Verona, Italy
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania
| |
Collapse
|
3
|
Vani BP, Aranganathan A, Wang D, Tiwary P. AlphaFold2-RAVE: From Sequence to Boltzmann Ranking. J Chem Theory Comput 2023; 19:4351-4354. [PMID: 37171364 PMCID: PMC10524496 DOI: 10.1021/acs.jctc.3c00290] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
While AlphaFold2 is rapidly being adopted as a new standard in protein structure predictions, it is limited to single structures. This can be insufficient for the inherently dynamic world of biomolecules. In this Letter, we propose AlphaFold2-RAVE, an efficient protocol for obtaining Boltzmann-ranked ensembles from sequence. The method uses structural outputs from AlphaFold2 as initializations for artificial intelligence-augmented molecular dynamics. We release the method as an open-source code and demonstrate results on different proteins.
Collapse
Affiliation(s)
- Bodhi P. Vani
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Akashnathan Aranganathan
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| | - Dedi Wang
- Biophysics Program and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park 20742, USA
| |
Collapse
|
4
|
Díaz O, Renault P, Giraldo J. Evaluating Allosteric Perturbations in Cannabinoid Receptor 1 by In Silico Single-Point Mutation. ACS OMEGA 2022; 7:37873-37884. [PMID: 36312415 PMCID: PMC9608382 DOI: 10.1021/acsomega.2c04980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Cannabinoid receptor 1 (CB1) is a promising drug target involved in many physiological processes. Using atomistic molecular dynamics (MD) simulations, we examined the structural effect of F237L mutation on CB1, a mutation that has qualitatively similar effects to allosteric ligand ORG27569 binding. This mutation showed a global effect on CB1 conformations. Among the observed effects, TM6 outward movement and the conformational change of the NPxxY motif upon receptor activation by CB1 agonist CP55940 were hindered compared to wt CB1. Within the orthosteric binding site, CP55940 interactions with CB1 were altered. Our results revealed that allosteric perturbations introduced by the mutation had a global impact on receptor conformations, suggesting that the mutation site is a key region for allosteric modulation in CB1.
Collapse
Affiliation(s)
- Oscar Díaz
- Laboratory
of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística
and Institut de Neurociències, Universitat
Autònoma de Barcelona, Bellaterra 08193, Spain
- Instituto
de Salud Carlos III, Centro de Investigación
Biomédica en Red de Salud Mental (CIBERSAM), Madrid 28029, Spain
- Unitat
de Neurociència Traslacional, Parc Taulí Hospital Universitari,
Institut d’Investigació i Innovació Parc Taulí
(I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Pedro Renault
- Laboratory
of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística
and Institut de Neurociències, Universitat
Autònoma de Barcelona, Bellaterra 08193, Spain
- Instituto
de Salud Carlos III, Centro de Investigación
Biomédica en Red de Salud Mental (CIBERSAM), Madrid 28029, Spain
- Unitat
de Neurociència Traslacional, Parc Taulí Hospital Universitari,
Institut d’Investigació i Innovació Parc Taulí
(I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Jesús Giraldo
- Laboratory
of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística
and Institut de Neurociències, Universitat
Autònoma de Barcelona, Bellaterra 08193, Spain
- Instituto
de Salud Carlos III, Centro de Investigación
Biomédica en Red de Salud Mental (CIBERSAM), Madrid 28029, Spain
- Unitat
de Neurociència Traslacional, Parc Taulí Hospital Universitari,
Institut d’Investigació i Innovació Parc Taulí
(I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| |
Collapse
|
5
|
Zhang H, Chu G, Wang G, Yao M, Lu S, Chen T. Mechanistic Understanding of the Palmitoylation of G o Protein in the Allosteric Regulation of Adhesion Receptor GPR97. Pharmaceutics 2022; 14:pharmaceutics14091856. [PMID: 36145604 PMCID: PMC9504338 DOI: 10.3390/pharmaceutics14091856] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Adhesion G-protein-coupled receptors (aGPCRs)—a major family of GPCRs—play critical roles in the regulation of tissue development and cancer progression. The orphan receptor GPR97, activated by glucocorticoid stress hormones, is a prototypical aGPCR. Although it has been established that the palmitoylation of the C-terminal Go protein is essential for Go’s efficient engagement with the active GPR97, the detailed allosteric mechanism remains to be clarified. Hence, we performed extensive large-scale molecular dynamics (MD) simulations of the GPR97−Go complex in the presence or absence of Go palmitoylation. The conformational landscapes analyzed by Markov state models revealed that the overall conformation of GPR97 is preferred to be fully active when interacting with palmitoylated Go protein. Structural and energetic analyses indicated that the palmitoylation of Go can allosterically stabilize the critical residues in the ligand-binding pocket of GPR97 and increase the affinity of the ligand for GPR97. Furthermore, the community network analysis suggests that the palmitoylation of Go not only allosterically strengthens the internal interactions between Gαo and Gβγ, but also enhances the coupling between Go and GPR97. Our study provides mechanistic insights into the regulation of aGPCRs via post-translational modifications of the Go protein, and offers guidance for future drug design of aGPCRs.
Collapse
Affiliation(s)
- Hao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, China
| | - Guojun Chu
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Gaoming Wang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Min Yao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200011, China
- Correspondence: (M.Y.); (S.L.); (T.C.)
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Correspondence: (M.Y.); (S.L.); (T.C.)
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
- Correspondence: (M.Y.); (S.L.); (T.C.)
| |
Collapse
|
6
|
Bello M. Molecular Basis of Inhibitory Mechanism of Naltrexone and Its Metabolites through Structural and Energetic Analyses. Molecules 2022; 27:molecules27154919. [PMID: 35956868 PMCID: PMC9369988 DOI: 10.3390/molecules27154919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Naltrexone is a potent opioid antagonist with good blood–brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of naltrexone and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. Naltrexone and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to the molecular mechanics–generalized Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that naltrexone and its derivatives showed differences in protein–ligand interactions; however, they shared contacts with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of naltrexone compared to its derivatives.
Collapse
Affiliation(s)
- Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Mexico City 11340, Mexico
| |
Collapse
|
7
|
Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
Collapse
Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
8
|
Abstract
Sphingosine-1-phosphate (S1P) receptors are valid therapeutic targets to treat autoimmune diseases, such as relapsing multiple sclerosis and ulcerative colitis. Particularly, S1PR1 is well characterized because of its nonredundant functions on T and B cells’ egress. However, the activation mechanism of S1PR1 is still poorly understood. Therefore, we determined active S1PR1–Gi complex structures bound to distinct agonists. Phosphorylated Fingolimod [(S)-FTY720-P] could modulate lymphocyte trafficking and treat multiple sclerosis. The nonlipid-like agonist CBP-307 is currently being evaluated in a global phase 2 clinical study in moderate to severe ulcerative colitis and Crohn’s disease. Meanwhile, two binding poses of CBP-307 and the unoccupied subpocket we observed may provide opportunities to improve further the efficacy and specificity of CBP-307 targeting different S1P receptors. As a critical sphingolipid metabolite, sphingosine-1-phosphate (S1P) plays an essential role in immune and vascular systems. There are five S1P receptors, designated as S1PR1 to S1PR5, encoded in the human genome, and their activities are governed by endogenous S1P, lipid-like S1P mimics, or nonlipid-like therapeutic molecules. Among S1PRs, S1PR1 stands out due to its nonredundant functions, such as the egress of T and B cells from the thymus and secondary lymphoid tissues, making it a potential therapeutic target. However, the structural basis of S1PR1 activation and regulation by various agonists remains unclear. Here, we report four atomic resolution cryo-electron microscopy (cryo-EM) structures of Gi-coupled human S1PR1 complexes: bound to endogenous agonist d18:1 S1P, benchmark lipid-like S1P mimic phosphorylated Fingolimod [(S)-FTY720-P], or nonlipid-like therapeutic molecule CBP-307 in two binding modes. Our results revealed the similarities and differences of activation of S1PR1 through distinct ligands binding to the amphiphilic orthosteric pocket. We also proposed a two-step “shallow to deep” transition process of CBP-307 for S1PR1 activation. Both binding modes of CBP-307 could activate S1PR1, but from shallow to deep transition may trigger the rotation of the N-terminal helix of Gαi and further stabilize the complex by increasing the Gαi interaction with the cell membrane. We combine with extensive biochemical analysis and molecular dynamic simulations to suggest key steps of S1P binding and receptor activation. The above results decipher the common feature of the S1PR1 agonist recognition and activation mechanism and will firmly promote the development of therapeutics targeting S1PRs.
Collapse
|
9
|
GPCR large-amplitude dynamics by 19F-NMR of aprepitant bound to the neurokinin 1 receptor. Proc Natl Acad Sci U S A 2022; 119:e2122682119. [PMID: 35377814 PMCID: PMC9169749 DOI: 10.1073/pnas.2122682119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Comparisons of G protein-coupled receptor (GPCR) complexes with agonists and antagonists based on X-ray crystallography and cryo-electron microscopy structure determinations show differences in the width of the orthosteric ligand binding groove over the range from 0.3 to 2.9 Å. Here, we show that there are transient structure fluctuations with amplitudes up to at least 6 Å. The experiments were performed with the neurokinin 1 receptor (NK1R), a GPCR of class A that is involved in inflammation, pain, and cancer. We used 19F-NMR observation of aprepitant, which is an approved drug that targets NK1R for the treatment of chemotherapy-induced nausea and vomiting. Aprepitant includes a bis-trifluoromethyl-phenyl ring attached with a single bond to the core of the molecule; 19F-NMR revealed 180° flipping motions of this ring about this bond. In the picture emerging from the 19F-NMR data, the GPCR transmembrane helices undergo large-scale floating motions in the lipid bilayer. The functional implication is of extensive promiscuity of initial ligand binding, primarily determined by size and shape of the ligand, with subsequent selection by unique interactions between atom groups of the ligand and the GPCR within the binding groove. This second step ensures the wide range of different efficacies documented for GPCR-targeting drugs. The NK1R data also provide a rationale for the observation that diffracting GPCR crystals are obtained for complexes with only very few of the ligands from libraries of approved drugs and lead compounds that bind to the receptors.
Collapse
|
10
|
Baccouch R, Rascol E, Stoklosa K, Alves ID. The role of the lipid environment in the activity of G protein coupled receptors. Biophys Chem 2022; 285:106794. [DOI: 10.1016/j.bpc.2022.106794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/11/2022] [Accepted: 03/08/2022] [Indexed: 12/21/2022]
|
11
|
Li L, Zhang J, Sun W, Gong W, Tian C, Shi P, Shi C. Allosteric conformational changes of G proteins upon its interaction with membrane and GPCR. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.07.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Topin J, Bouysset C, Pacalon J, Kim Y, Rhyu MR, Fiorucci S, Golebiowski J. Functional molecular switches of mammalian G protein-coupled bitter-taste receptors. Cell Mol Life Sci 2021; 78:7605-7615. [PMID: 34687318 PMCID: PMC11073308 DOI: 10.1007/s00018-021-03968-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Bitter taste receptors (TAS2Rs) are a poorly understood subgroup of G protein-coupled receptors (GPCRs). The experimental structure of these receptors has yet to be determined, and key-residues controlling their function remain mostly unknown. We designed an integrative approach to improve comparative modeling of TAS2Rs. Using current knowledge on class A GPCRs and existing experimental data in the literature as constraints, we pinpointed conserved motifs to entirely re-align the amino-acid sequences of TAS2Rs. We constructed accurate homology models of human TAS2Rs. As a test case, we examined the accuracy of the TAS2R16 model with site-directed mutagenesis and in vitro functional assays. This combination of in silico and in vitro results clarifies sequence-function relationships and proposes functional molecular switches that encode agonist sensing and downstream signaling mechanisms within mammalian TAS2Rs sequences.
Collapse
Affiliation(s)
- Jérémie Topin
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Cédric Bouysset
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Jody Pacalon
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Yiseul Kim
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Mee-Ra Rhyu
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Sébastien Fiorucci
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Jérôme Golebiowski
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, 711-873, Republic of Korea
| |
Collapse
|
13
|
van Aalst E, Koneri J, Wylie BJ. In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3. MEMBRANES 2021; 11:570. [PMID: 34436333 PMCID: PMC8401243 DOI: 10.3390/membranes11080570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/14/2023]
Abstract
CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms of cancer. However, little is known about how CCR3 functionally interacts with its bilayer environment. Here, we investigate cholesterol binding sites in silico through Coarse-Grained Molecular Dynamics (MD) and Pylipid analysis using an extensively validated homology model based on the crystal structure of CCR5. These simulations identified several cholesterol binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs in CCR3. One such site, a CARC site in TM1, in conjunction with aliphatic residues in TM7, emerged as a candidate for future investigation based on the cholesterol residency time within the binding pocket. This site forms the core of a cholesterol binding site previously observed in computational studies of CCR2 and CCR5. Most importantly, these cholesterol binding sites are conserved in other chemokine receptors and may provide clues to cholesterol regulation mechanisms in this subfamily of Class A GPCRs.
Collapse
Affiliation(s)
| | | | - Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.v.A.); (J.K.)
| |
Collapse
|
14
|
Ricarte A, Dalton JAR, Giraldo J. Structural Assessment of Agonist Efficacy in the μ-Opioid Receptor: Morphine and Fentanyl Elicit Different Activation Patterns. J Chem Inf Model 2021; 61:1251-1274. [PMID: 33448226 DOI: 10.1021/acs.jcim.0c00890] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the past two decades, the opioid epidemic in the United States and Canada has evidenced the need for a better understanding of the molecular mechanisms of medications used to fight pain. Morphine and fentanyl are widely used in opiate-mediated analgesia for the treatment of chronic pain. These compounds target the μ-opioid receptor (MOR), a class A G protein-coupled receptor (GPCR). In light of described higher efficacy of fentanyl with respect to morphine, we have performed independent μs-length unbiased molecular dynamics (MD) simulations of MOR complexes with each of these ligands, including the MOR antagonist naltrexone as a negative control. Consequently, MD simulations totaling 58 μs have been conducted to elucidate at the atomic level ligand-specific receptor activity and signal transmission in the MOR. In particular, we have identified stable binding poses of morphine and fentanyl, which interact differently with the MOR. Different ligand-receptor interaction landscapes directly induce sidechain conformational changes of orthosteric pocket residues: Asp1493.32, Tyr1503.33, Gln1262.60, and Lys2355.39. The induced conformations determine Asp1493.32-Tyr3287.43 sidechain-sidechain interactions and Trp2956.48-Ala2425.46 sidechain-backbone H-bond formations, as well as Met1533.36 conformational changes. In addition to differences in ligand binding, different intracellular receptor conformational changes are observed as morphine preferentially activates transmembrane (TM) helices: TM3 and TM5, while fentanyl preferentially activates TM6 and TM7. As conformational changes in TM6 and TM7 are widely described as being the most crucial aspect in GPCR activation, this may contribute to the greater efficacy of fentanyl over morphine. These computationally observed functional differences between fentanyl and morphine may provide new avenues for the design of safer but not weaker opioid drugs because it is desirable to increase the safety of medicines without sacrificing their efficacy.
Collapse
Affiliation(s)
- Adrián Ricarte
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 28029 Madrid, Spain
| | - James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 28029 Madrid, Spain
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 28029 Madrid, Spain
| |
Collapse
|
15
|
Baldessari F, Capelli R, Carloni P, Giorgetti A. Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors. Comput Struct Biotechnol J 2020; 18:1153-1159. [PMID: 32489528 PMCID: PMC7260681 DOI: 10.1016/j.csbj.2020.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 12/26/2022] Open
Abstract
We present an approach that, by integrating structural data with Direct Coupling Analysis, is able to pinpoint most of the interaction hotspots (i.e. key residues for the biological activity) across very sparse protein families in a single run. An application to the Class A G-protein coupled receptors (GPCRs), both in their active and inactive states, demonstrates the predictive power of our approach. The latter can be easily extended to any other kind of protein family, where it is expected to highlight most key sites involved in their functional activity.
Collapse
Affiliation(s)
- Filippo Baldessari
- Department of Biotechnology, Università di Verona, Ca Vignal 1, strada Le Grazie 15, I-37134 Verona, Italy
| | - Riccardo Capelli
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
| | - Alejandro Giorgetti
- Department of Biotechnology, Università di Verona, Ca Vignal 1, strada Le Grazie 15, I-37134 Verona, Italy
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
| |
Collapse
|
16
|
Doi T, Kikuta K, Tani K. Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal. Biochemistry 2020; 59:1718-1727. [PMID: 32343134 DOI: 10.1021/acs.biochem.0c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously reported the crystal structures of endothelin-1 (ET-1)-bound, ligand-free, and antagonist bosentan-bound forms of the thermostabilized ET type B receptor (ETB). Although other agonist-bound structures of ETB have been determined, the interactions for high-affinity binding and ETB receptor activation, as well as the roles of rearrangement of the hydrogen-bond network surrounding the ligand in G protein activation, remain elusive. ET-1, a 21-amino acid residue peptide, plays fundamental roles in basal vascular tone, sodium balance, cell proliferation, and stress-responsive regulation. We studied the interactions between the ET-1(8-21) peptide and ETB in the ligand binding and activation of ETB using a series of Ala-substituted ET-1(8-21) analogues and the mutated ETB. We found that while D8, L17, D18, I20, and W21 were responsible for high-affinity binding and potent G protein activation, Y13 and F14 in the helical region of ET-1 are prerequisites for the full activation of ETB via interactions near the extracellular side. Furthermore, we introduced the mutation into the residues around the ET-1 binding pocket of ETB. The results showed that while S1843.35, W3366.48, N3787.45, and S3797.46 in a conserved polar network are required for full activation, N1191.50, D1472.50, and N3827.49 are essential for G protein activation via direct interactions after rearrangement upon ET-1 binding. These results demonstrate that both interactions near the extracellular side and within the transmembrane helices with ET-1 play crucial roles in the full activation of the ETB receptor.
Collapse
Affiliation(s)
- Tomoko Doi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kohei Kikuta
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Tani
- Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| |
Collapse
|
17
|
Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18. Biomolecules 2020; 10:biom10050686. [PMID: 32365486 PMCID: PMC7277601 DOI: 10.3390/biom10050686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.
Collapse
|
18
|
Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions. PLoS Comput Biol 2020; 16:e1007818. [PMID: 32298258 PMCID: PMC7188303 DOI: 10.1371/journal.pcbi.1007818] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/28/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.
Collapse
|
19
|
Lans I, Díaz Ó, Dalton JAR, Giraldo J. Exploring the Activation Mechanism of the mGlu5 Transmembrane Domain. Front Mol Biosci 2020; 7:38. [PMID: 32211419 PMCID: PMC7069277 DOI: 10.3389/fmolb.2020.00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/18/2020] [Indexed: 01/14/2023] Open
Abstract
As a class C GPCR and regulator of synaptic activity, mGlu5 is an attractive drug target, potentially offering treatment for several neurologic and psychiatric disorders. As little is known about the activation mechanism of mGlu5 at a structural level, potential of mean force calculations linked to molecular dynamics simulations were performed on the mGlu5 transmembrane domain crystal structure to explore various internal mechanisms responsible for its activation. Our results suggest that the hydrophilic interactions between intracellular loop 1 and the intracellular side of TM6 have to be disrupted to reach a theoretically active-like conformation. In addition, interactions between residues that are key for mGlu5 activation (Tyr6593.44 and Ile7515.51) and mGlu5 inactivation (Tyr6593.44 and Ser8097.39) have been identified. Inasmuch as mGlu5 receptor signaling is poorly understood, potentially showing a complex network of micro-switches and subtle structure-activity relationships, the present study represents a step forward in the understanding of mGlu5 transmembrane domain activation.
Collapse
Affiliation(s)
- Isaias Lans
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, Colombia
| | - Óscar Díaz
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Madrid, Spain
| | - James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Madrid, Spain
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Madrid, Spain
| |
Collapse
|
20
|
Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 304] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
Collapse
Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| |
Collapse
|
21
|
Díaz Ó, Dalton JAR, Giraldo J. Revealing the Mechanism of Agonist-Mediated Cannabinoid Receptor 1 (CB1) Activation and Phospholipid-Mediated Allosteric Modulation. J Med Chem 2019; 62:5638-5654. [DOI: 10.1021/acs.jmedchem.9b00612] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Óscar Díaz
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - James A. R. Dalton
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| |
Collapse
|
22
|
Falls BA, Zhang Y. Insights into the Allosteric Mechanism of Setmelanotide (RM-493) as a Potent and First-in-Class Melanocortin-4 Receptor (MC4R) Agonist To Treat Rare Genetic Disorders of Obesity through an in Silico Approach. ACS Chem Neurosci 2019; 10:1055-1065. [PMID: 30048591 DOI: 10.1021/acschemneuro.8b00346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human melanocortin-4 receptor (hMC4R) mutations have been implicated as the cause for about 6-8% of all severe obesity cases. Drug-like molecules that are able to rescue the functional activity of mutated receptors are highly desirable to combat genetic obesity among this population of patients. One such molecule is the selective MC4R agonist RM-493 (setmelanotide). While this molecule has been shown to activate mutated receptors with 20-fold higher potency over the endogenous agonist, little is known about its binding mode and how it effectively interacts with hMC4R despite the presence of mutations. In this study, a MC4R homology model was constructed based on the X-ray crystal structure of the adenosine A2A receptor in the active state. Four MC4R mutations commonly found in genetically obese patients and known to effect ligand binding in vitro were introduced into the constructed model. RM-493 was then docked into the wild-type and mutated models in order to better elucidate the possible binding modes for this promising drug candidate and assess how it may be interacting with MC4R to effectively activate receptor polymorphisms. The results reflected the orthosteric interactions of both the endogenous and synthetic ligands with the MC4R, which is supported by the site-directed mutagenesis studies. Meanwhile it helped explain the decremental affinity and potency of these ligands with the receptor polymorphisms. More significantly, our findings indicated that the structural characteristics of RM-493 may allow for enhanced receptor-ligand interactions, particularly through those with the putative allosteric binding sites, which facilitated the ligand to stabilize the active state of native and mutant MC4Rs to maintain reasonably high affinity and potency.
Collapse
Affiliation(s)
- Bethany A. Falls
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23298, United States
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, Virginia 23298, United States
| |
Collapse
|
23
|
Yoshida K, Nagatoishi S, Kuroda D, Suzuki N, Murata T, Tsumoto K. Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium. Biochemistry 2019; 58:504-508. [DOI: 10.1021/acs.biochem.8b01194] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Kouhei Yoshida
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Nanao Suzuki
- Graduate School of Science, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
24
|
Wang L, Yan F. Trans and Cis Conformations of the Antihypertensive Drug Valsartan Respectively Lock the Inactive and Active-like States of Angiotensin II Type 1 Receptor: A Molecular Dynamics Study. J Chem Inf Model 2018; 58:2123-2130. [DOI: 10.1021/acs.jcim.8b00364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Lingyun Wang
- Division of Nephrology, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Feng Yan
- School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin 300387, People’s Republic of China
- State Key Laboratory of Separation Membranes and Membrane Processes, Tianjin Polytechnic University, Tianjin 300387, People’s Republic of China
| |
Collapse
|
25
|
Cao C, Zhang H, Yang Z, Wu B. Peptide recognition, signaling and modulation of class B G protein-coupled receptors. Curr Opin Struct Biol 2018; 51:53-60. [PMID: 29567494 DOI: 10.1016/j.sbi.2018.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/01/2018] [Accepted: 03/07/2018] [Indexed: 01/23/2023]
Abstract
Class B G protein-coupled receptors (GPCRs) are important drug targets in many human diseases, including type 2 diabetes, obesity, cardiovascular disease and neurodegeneration. Peptide hormones bind to these receptors through interactions with both the extracellular domain and transmembrane domain. Despite remarkable advances in structural studies of GPCRs, structural characterization of the full-length class B receptors remains extremely challenging due to their conformational complexity. The recently solved structures of class B GPCRs reveal the structural basis of peptide ligand recognition and modulation mechanisms of small molecule allosteric modulators. Furthermore, these structures provide essential insights into molecular mechanisms of class B GPCR signal transduction and modulation.
Collapse
Affiliation(s)
- Can Cao
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Haonan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhenlin Yang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
| |
Collapse
|
26
|
Structural insights into positive and negative allosteric regulation of a G protein-coupled receptor through protein-lipid interactions. Sci Rep 2018. [PMID: 29535353 PMCID: PMC5849739 DOI: 10.1038/s41598-018-22735-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lipids are becoming known as essential allosteric modulators of G protein-coupled receptor (GPCRs). However, how they exert their effects on GPCR conformation at the atomic level is still unclear. In light of recent experimental data, we have performed several long-timescale molecular dynamics (MD) simulations, totalling 24 μs, to rigorously map allosteric modulation and conformational changes in the β2 adrenergic receptor (β2AR) that occur as a result of interactions with three different phospholipids. In particular, we identify different sequential mechanisms behind receptor activation and deactivation, respectively, mediated by specific lipid interactions with key receptor regions. We show that net negatively charged lipids stabilize an active-like state of β2AR that is able to dock Gsα protein. Clustering of anionic lipids around the receptor with local distortion of membrane thickness is also apparent. On the other hand, net-neutral zwitterionic lipids inactivate the receptor, generating either fully inactive or intermediate states, with kinetics depending on lipid headgroup charge distribution and hydrophobicity. These chemical differences alter membrane thickness and density, which differentially destabilize the β2AR active state through lateral compression effects.
Collapse
|
27
|
Thangappan J, Madan B, Wu S, Lee SG. Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor. Sci Rep 2017; 7:15205. [PMID: 29123217 PMCID: PMC5680341 DOI: 10.1038/s41598-017-15513-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/27/2017] [Indexed: 01/19/2023] Open
Abstract
Joint-based descriptor is a new level of macroscopic descriptor for protein structure using joints of secondary structures as a basic element. Here, we propose how the joint-based descriptor can be applied to examine the conformational distances or differences of transmembrane (TM) proteins. Specifically, we performed three independent studies that measured the global and conformational distances between GPCR A family and its related structures. First, the conformational distances of GPCR A family and other 7TM proteins were evaluated. This provided the information on the distant and close families or superfamilies to GPCR A family and permitted the identification of conserved local conformations. Second, computational models of GPCR A family proteins were validated, which enabled us to estimate how much they reproduce the native conformation of GPCR A proteins at global and local conformational level. Finally, the conformational distances between active and inactive states of GPCR proteins were estimated, which identified the difference of local conformation. The proposed macroscopic joint-based approach is expected to allow us to investigate structural features, evolutionary relationships, computational models and conformational changes of TM proteins in a more simplistic manner.
Collapse
Affiliation(s)
- Jayaraman Thangappan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea
| | - Bharat Madan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea
| | - Sangwook Wu
- Department of Physics, Pukyong National University, Busan, 608-737, Republic of Korea.
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea.
| |
Collapse
|
28
|
Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity 2017. [PMID: 28636951 DOI: 10.1016/j.immuni.2017.05.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc. Molecular modeling indicated that HIV gp120 mimicked the chemokine interaction with CCR5, providing an explanation for the ability of CCR5 to recognize diverse ligands and gp120 variants. Our findings reveal that structural plasticity facilitates receptor-chemokine specificity and enables exploitation by HIV, and provide insight into the design of small molecule and protein inhibitors for HIV and other CCR5-mediated diseases.
Collapse
Affiliation(s)
- Yi Zheng
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Gye Won Han
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Ruben Abagyan
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Raymond C Stevens
- Bridge Institute, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Irina Kufareva
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
| | - Tracy M Handel
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
| |
Collapse
|
29
|
Dalton JAR, Pin JP, Giraldo J. Analysis of positive and negative allosteric modulation in metabotropic glutamate receptors 4 and 5 with a dual ligand. Sci Rep 2017; 7:4944. [PMID: 28694498 PMCID: PMC5504000 DOI: 10.1038/s41598-017-05095-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/25/2017] [Indexed: 12/24/2022] Open
Abstract
As class C GPCRs and regulators of synaptic activity, human metabotropic glutamate receptors (mGluRs) 4 and 5 are prime targets for allosteric modulation, with mGlu5 inhibition or mGlu4 stimulation potentially treating conditions like chronic pain and Parkinson’s disease. As an allosteric modulator that can bind both receptors, 2-Methyl-6-(phenylethynyl)pyridine (MPEP) is able to negatively modulate mGlu5 or positively modulate mGlu4. At a structural level, how it elicits these responses and how mGluRs undergo activation is unclear. Here, we employ homology modelling and 30 µs of atomistic molecular dynamics (MD) simulations to probe allosteric conformational change in mGlu4 and mGlu5, with and without docked MPEP. Our results identify several structural differences between mGlu4 and mGlu5, as well as key differences responsible for MPEP-mediated positive and negative allosteric modulation, respectively. A novel mechanism of mGlu4 activation is revealed, which may apply to all mGluRs in general. This involves conformational changes in TM3, TM4 and TM5, separation of intracellular loop 2 (ICL2) from ICL1/ICL3, and destabilization of the ionic-lock. On the other hand, mGlu5 experiences little disturbance when MPEP binds, maintaining its inactive state with reduced conformational fluctuation. In addition, when MPEP is absent, a lipid molecule can enter the mGlu5 allosteric pocket.
Collapse
Affiliation(s)
- James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Network Biomedical Research Centre on Mental Health (CIBERSAM), Madrid, Spain
| | - Jean-Philippe Pin
- Institute of Functional Genomics, Université de Montpellier, Unité Mixte de Recherche 5302 CNRS, Montpellier, France.,Unité de recherche U1191, INSERM, Montpellier, France
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Network Biomedical Research Centre on Mental Health (CIBERSAM), Madrid, Spain.
| |
Collapse
|
30
|
Sutcliffe KJ, Henderson G, Kelly E, Sessions RB. Drug Binding Poses Relate Structure with Efficacy in the μ Opioid Receptor. J Mol Biol 2017; 429:1840-1851. [PMID: 28502792 PMCID: PMC5472181 DOI: 10.1016/j.jmb.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/07/2017] [Accepted: 05/08/2017] [Indexed: 12/18/2022]
Abstract
The μ-opioid receptor (MOPr) is a clinically important G protein-coupled receptor that couples to Gi/o proteins and arrestins. At present, the receptor conformational changes that occur following agonist binding and activation are poorly understood. This study has employed molecular dynamics simulations to investigate the binding mode and receptor conformational changes induced by structurally similar opioid ligands of widely differing intrinsic agonist efficacy, norbuprenorphine, buprenorphine, and diprenorphine. Bioluminescence resonance energy transfer assays for Gi activation and arrestin-3 recruitment in human embryonic kidney 293 cells confirmed that norbuprenorphine is a high efficacy agonist, buprenorphine a low efficacy agonist, and diprenorphine an antagonist at the MOPr. Molecular dynamics simulations revealed that these ligands adopt distinct binding poses and engage different subsets of residues, despite sharing a common morphinan scaffold. Notably, norbuprenorphine interacted with sodium ion-coordinating residues W2936.48 and N1503.35, whilst buprenorphine and diprenorphine did not. Principal component analysis of the movements of the receptor transmembrane domains showed that the buprenorphine-bound receptor occupied a distinct set of conformations to the norbuprenorphine-bound receptor. Addition of an allosteric sodium ion caused the receptor and ligand to adopt an inactive conformation. The differences in ligand-residue interactions and receptor conformations observed here may underlie the differing efficacies for cellular signalling outputs for these ligands.
Collapse
Affiliation(s)
- Katy J Sutcliffe
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Graeme Henderson
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK
| | - Eamonn Kelly
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK
| | | |
Collapse
|
31
|
Structural heterogeneity of the μ-opioid receptor's conformational ensemble in the apo state. Sci Rep 2017; 8:45761. [PMID: 28368046 PMCID: PMC5377942 DOI: 10.1038/srep45761] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/03/2017] [Indexed: 01/17/2023] Open
Abstract
G-protein coupled receptors (GPCRs) are the largest and most pharmaceutically relevant family of membrane proteins. Here, fully unbiased, enhanced sampling simulations of a constitutively active mutant (CAM) of a class A GPCR, the μ-opioid receptor (μOR), demonstrates repeated transitions between the inactive (IS) and active-like (AS-L) states. The interconversion features typical activation/inactivation patterns involving established conformational rearrangements of conserved residues. By contrast, wild-type μOR remains in IS during the same course of simulation, consistent with the low basal activity of the protein. The simulations point to an important role of residue W2936.48 at the "toggle switch" in the mutation-induced constitutive activation. Such role has been already observed for other CAMs of class A GPCRs. We also find a significantly populated intermediate state, rather similar to IS. Based on the remarkable accord between simulations and experiments, we suggest here that this state, which has escaped so far experimental characterization, might constitute an early step in the activation process of the apo μOR CAM.
Collapse
|
32
|
7×7 RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors. J Struct Biol 2017; 199:87-101. [PMID: 28223044 DOI: 10.1016/j.jsb.2017.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 01/14/2023]
Abstract
The G-protein coupled receptors (GPCRs) share a conserved heptahelical fold in the transmembrane (TM) region, but the exact arrangements of the seven TM helices vary with receptors and their activation states. The differences or the changes have been observed in the experimentally solved structures, but have not been systematically and quantitatively investigated due to lack of suitable methods. In this work, we describe a novel method, called 7×7 RMSD matrix that is proposed specifically for comparing the characteristic 7TM bundle structures of GPCRs. Compared to the commonly used overall TM bundle RMSD as a single parameter, a 7×7 RMSD matrix contains 49 parameters, which reveal changes of the relative orientations of the seven TMs. We demonstrate the novelty and advantages of this method by tackling two problems that are challenging for the existing methods. With this method, we are able to identify and quantify the helix movements in the activated receptor structures and reveal structural conservation and divergence as well as the structural relationships of different GPCRs in terms of the relative orientations of the seven TMs.
Collapse
|
33
|
Ponzoni L, Rossetti G, Maggi L, Giorgetti A, Carloni P, Micheletti C. Unifying view of mechanical and functional hotspots across class A GPCRs. PLoS Comput Biol 2017; 13:e1005381. [PMID: 28158180 PMCID: PMC5315405 DOI: 10.1371/journal.pcbi.1005381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 02/17/2017] [Accepted: 01/25/2017] [Indexed: 01/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors’ functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. The biological functionality of several receptors and enzymes depends on their capability to sustain large-scale structural fluctuations and adopt different conformational states in response to ligand binding. This is the case for G protein-coupled receptors (GPCRs), the largest superfamily of signaling proteins in mammals and a primary pharmaceutical target. To better understand the functional dynamics of GPCRs, we have analysed the inter-residue distance variations across the available structures for several receptors of the rhodopsin-like family (class A). We first reconstructed the network of mechanical, rigid-like couplings between nearby amino acids and then identified those acting as dynamical/mechanical hubs. These were the sites whose virtual removal led to a significant softening of the overall mechanical network. After validating the biological relevance of these sites by comparison against known key functional sites, we singled out those regions which emerge as prominent mechanical hubs and yet have an otherwise still unknown functional role. The most relevant of such novel putative functional sites, which could be probed by mutagenesis experiments, is at interface of two transmembrane helices and we expect it to be crucial for assisting GPCRs conformational response to agonist binding.
Collapse
Affiliation(s)
| | - Giulia Rossetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- JSC: Division Computational Science – Simulation Laboratory Biology – Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich, Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- * E-mail: (LP); (GR)
| | - Luca Maggi
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
| | - Alejandro Giorgetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
| | | |
Collapse
|
34
|
Suku E, Giorgetti A. Common evolutionary binding mode of rhodopsin-like GPCRs: Insights from structural bioinformatics. AIMS BIOPHYSICS 2017. [DOI: 10.3934/biophy.2017.4.543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
35
|
Ichikawa O, Fujimoto K, Yamada A, Okazaki S, Yamazaki K. G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation. PLoS One 2016; 11:e0155816. [PMID: 27187591 PMCID: PMC4871340 DOI: 10.1371/journal.pone.0155816] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 01/14/2023] Open
Abstract
The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand—receptor interactions is complicated. Here, we identified the G-protein/β-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the β2-adrenergic receptor (β2AR) with a diverse collection of ligands and correlation analysis of their G protein/β-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the β-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/β-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs.
Collapse
Affiliation(s)
- Osamu Ichikawa
- Genomic Science Laboratories, Sumitomo Dainippon Pharma. Co. Ltd, Osaka, Osaka, Japan
| | - Kazushi Fujimoto
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Atsushi Yamada
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Susumu Okazaki
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuto Yamazaki
- Genomic Science Laboratories, Sumitomo Dainippon Pharma. Co. Ltd, Osaka, Osaka, Japan
| |
Collapse
|
36
|
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PLoS Comput Biol 2016; 12:e1004805. [PMID: 27028541 PMCID: PMC4814114 DOI: 10.1371/journal.pcbi.1004805] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/11/2016] [Indexed: 11/23/2022] Open
Abstract
The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs. These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms. G-protein coupled receptors (GPCRs) are a large superfamily of integral membrane proteins that share a characteristic 7 transmembrane helix fold. They detect various molecules outside of the cell and signal their presence to the inside of the cell. At least half of the 800 human GPCRs are potential drug targets, so understanding their structure and function is critical. Experimental structures are now available for at least one receptor from each GPCR class. The structure of the 7 helix fold is highly conserved even for receptors with very low sequence similarity. We analyze the available experimental structures and compare the common inter-helical contacts. Our analysis leads to a unified sequence-structure alignment of the GPCR superfamily that can then be used as the starting point for structure prediction of all other GPCRs. A key result of our analysis is a list of conserved contact residues and activation “hot-spots” residues that are critical for GPCR folding and function. We propose that mutations and natural variants of amino acids at these locations in the GPCRs can dramatically influence their activation state and alter intracellular signaling. This provides hypotheses for the molecular mechanisms underlying disease causing mutants for any GPCR.
Collapse
|
37
|
Helix 3 acts as a conformational hinge in Class A GPCR activation: An analysis of interhelical interaction energies in crystal structures. J Struct Biol 2015; 192:545-553. [PMID: 26522273 DOI: 10.1016/j.jsb.2015.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/21/2023]
Abstract
A collection of crystal structures of rhodopsin, β2-adrenergic and adenosine A2A receptors in active, intermediate and inactive states were selected for structural and energetic analyses to identify the changes involved in the activation/deactivation of Class A GPCRs. A set of helix interactions exclusive to either inactive or active/intermediate states were identified. The analysis of these interactions distinguished some local conformational changes involved in receptor activation, in particular, a packing between the intracellular domains of transmembrane helices H3 and H7 and a separation between those of H2 and H6. Also, differential movements of the extracellular and intracellular domains of these helices are apparent. Moreover, a segment of residues in helix H3, including residues L/I3.40 to L3.43, is identified as a key component of the activation mechanism, acting as a conformational hinge between extracellular and intracellular regions. Remarkably, the influence on the activation process of some glutamic and aspartic acidic residues and, as a consequence, the influence of variations on local pH is highlighted. Structural hypotheses that arose from the analysis of rhodopsin, β2-adrenergic and adenosine A2A receptors were tested on the active and inactive M2 muscarinic acetylcholine receptor structures and further discussed in the context of the new mechanistic insights provided by the recently determined active and inactive crystal structures of the μ-opioid receptor. Overall, the structural and energetic analyses of the interhelical interactions present in this collection of Class A GPCRs suggests the existence of a common general activation mechanism featuring a chemical space useful for drug discovery exploration.
Collapse
|
38
|
Lans I, Dalton JAR, Giraldo J. Selective Protonation of Acidic Residues Triggers Opsin Activation. J Phys Chem B 2015; 119:9510-9. [DOI: 10.1021/acs.jpcb.5b01908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Isaias Lans
- Laboratory of Molecular Neuropharmacology
and Bioinformatics, Institut de Neurociències and Unitat de
Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - James A. R. Dalton
- Laboratory of Molecular Neuropharmacology
and Bioinformatics, Institut de Neurociències and Unitat de
Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology
and Bioinformatics, Institut de Neurociències and Unitat de
Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| |
Collapse
|