1
|
Gaiser BI, Danielsen M, Xu X, Røpke Jørgensen K, Fronik P, Märcher-Rørsted E, Wróbel TM, Liu X, Mosolff Mathiesen J, Sejer Pedersen D. Bitopic Ligands Support the Presence of a Metastable Binding Site at the β 2 Adrenergic Receptor. J Med Chem 2024; 67:11053-11068. [PMID: 38952152 DOI: 10.1021/acs.jmedchem.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Metastable binding sites (MBS) have been observed in a multitude of molecular dynamics simulations and can be considered low affinity allosteric binding sites (ABS) that function as stepping stones as the ligand moves toward the orthosteric binding site (OBS). Herein, we show that MBS can be utilized as ABS in ligand design, resulting in ligands with improved binding kinetics. Four homobivalent bitopic ligands (1-4) were designed by molecular docking of (S)-alprenolol ((S)-ALP) in the cocrystal structure of the β2 adrenergic receptor (β2AR) bound to the antagonist ALP. Ligand 4 displayed a potency and affinity similar to (S)-ALP, but with a >4-fold increase in residence time. The proposed binding mode was confirmed by X-ray crystallography of ligand 4 in complex with the β2AR. This ligand design principle can find applications beyond the β2AR and G protein-coupled receptors (GPCRs) as a general approach for improving the pharmacological profile of orthosteric ligands by targeting the OBS and an MBS simultaneously.
Collapse
Affiliation(s)
- Birgit Isabel Gaiser
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Mia Danielsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Xinyu Xu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084 ,China
| | - Kira Røpke Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Philipp Fronik
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Emil Märcher-Rørsted
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Tomasz M Wróbel
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Chodźki 4a, 20093 Lublin, Poland
| | - Xiangyu Liu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084 ,China
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| |
Collapse
|
2
|
Agyemang E, Gonneville AN, Tiruvadi-Krishnan S, Lamichhane R. Exploring GPCR conformational dynamics using single-molecule fluorescence. Methods 2024; 226:35-48. [PMID: 38604413 PMCID: PMC11098685 DOI: 10.1016/j.ymeth.2024.03.011] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins that transmit specific external stimuli into cells by changing their conformation. This conformational change allows them to couple and activate G-proteins to initiate signal transduction. A critical challenge in studying and inferring these structural dynamics arises from the complexity of the cellular environment, including the presence of various endogenous factors. Due to the recent advances in cell-expression systems, membrane-protein purification techniques, and labeling approaches, it is now possible to study the structural dynamics of GPCRs at a single-molecule level both in vitro and in live cells. In this review, we discuss state-of-the-art techniques and strategies for expressing, purifying, and labeling GPCRs in the context of single-molecule research. We also highlight four recent studies that demonstrate the applications of single-molecule microscopy in revealing the dynamics of GPCRs. These techniques are also useful as complementary methods to verify the results obtained from other structural biology tools like cryo-electron microscopy and x-ray crystallography.
Collapse
Affiliation(s)
- Eugene Agyemang
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Alyssa N Gonneville
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996, USA; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
3
|
Brunetti L, Francavilla F, Leopoldo M, Lacivita E. Allosteric Modulators of Serotonin Receptors: A Medicinal Chemistry Survey. Pharmaceuticals (Basel) 2024; 17:695. [PMID: 38931362 PMCID: PMC11206742 DOI: 10.3390/ph17060695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/15/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Serotonin (5-hydroxytryptamine, 5-HT) is a neurotransmitter regulating numerous physiological functions, and its dysregulation is a crucial component of the pathological processes of schizophrenia, depression, migraines, and obesity. 5-HT interacts with 14 different receptors, of which 5-HT1A-1FRs, 5-HT2A-CRs, and 5-HT4-7Rs are G protein-coupled receptors (GPCRs), while 5-HT3R is a ligand-gated ion channel. Over the years, selective orthosteric ligands have been identified for almost all serotonin receptors, yielding several clinically relevant drugs. However, the high degree of homology between 5-HTRs and other GPCRs means that orthosteric ligands can have severe side effects. Thus, there has recently been increased interest in developing safer ligands of GPCRs, which bind to less conserved, more specific sites, distinct from that of the receptor's natural ligand. The present review describes the identification of allosteric ligands of serotonin receptors, which are largely natural compounds (oleamide, cannabidiol, THC, and aporphine alkaloids), complemented by synthetic modulators developed in large part for the 5-HT2C receptor. The latter are positive allosteric modulators sought after for their potential as drugs preferable over the orthosteric agonists as antiobesity agents for their potentially safer profile. When available, details on the interactions between the ligand and allosteric binding site will be provided. An outlook on future research in the field will also be provided.
Collapse
Affiliation(s)
| | | | - Marcello Leopoldo
- Department of Pharmacy–Drug Sciences, University of Bari Aldo Moro, 70125 Bari, Italy; (L.B.); (F.F.); (E.L.)
| | | |
Collapse
|
4
|
Apweiler M, Saliba SW, Sun L, Streyczek J, Normann C, Hellwig S, Bräse S, Fiebich BL. Modulation of neuroinflammation and oxidative stress by targeting GPR55 - new approaches in the treatment of psychiatric disorders. Mol Psychiatry 2024:10.1038/s41380-024-02614-5. [PMID: 38796643 DOI: 10.1038/s41380-024-02614-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/28/2024]
Abstract
Pharmacological treatment of psychiatric disorders remains challenging in clinical, pharmacological, and scientific practice. Even if many different substances are established for treating different psychiatric conditions, subgroups of patients show only small or no response to the treatment. The neuroinflammatory hypothesis of the genesis of psychiatric disorders might explain underlying mechanisms in these non-responders. For that reason, recent research focus on neuroinflammatory processes and oxidative stress as possible causes of psychiatric disorders. G-protein coupled receptors (GPCRs) form the biggest superfamily of membrane-bound receptors and are already well known as pharmacological targets in various diseases. The G-protein coupled receptor 55 (GPR55), a receptor considered part of the endocannabinoid system, reveals promising modulation of neuroinflammatory and oxidative processes. Different agonists and antagonists reduce pro-inflammatory cytokine release, enhance the synthesis of anti-inflammatory mediators, and protect cells from oxidative damage. For this reason, GPR55 ligands might be promising compounds in treating subgroups of patients suffering from psychiatric disorders related to neuroinflammation or oxidative stress. New approaches in drug design might lead to new compounds targeting different pathomechanisms of those disorders in just one molecule.
Collapse
Affiliation(s)
- Matthias Apweiler
- Neuroimmunology and Neurochemistry Research Group, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany
- Department of Cardiology and Angiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79106 Freiburg, Germany
| | - Soraya Wilke Saliba
- Neuroimmunology and Neurochemistry Research Group, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany
| | - Lu Sun
- Neuroimmunology and Neurochemistry Research Group, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany
| | - Jana Streyczek
- Neuroimmunology and Neurochemistry Research Group, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany
| | - Claus Normann
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany
| | - Sabine Hellwig
- Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, D-76131, Karlsruhe, Germany
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, D-76131, Karlsruhe, Germany
| | - Bernd L Fiebich
- Neuroimmunology and Neurochemistry Research Group, Department of Psychiatry and Psychotherapy, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, D-79104, Freiburg, Germany.
| |
Collapse
|
5
|
Mendoza-Hoffmann F, Guo C, Song Y, Feng D, Yang L, Wüthrich K. 19F-NMR studies of the impact of different detergents and nanodiscs on the A 2A adenosine receptor. JOURNAL OF BIOMOLECULAR NMR 2024; 78:31-37. [PMID: 38072902 DOI: 10.1007/s10858-023-00430-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/07/2023] [Indexed: 04/02/2024]
Abstract
For the A2A adenosine receptor (A2AAR), a class A G-protein-coupled receptor (GPCR), reconstituted in n-dodecyl-β-D-maltoside (DDM)/cholesteryl hemisuccinate (CHS) mixed micelles, previous 19F-NMR studies revealed the presence of multiple simultaneously populated conformational states. Here, we study the influence of a different detergent, lauryl maltose neopentyl glycol (LMNG) in mixed micelles with CHS, and of lipid bilayer nanodiscs on these conformational equilibria. The populations of locally different substates are pronouncedly different in DDM/CHS and LMNG/CHS micelles, whereas the A2AAR conformational manifold in LMNG/CHS micelles is closely similar to that in the lipid bilayer nanodiscs. Considering that nanodiscs represent a closer match of the natural lipid bilayer membrane, these observations support that LMNG/CHS micelles are a good choice for reconstitution trials of class A GPCRs for NMR studies in solution.
Collapse
Affiliation(s)
- Francisco Mendoza-Hoffmann
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- Faculty of Chemistry Sciences and Engineering, Autonomous University of Baja California (UABC), Tijuana, México
| | - Canyong Guo
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yanzhuo Song
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- DGI Tech (Qingdao) Co., Ltd., Qingdao, China
| | - Dandan Feng
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
6
|
Do HN, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. JACS AU 2023; 3:3165-3180. [PMID: 38034960 PMCID: PMC10685416 DOI: 10.1021/jacsau.3c00503] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
G-protein-coupled receptors (GPCRs) make up the largest superfamily of human membrane proteins and represent primary targets of ∼1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon the binding of positive and negative allosteric modulators (PAMs and NAMs). The mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), deep learning (DL), and free energy prOfiling Workflow (GLOW). GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence and absence of the modulator. DL and free energy calculations revealed significantly reduced dynamic fluctuations and conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G-protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes. Therefore, GPCR allostery exhibits a dynamic "conformational selection" mechanism. In the absence of available modulator-bound structures as for most current GPCRs, it is critical to use a structural ensemble of representative GPCR conformations rather than a single structure for compound docking ("ensemble docking"), which will potentially improve structure-based design of novel allosteric drugs of GPCRs.
Collapse
Affiliation(s)
| | - Jinan Wang
- Computational Biology Program
and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | | |
Collapse
|
7
|
Zhou J, Xu W, Wu Y, Wang M, Zhang N, Wang L, Feng Y, Zhang T, Wang L, Mao A. GPR37 promotes colorectal cancer liver metastases by enhancing the glycolysis and histone lactylation via Hippo pathway. Oncogene 2023; 42:3319-3330. [PMID: 37749229 DOI: 10.1038/s41388-023-02841-0] [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: 12/30/2022] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Liver metastases are commonly detected in a range of malignancies including colorectal cancer (CRC), unfortunately no effectively strategies for CRC liver metastasis (CRLM). In this study, we found GPR37 expression dramatically increased in human CRLM specimens and associated poor prognosis. GPR37 depletion greatly suppressed the liver metastasis in the mouse models of CRLM. Functional experiments showed that GPR37 knockdown inhibited the growth by reducing the glycolysis of CRC cells. Also, GPR37 knockdown in tumor cells produced decreased levels of two chemokines involved in neutrophil accumulation, which abrogated neutrophil recruitment in the tumor microenvironment of CRLM. Finally, the mechanism studies revealed that GPR37 could activate the hippo pathway, thereby promoting LDHA expression and glycolysis. This leads to increased lactylation of H3K18la, resulting in up-regulation of CXCL1 and CXCL5. These results support a role of the GPR37 in modulating the tumor metabolism and microenvironment in CRLM and GPR37 could be a potential therapeutic target.
Collapse
Affiliation(s)
- Jiamin Zhou
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Weiqi Xu
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Yibin Wu
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Miao Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Ning Zhang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Longrong Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Yun Feng
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Ti Zhang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China
| | - Lu Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China.
| | - Anrong Mao
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, 200032, PR China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, PR China.
| |
Collapse
|
8
|
Faas F, Nørskov A, Holst PJ, Andersson AM, Qvortrup K, Mathiasen S, Rosenkilde MM. Re-routing GPR56 signalling using Gα 12/13 G protein chimeras. Basic Clin Pharmacol Toxicol 2023; 133:378-389. [PMID: 37621135 DOI: 10.1111/bcpt.13935] [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: 04/20/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Adhesion G protein-coupled receptors (aGPCRs) constitute the second largest subclass of the GPCR superfamily. Although canonical GPCRs are explored pharmacologically as drug targets, no clinically approved drugs target the aGPCR family so far. The aGPCR GPR56/ADGRG1 stands out as an especially promising target, given its direct link to the monogenetic disease bilateral frontoparietal polymicrogyria and implications in cancers. Key to understanding GPCR pharmacology has been mapping out intracellular signalling activity. Detection of GPCR signalling in the Gαs /Gαi /Gαq G protein pathways is feasible with second messenger detection systems. However, in the case of Gα12/13 -coupled receptors, like GPR56, signalling detection is more challenging due to the lack of direct second messenger generation. To overcome this challenge, we engineered a Gαq chimera to translate Gα12/13 signalling. We show the ability of the chimeric GαΔ6q12myr and GαΔ6q13myr to translate basal Gα12/13 signalling of GPR56 to a Gαq readout in transcription factor luciferase reporter systems and show that the established peptide ligands (P7 and P19) function to enhance this signal. We further demonstrate the ability to directly influence the generation of second messengers in inositol-3-phosphate assays. In the future, these chimeric G proteins could facilitate basic functional studies, drug screenings and deorphanization of other aGPCRs.
Collapse
Affiliation(s)
- Felix Faas
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amalie Nørskov
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Peter J Holst
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- InProTher APS, Copenhagen, Denmark
| | | | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Signe Mathiasen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette M Rosenkilde
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
9
|
Parajulee A, Kim K. Structural studies of serotonin receptor family. BMB Rep 2023; 56:527-536. [PMID: 37817438 PMCID: PMC10618075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Serotonin receptors, also known as 5-HT receptors, belong to the G protein-coupled receptors (GPCRs) superfamily. They mediate the effects of serotonin, a neurotransmitter that plays a key role in a wide range of functions including mood regulation, cognition and appetite. The functions of serotonin are mediated by a family of 5-HT receptors including 12 GPCRs belonging to six major families: 5-HT1, 5-HT2, 5-HT4, 5-HT5, 5-HT6 and 5-HT7. Despite their distinct characteristics and functions, these receptors' subtypes share common structural features and signaling mechanisms. Understanding the structure, functions and pharmacology of the serotonin receptor family is essential for unraveling the complexities of serotonin signaling and developing targeted therapeutics for neuropsychiatric disorders. However, developing drugs that selectively target specific receptor subtypes is challenging due to the structural similarities in their orthosteric binding sites. This review focuses on the recent advancements in the structural studies of 5-HT receptors, highlighting the key structural features of each subtype and shedding light on their potential as targets for mental health and neurological disorders (such as depression, anxiety, schizophrenia, and migraine) drugs. [BMB Reports 2023; 56(10): 527-536].
Collapse
Affiliation(s)
- Apeksha Parajulee
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Korea
| | - Kuglae Kim
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Korea
| |
Collapse
|
10
|
Guo C, Yang L, Liu Z, Liu D, Wüthrich K. Two-Dimensional NMR Spectroscopy of the G Protein-Coupled Receptor A 2AAR in Lipid Nanodiscs. Molecules 2023; 28:5419. [PMID: 37513291 PMCID: PMC10383251 DOI: 10.3390/molecules28145419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Eight hundred and twenty-six human G protein-coupled receptors (GPCRs) mediate the actions of two-thirds of the human hormones and neurotransmitters and over one-third of clinically used drugs. Studying the structure and dynamics of human GPCRs in lipid bilayer environments resembling the native cell membrane milieu is of great interest as a basis for understanding structure-function relationships and thus benefits continued drug development. Here, we incorporate the human A2A adenosine receptor (A2AAR) into lipid nanodiscs, which represent a detergent-free environment for structural studies using nuclear magnetic resonance (NMR) in solution. The [15N,1H]-TROSY correlation spectra confirmed that the complex of [u-15N, ~70% 2H]-A2AAR with an inverse agonist adopts its global fold in lipid nanodiscs in solution at physiological temperature. The global assessment led to two observations of practical interest. First, A2AAR in nanodiscs can be stored for at least one month at 4 °C in an aqueous solvent. Second, LMNG/CHS micelles are a very close mimic of the environment of A2AAR in nanodiscs. The NMR signal of five individually assigned tryptophan indole 15N-1H moieties located in different regions of the receptor structure further enabled a detailed assessment of the impact of nanodiscs and LMNG/CHS micelles on the local structure and dynamics of A2AAR. As expected, the largest effects were observed near the lipid-water interface along the intra- and extracellular surfaces, indicating possible roles of tryptophan side chains in stabilizing GPCRs in lipid bilayer membranes.
Collapse
Affiliation(s)
- Canyong Guo
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| |
Collapse
|
11
|
Dahl L, Kotliar IB, Bendes A, Dodig-Crnković T, Fromm S, Elofsson A, Uhlén M, Sakmar TP, Schwenk JM. Multiplexed selectivity screening of anti-GPCR antibodies. SCIENCE ADVANCES 2023; 9:eadf9297. [PMID: 37134173 PMCID: PMC10156119 DOI: 10.1126/sciadv.adf9297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/31/2023] [Indexed: 05/05/2023]
Abstract
G protein-coupled receptors (GPCRs) control critical cellular signaling pathways. Therapeutic agents including anti-GPCR antibodies (Abs) are being developed to modulate GPCR function. However, validating the selectivity of anti-GPCR Abs is challenging because of sequence similarities among individual receptors within GPCR subfamilies. To address this challenge, we developed a multiplexed immunoassay to test >400 anti-GPCR Abs from the Human Protein Atlas targeting a customized library of 215 expressed and solubilized GPCRs representing all GPCR subfamilies. We found that ~61% of Abs tested were selective for their intended target, ~11% bound off-target, and ~28% did not bind to any GPCR. Antigens of on-target Abs were, on average, significantly longer, more disordered, and less likely to be buried in the interior of the GPCR protein than the other Abs. These results provide important insights into the immunogenicity of GPCR epitopes and form a basis for designing therapeutic Abs and for detecting pathological auto-Abs against GPCRs.
Collapse
Affiliation(s)
- Leo Dahl
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Ilana B. Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, USA
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Samuel Fromm
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Arne Elofsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 171 64 Solna, Sweden
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| |
Collapse
|
12
|
Do H, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. RESEARCH SQUARE 2023:rs.3.rs-2543463. [PMID: 36865316 PMCID: PMC9980202 DOI: 10.21203/rs.3.rs-2543463/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest superfamily of human membrane proteins and represent primary targets of ~ 1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon binding of positive and negative allosteric modulators (PAMs and NAMs). Mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), Deep Learning (DL) and free energy prOfiling Workflow (GLOW). A total of 18 available high-resolution experimental structures of allosteric modulator-bound class A and B GPCRs were collected for simulations. A number of 8 computational models were generated to examine selectivity of the modulators by changing their target receptors to different subtypes. All-atom GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence/absence of the modulator. DL and free energy calculations revealed significantly reduced conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes in the computational models. Therefore, comprehensive DL of extensive GaMD simulations has revealed a general dynamic mechanism of GPCR allostery, which will greatly facilitate rational design of selective allosteric drugs of GPCRs.
Collapse
|
13
|
Do HN, Wang J, Miao Y. Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.15.524128. [PMID: 36711515 PMCID: PMC9882226 DOI: 10.1101/2023.01.15.524128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest superfamily of human membrane proteins and represent primary targets of ~1/3 of currently marketed drugs. Allosteric modulators have emerged as more selective drug candidates compared with orthosteric agonists and antagonists. However, many X-ray and cryo-EM structures of GPCRs resolved so far exhibit negligible differences upon binding of positive and negative allosteric modulators (PAMs and NAMs). Mechanism of dynamic allosteric modulation in GPCRs remains unclear. In this work, we have systematically mapped dynamic changes in free energy landscapes of GPCRs upon binding of allosteric modulators using the Gaussian accelerated molecular dynamics (GaMD), Deep Learning (DL) and free energy prOfiling Workflow (GLOW). A total of 18 available high-resolution experimental structures of allosteric modulator-bound class A and B GPCRs were collected for simulations. A number of 8 computational models were generated to examine selectivity of the modulators by changing their target receptors to different subtypes. All-atom GaMD simulations were performed for a total of 66 μs on 44 GPCR systems in the presence/absence of the modulator. DL and free energy calculations revealed significantly reduced conformational space of GPCRs upon modulator binding. While the modulator-free GPCRs often sampled multiple low-energy conformational states, the NAMs and PAMs confined the inactive and active agonist-G protein-bound GPCRs, respectively, to mostly only one specific conformation for signaling. Such cooperative effects were significantly reduced for binding of the selective modulators to "non-cognate" receptor subtypes in the computational models. Therefore, comprehensive DL of extensive GaMD simulations has revealed a general dynamic mechanism of GPCR allostery, which will greatly facilitate rational design of selective allosteric drugs of GPCRs.
Collapse
Affiliation(s)
- Hung N. Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047
| |
Collapse
|
14
|
Ferrero KM, Koch WJ. GRK2 in cardiovascular disease and its potential as a therapeutic target. J Mol Cell Cardiol 2022; 172:14-23. [PMID: 35878706 DOI: 10.1016/j.yjmcc.2022.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 01/25/2023]
Abstract
Cardiovascular diseases (CVDs) represent the leading cause of death globally. Despite major advances in the field of pharmacological CVD treatments, particularly in the field of heart failure (HF) research, case numbers and overall mortality remain high and have trended upwards over the last few years. Thus, identifying novel molecular targets for developing HF therapeutics remains a key research focus. G protein-coupled receptors (GPCRs) are critical myocardial signal transducers which regulate cardiac contractility, growth, adaptation and metabolism. Additionally, GPCR dysregulation underlies multiple models of cardiac pathology, and most pharmacological therapeutics currently used in HF target these receptors. Currently-approved treatments have improved patient outcomes, but therapies to stop or reverse HF are lacking. A recent focus on GPCR intracellular-regulating proteins such as GPCR kinases (GRKs) has uncovered GRK2 as a promising target for combating HF. Current literature strongly establishes increased levels and activity of GRK2 in multiple models of CVD. Additionally, the GRK2 interactome includes numerous proteins which interact with differential domains of GRK2 to modulate both beneficial and deleterious signaling pathways in the heart, indicating that these domains can be targeted with a high level of specificity unique to various cardiac pathologies. These data support the premise that GRK2 should be at the forefront of a novel investigative drug search. This perspective reviews cardiac GPCRs, describes the structure and functions of GRK2 in cardiac function and maladaptive pathology, and summarizes the ongoing and future research for targeting this critical kinase across cellular, animal and human models of cardiac dysfunction and HF.
Collapse
Affiliation(s)
- Kimberly M Ferrero
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Philadelphia, PA, USA; Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, USA
| | - Walter J Koch
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Philadelphia, PA, USA; Lewis Katz School of Medicine at Temple University, Center for Translational Medicine, Philadelphia, PA, USA.
| |
Collapse
|
15
|
Meikle TG, Keizer DW, Separovic F, Yao S. A solution NMR view of Lipidic Cubic Phases: Structure, dynamics, and beyond. BBA ADVANCES 2022; 2:100062. [PMID: 37082598 PMCID: PMC10074910 DOI: 10.1016/j.bbadva.2022.100062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is well-established nowadays for the elucidation of the 3D structures of proteins and protein complexes, the evaluation of biomolecular dynamics with atomistic resolution across a range of time scales, the screening of drug candidates with site specificity, and for the quantitation of molecular translational diffusion. Lyotropic lipidic cubic phases (LCPs) are lipid bilayer-based materials with a complex geometry, formed via the spontaneous self-assembly of certain lipids in an aqueous environment at specific temperature ranges. LCPs have been successfully applied to the in meso crystallization of membrane proteins for structural studies by X-ray crystallography, and have also shown promising potential for serving as matrices for drug and nutrient delivery/release in vivo. The characterization of the structural and dynamics properties of LCPs is of significant interest for the application of these materials. Here we present a systematic review detailing the characterization of LCPs by solution NMR. Using LCPs formed by monoolein (MO) as an example, various aspects of LCPs readily accessible by solution NMR are covered, including spectral perturbation in the presence of additives, quantification of hydration levels, 13C relaxation-based measurements for studying atom-specific dynamics along the MO hydrocarbon chain, PGSE NMR measurement of translational diffusion and its correlation with release profiles, and the encapsulation of soluble proteins in LCPs. A brief discussion of future perspectives for the characterization of LCPs by solution NMR is also presented.
Collapse
|
16
|
Mind the Gap—Deciphering GPCR Pharmacology Using 3D Pharmacophores and Artificial Intelligence. Pharmaceuticals (Basel) 2022; 15:ph15111304. [DOI: 10.3390/ph15111304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. Three-dimensional pharmacophore models are powerful computational tools in in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, the discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and the elucidation of ligand–receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning are highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs.
Collapse
|
17
|
MAS-related G protein-coupled receptors X (MRGPRX): Orphan GPCRs with potential as targets for future drugs. Pharmacol Ther 2022; 238:108259. [DOI: 10.1016/j.pharmthera.2022.108259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022]
|
18
|
GPR125 (ADGRA3) is an autocleavable adhesion GPCR that traffics with Dlg1 to the basolateral membrane and regulates epithelial apico-basal polarity. J Biol Chem 2022; 298:102475. [PMID: 36089063 PMCID: PMC9539791 DOI: 10.1016/j.jbc.2022.102475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 01/12/2023] Open
Abstract
The adhesion family of G protein–coupled receptors (GPCRs) is defined by an N-terminal large extracellular region that contains various adhesion-related domains and a highly-conserved GPCR-autoproteolysis-inducing (GAIN) domain, the latter of which is located immediately before a canonical seven-transmembrane domain. These receptors are expressed widely and involved in various functions including development, angiogenesis, synapse formation, and tumorigenesis. GPR125 (ADGRA3), an orphan adhesion GPCR, has been shown to modulate planar cell polarity in gastrulating zebrafish, but its biochemical properties and role in mammalian cells have remained largely unknown. Here, we show that human GPR125 likely undergoes cis-autoproteolysis when expressed in canine kidney epithelial MDCK cells and human embryonic kidney HEK293 cells. The cleavage appears to occur at an atypical GPCR proteolysis site within the GAIN domain during an early stage of receptor biosynthesis. The products, i.e., the N-terminal and C-terminal fragments, seem to remain associated after self-proteolysis, as observed in other adhesion GPCRs. Furthermore, in polarized MDCK cells, GPR125 is exclusively recruited to the basolateral domain of the plasma membrane. The recruitment likely requires the C-terminal PDZ-domain–binding motif of GPR125 and its interaction with the cell polarity protein Dlg1. Knockdown of GPR125 as well as that of Dlg1 results in formation of aberrant cysts with multiple lumens in Matrigel 3D culture of MDCK cells. Consistent with the multilumen phenotype, mitotic spindles are incorrectly oriented during cystogenesis in GPR125-KO MDCK cells. Thus, the basolateral protein GPR125, an autocleavable adhesion GPCR, appears to play a crucial role in apicobasal polarization in epithelial cells.
Collapse
|
19
|
Oh J, Ceong HT, Na D, Park C. A machine learning model for classifying G-protein-coupled receptors as agonists or antagonists. BMC Bioinformatics 2022; 23:346. [PMID: 35982407 PMCID: PMC9389651 DOI: 10.1186/s12859-022-04877-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background G-protein coupled receptors (GPCRs) sense and transmit extracellular signals into the intracellular machinery by regulating G proteins. GPCR malfunctions are associated with a variety of signaling-related diseases, including cancer and diabetes; at least a third of the marketed drugs target GPCRs. Thus, characterization of their signaling and regulatory mechanisms is crucial for the development of effective drugs. Results In this study, we developed a machine learning model to identify GPCR agonists and antagonists. We designed two-step prediction models: the first model identified the ligands binding to GPCRs and the second model classified the ligands as agonists or antagonists. Using 990 selected subset features from 5270 molecular descriptors calculated from 4590 ligands deposited in two drug databases, our model classified non-ligands, agonists, and antagonists of GPCRs, and achieved an area under the ROC curve (AUC) of 0.795, sensitivity of 0.716, specificity of 0.744, and accuracy of 0.733. In addition, we verified that 70% (44 out of 63) of FDA-approved GPCR-targeting drugs were correctly classified into their respective groups. Conclusions Studies of ligand–GPCR interaction recognition are important for the characterization of drug action mechanisms. Our GPCR–ligand interaction prediction model can be employed in the pharmaceutical sciences for the efficient virtual screening of putative GPCR-binding agonists and antagonists. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04877-7.
Collapse
Affiliation(s)
- Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyi-Thaek Ceong
- Department of Multimedia, Chonnam National University, Yeosu, 59626, Republic of Korea.
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| |
Collapse
|
20
|
Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses. Nat Commun 2022; 13:4728. [PMID: 35970889 PMCID: PMC9378622 DOI: 10.1038/s41467-022-32390-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 07/28/2022] [Indexed: 11/30/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate processes ranging from immune responses to neuronal signaling. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additionally, dissecting cell type-specific responses is challenging when the same GPCR is expressed on different cells within a tissue. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that bind clozapine-N-oxide and mimic a GPCR-of-interest. We show that chimeric DREADD-β2AR triggers responses comparable to β2AR on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in microglia, an immune cell capable of driving central nervous system inflammation. When dissecting microglial inflammation, we included two additional DREADD-based chimeras mimicking microglia-enriched GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with high similarity to endogenous β2AR, while DREADD-GPR109A shows no impact. Our DREADD-based approach allows investigation of cell type-dependent pathways without known endogenous ligands. Understanding the function of GPCRs requires stimulation with their specific ligands. Here, the authors design chemogenetic G-protein coupled receptors that allows for the study of receptors without knowing the immediate ligand, and demonstrate its use for the β2-adrenergic receptor in microglia.
Collapse
|
21
|
Genomics-based strategies toward the identification of a Z-ISO carotenoid biosynthetic enzyme suitable for structural studies. Methods Enzymol 2022; 671:171-205. [PMID: 35878977 DOI: 10.1016/bs.mie.2021.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Over the past 20years, structural genomics efforts have proven enormously successful for the determination of integral membrane protein structures, particularly for those of prokaryotic origin. However, traditional genomic expansion screens have included up to hundreds of targets, necessitating the use of robotics and other automation not available to most laboratories. Moreover, such large-scale screens of eukaryotic targets are not easily performed at such a scale. To have broader appeal, traditional structural genomic approaches need to be modified and improved such that they are feasible for most laboratories and especially so for proteins from eukaryotic organisms. One such refinement, termed "microgenomic expansion," has been recently described. This approach improves the process of target selection by making target screening a two-step process, with a minimal number of targets tested at each step. Microgenomic expansion methods are applied here theoretically to a project that has the objective of acquiring a structure for the plant 15-cis-ζ-carotene isomerase, Z-ISO.
Collapse
|
22
|
Gado F, Ferrisi R, Polini B, Mohamed KA, Ricardi C, Lucarini E, Carpi S, Domenichini F, Stevenson LA, Rapposelli S, Saccomanni G, Nieri P, Ortore G, Pertwee RG, Ghelardini C, Di Cesare Mannelli L, Chiellini G, Laprairie RB, Manera C. Design, Synthesis, and Biological Activity of New CB2 Receptor Ligands: from Orthosteric and Allosteric Modulators to Dualsteric/Bitopic Ligands. J Med Chem 2022; 65:9918-9938. [PMID: 35849804 PMCID: PMC10168668 DOI: 10.1021/acs.jmedchem.2c00582] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design of dualsteric/bitopic agents as single chemical entities able to simultaneously interact with both the orthosteric and an allosteric binding site represents a novel approach in medicinal chemistry. Biased dualsteric/bitopic agents could enhance certain signaling pathways while diminishing the others that cause unwanted side effects. We have designed, synthesized, and functionally characterized the first CB2R heterobivalent bitopic ligands. In contrast to the parent orthosteric compound, our bitopic ligands selectively target CB2R versus CB1R and show a functional selectivity for the cAMP signaling pathway versus βarrestin2 recruitment. Moreover, the most promising bitopic ligand FD-22a displayed anti-inflammatory activity in a human microglial cell inflammatory model and antinociceptive activity in vivo in an experimental mouse model of neuropathic pain. Finally, computational studies clarified the binding mode of these compounds inside the CB2R, further confirming their bitopic nature.
Collapse
Affiliation(s)
- Francesca Gado
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy
| | - Rebecca Ferrisi
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy
| | - Beatrice Polini
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy.,Department of Pathology, University of Pisa, Pisa 56126, Italy
| | - Kawthar A Mohamed
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | | | - Elena Lucarini
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology and Toxicology, University of Florence, Florence 50139, Italy
| | - Sara Carpi
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy.,NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, Pisa 56126, Italy
| | | | - Lesley A Stevenson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Simona Rapposelli
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy.,CISUP, Centre for Instrumentation Sharing Pisa University, Lungarno Pacinotti 43, Pisa 56126, Italy
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy
| | | | - Roger G Pertwee
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Carla Ghelardini
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology and Toxicology, University of Florence, Florence 50139, Italy
| | - Lorenzo Di Cesare Mannelli
- Department of Neuroscience, Psychology, Drug Research and Child Health, Section of Pharmacology and Toxicology, University of Florence, Florence 50139, Italy
| | - Grazia Chiellini
- Department of Pathology, University of Pisa, Pisa 56126, Italy.,CISUP, Centre for Instrumentation Sharing Pisa University, Lungarno Pacinotti 43, Pisa 56126, Italy
| | - Robert B Laprairie
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.,Department of Pharmacology, College of Medicine, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Clementina Manera
- Department of Pharmacy, University of Pisa, Pisa 56126, Italy.,CISUP, Centre for Instrumentation Sharing Pisa University, Lungarno Pacinotti 43, Pisa 56126, Italy
| |
Collapse
|
23
|
Woo S, Shenvi RA. Synthesis and target annotation of the alkaloid GB18. Nature 2022; 606:917-921. [PMID: 35551513 PMCID: PMC10036212 DOI: 10.1038/s41586-022-04840-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/06/2022] [Indexed: 11/08/2022]
Abstract
Ingestion of alkaloid metabolites from the bark of Galbulimima (GB) sp. leads to psychotropic and excitatory effects in humans1-4. Limited, variable supply of GB alkaloids5, however, has impeded their biological exploration and clinical development6. Here we report a solution to the supply of GB18, a structural outlier and putative psychotropic principle of Galbulimima bark. Efficient access to its challenging tetrahedral attached-ring motif required the development of a ligand-controlled endo-selective cross-electrophile coupling and a diastereoselective hydrogenation of a rotationally dynamic pyridine. Reliable, gram-scale access to GB18 enabled its assignment as a potent antagonist of κ- and μ-opioid receptors-the first new targets in 35 years-and lays the foundation to navigate and understand the biological activity of Galbulimima metabolites.
Collapse
Affiliation(s)
- Stone Woo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Ryan A Shenvi
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
| |
Collapse
|
24
|
Abstract
Although G-protein–coupled receptors (GPCRs) control vast physiological pathways, their activation remains chemically and physically enigmatic. Our osmotic stress studies of the visual receptor rhodopsin have redefined the standard model of GPCR signaling by revealing the essential role of bulk water. We show results consistent with a large number of water molecules flooding the rhodopsin interior during activation to stabilize the effector binding conformation. These results suggest a model of GPCR activation in which the receptor becomes solvent-swollen upon formation of the active state. We thus demonstrate the mechanism whereby water acts as a powerful allosteric modulator of a pharmacologically important membrane protein family. The Rhodopsin family of G-protein–coupled receptors (GPCRs) comprises the targets of nearly a third of all pharmaceuticals. Despite structural water present in GPCR X-ray structures, the physiological relevance of these solvent molecules to rhodopsin signaling remains unknown. Here, we show experimental results consistent with the idea that rhodopsin activation in lipid membranes is coupled to bulk water movements into the protein. To quantify hydration changes, we measured reversible shifting of the metarhodopsin equilibrium due to osmotic stress using an extensive series of polyethylene glycol (PEG) osmolytes. We discovered clear evidence that light activation entails a large influx of bulk water (∼80–100 molecules) into the protein, giving insight into GPCR activation mechanisms. Various size polymer osmolytes directly control rhodopsin activation, in which large solutes are excluded from rhodopsin and dehydrate the protein, favoring the inactive state. In contrast, small osmolytes initially forward shift the activation equilibrium until a quantifiable saturation point is reached, similar to gain-of-function protein mutations. For the limit of increasing osmolyte size, a universal response of rhodopsin to osmotic stress is observed, suggesting it adopts a dynamic, hydrated sponge-like state upon photoactivation. Our results demand a rethinking of the role of water dynamics in modulating various intermediates in the GPCR energy landscape. We propose that besides bound water, an influx of bulk water plays a necessary role in establishing the active GPCR conformation that mediates signaling.
Collapse
|
25
|
Fu X, Wei S, Wang T, Fan H, Zhang Y, Costa CD, Brandner S, Yang G, Pan Y, He Y, Li N. Research Status of the Orphan G Protein Coupled Receptor 158 and Future Perspectives. Cells 2022; 11:cells11081334. [PMID: 35456013 PMCID: PMC9027133 DOI: 10.3390/cells11081334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) remain one of the most successful targets for therapeutic drugs approved by the US Food and Drug Administration (FDA). Many novel orphan GPCRs have been identified by human genome sequencing and considered as putative targets for refractory diseases. Of note, a series of studies have been carried out involving GPCR 158 (or GPR158) since its identification in 2005, predominantly focusing on the characterization of its roles in the progression of cancer and mental illness. However, advances towards an in-depth understanding of the biological mechanism(s) involved for clinical application of GPR158 are lacking. In this paper, we clarify the origin of the GPR158 evolution in different species and summarize the relationship between GPR158 and different diseases towards potential drug target identification, through an analysis of the sequences and substructures of GPR158. Further, we discuss how recent studies set about unraveling the fundamental features and principles, followed by future perspectives and thoughts, which may lead to prospective therapies involving GPR158.
Collapse
Affiliation(s)
- Xianan Fu
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Shoupeng Wei
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Tao Wang
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Hengxin Fan
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Ying Zhang
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Clive Da Costa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK;
| | - Guang Yang
- Department of Burn and Plastic Surgery, Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen 518039, China;
| | - Yihang Pan
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Yulong He
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
- Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China
- Correspondence: (Y.H.); (N.L.)
| | - Ningning Li
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
- China-UK Institute for Frontier Science, Shenzhen 518107, China
- Correspondence: (Y.H.); (N.L.)
| |
Collapse
|
26
|
IBD-associated G protein-coupled receptor 65 variant compromises signalling and impairs key functions involved in inflammation. Cell Signal 2022; 93:110294. [PMID: 35218908 PMCID: PMC9536022 DOI: 10.1016/j.cellsig.2022.110294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/06/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases (IBD) result in chronic inflammation of the gastrointestinal tract. Genetic studies have shown that the GPR65 gene, as well as its missense coding variant, GPR65*Ile231Leu, is associated with IBD. We aimed to define the signalling and biological pathways downstream of GPR65 activation and evaluate the impact of GPR65*231Leu on these. METHODS We used HEK 293 cells stably expressing GPR65 and deficient for either Gαs, Gαq/11 or Gα12/13, to define GPR65 signalling pathways, IBD patient biopsies and a panel of human tissues, primary immune cells and cell lines to determine biologic context, and genetic modulation of human THP-1-derived macrophages to examine the impact of GPR65 in bacterial phagocytosis and NLRP3 inflammasome activation. RESULTS We confirmed that GPR65 signals via the Gαs pathway, leading to cAMP accumulation. GPR65 can also signal via the Gα12/13 pathway leading to formation of stress fibers, actin remodeling and RhoA activation; all impaired by the IBD-associated GPR65*231Leu allele. Gene expression profiling revealed greater expression of GPR65 in biopsies from inflamed compared to non-inflamed tissues from IBD patients or control individuals, potentially explained by infiltration of inflammatory immune cells. Decreased GPR65 expression in THP-1-derived macrophages leads to impaired bacterial phagocytosis, increased NLRP3 inflammasome activation and IL-1β secretion in response to an inflammatory stimulus. CONCLUSIONS We demonstrate that GPR65 exerts its effects through Gαs- and Gα12/13-mediated pathways, that the IBD-associated GPR65*231Leu allele has compromised interactions with Gα12/13 and that KD of GPR65 leads to impaired bacterial phagocytosis and increased inflammatory signalling via the NLRP3 inflammasome. This work identifies a target for development of small molecule therapies.
Collapse
|
27
|
Nakai H, Isshiki K, Hattori M, Maehira H, Yamaguchi T, Masuda K, Shimizu Y, Watanabe T, Hohsaka T, Shihoya W, Nureki O, Kato Y, Watanabe H, Matsuura T. Cell-Free Synthesis of Human Endothelin Receptors and Its Application to Ribosome Display. Anal Chem 2022; 94:3831-3839. [PMID: 35188389 DOI: 10.1021/acs.analchem.1c04714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Engineering G-protein-coupled receptors (GPCRs) for improved stability or altered function is of great interest, as GPCRs consist of the largest protein family, are involved in many important signaling pathways, and thus, are one of the major drug targets. Here, we report the development of a high-throughput screening method for GPCRs using a reconstituted in vitro transcription-translation (IVTT) system. Human endothelin receptor type-B (ETBR), a class A GPCR that binds endothelin-1 (ET-1), a 21-residue peptide hormone, was synthesized in the presence of nanodisc (ND) composed of a phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG). The ET-1 binding of ETBR was significantly reduced or was undetectable when other phospholipids were used for ND preparation. However, when functional ETBR purified from Sf9 cells was reconstituted into NDs, ET-1 binding was observed with two different phospholipids tested, including POPG. These results suggest that POPG likely supports the folding of ETBR into its functional form in the IVTT system. Using the same conditions as ETBR, whose three-dimensional structure has been solved, human endothelin receptor type-A (ETAR), whose three-dimensional structure remains unsolved, was also synthesized in its functional form. By adding POPG-ND to the IVTT system, both ETAR and ETBR were successfully subjected to ribosome display, a method of in vitro directed evolution that facilitates the screening of up to 1012 mutants. Finally, using a mock library, we showed that ribosome display can be applied for gene screening of ETBR, suggesting that high-throughput screening and directed evolution of GPCRs is possible in vitro.
Collapse
Affiliation(s)
- Hiroki Nakai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kinuka Isshiki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masato Hattori
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiromasa Maehira
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsumi Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystem Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystem Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yasuhiko Kato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
| |
Collapse
|
28
|
Hou W, Hao Y, Sun L, Zhao Y, Zheng X, Song L. The dual roles of autophagy and the GPCRs-mediating autophagy signaling pathway after cerebral ischemic stroke. Mol Brain 2022; 15:14. [PMID: 35109896 PMCID: PMC8812204 DOI: 10.1186/s13041-022-00899-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/20/2022] [Indexed: 12/17/2022] Open
Abstract
Ischemic stroke, caused by a lack of blood supply in brain tissues, is the third leading cause of human death and disability worldwide, and usually results in sensory and motor dysfunction, cognitive impairment, and in severe cases, even death. Autophagy is a highly conserved lysosome-dependent process in which eukaryotic cells removal misfolded proteins and damaged organelles in cytoplasm, which is critical for energy metabolism, organelle renewal, and maintenance of intracellular homeostasis. Increasing evidence suggests that autophagy plays important roles in pathophysiological mechanisms under ischemic conditions. However, there are still controversies about whether autophagy plays a neuroprotective or damaging role after ischemia. G-protein-coupled receptors (GPCRs), one of the largest protein receptor superfamilies in mammals, play crucial roles in various physiological and pathological processes. Statistics show that GPCRs are the targets of about one-fifth of drugs known in the world, predicting potential values as targets for drug research. Studies have demonstrated that nutritional deprivation can directly or indirectly activate GPCRs, mediating a series of downstream biological processes, including autophagy. It can be concluded that there are interactions between autophagy and GPCRs signaling pathway, which provides research evidence for regulating GPCRs-mediated autophagy. This review aims to systematically discuss the underlying mechanism and dual roles of autophagy in cerebral ischemia, and describe the GPCRs-mediated autophagy, hoping to probe promising therapeutic targets for ischemic stroke through in-depth exploration of the GPCRs-mediated autophagy signaling pathway.
Collapse
Affiliation(s)
- Weichen Hou
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin Street 71#, Changchun, 130021, China
| | - Yulei Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin Street 71#, Changchun, 130021, China
| | - Li Sun
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin Street 71#, Changchun, 130021, China
| | - Yang Zhao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin Street 71#, Changchun, 130021, China
| | - Xiangyu Zheng
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Xinmin Street 71#, Changchun, 130021, China.
| | - Lei Song
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Xinmin Street 71#, Changchun, 130021, China.
| |
Collapse
|
29
|
Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins 2022; 90:601-614. [PMID: 34599827 PMCID: PMC8738117 DOI: 10.1002/prot.26256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 02/03/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and represent the primary targets of about one third of currently marketed drugs. Despite the critical importance, experimental structures have been determined for only a limited portion of GPCRs and functional mechanisms of GPCRs remain poorly understood. Here, we have constructed novel sequence coevolutionary models of the A and B classes of GPCRs and compared them with residue contact frequency maps generated with available experimental structures. Significant portions of structural residue contacts were successfully detected in the sequence-based covariational models. "Exception" residue contacts predicted from sequence coevolutionary models but not available structures added missing links that were important for GPCR activation and allosteric modulation. Moreover, we identified distinct residue contacts involving different sets of functional motifs for GPCR activation, such as the Na+ pocket, CWxP, DRY, PIF, and NPxxY motifs in the class A and the HETx and PxxG motifs in the class B. Finally, we systematically uncovered critical residue contacts tuned by allosteric modulation in the two classes of GPCRs, including those from the activation motifs and particularly the extracellular and intracellular loops in class A GPCRs. These findings provide a promising framework for rational design of ligands to regulate GPCR activation and allosteric modulation.
Collapse
Affiliation(s)
- Hung N Do
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Allan Haldane
- Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122,Corresponding authors: and
| | - Ronald M Levy
- Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122
| | - Yinglong Miao
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047,Corresponding authors: and
| |
Collapse
|
30
|
Conrad M, Söldner CA, Sticht H. Effect of Ions and Sequence Variants on the Antagonist Binding Properties of the Histamine H 1 Receptor. Int J Mol Sci 2022; 23:ijms23031420. [PMID: 35163341 PMCID: PMC8836275 DOI: 10.3390/ijms23031420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
The histamine H1 receptor (H1R) is a G protein-coupled receptor (GPCR) and represents a main target in the treatment of allergic reactions as well as inflammatory reactions and depressions. Although the overall effect of antagonists on H1 function has been extensively investigated, rather little is known about the potential modulatory effect of ions or sequence variants on antagonist binding. We investigated the dynamics of a phosphate ion present in the crystal structure and of a sodium ion, for which we determined the position in the allosteric pocket by metadynamics simulations. Both types of ions exhibit significant dynamics within their binding site; however, some key contacts remain stable over the simulation time, which might be exploited to develop more potent drugs targeting these sites. The dynamics of the ions is almost unaffected by the presence or absence of doxepin, as also reflected in their small effect (less than 1 kcal·mol-1) on doxepin binding affinity. We also examined the effect of four H1R sequence variants observed in the human population on doxepin binding. These variants cause a reduction in doxepin affinity of up to 2.5 kcal·mol-1, indicating that personalized medical treatments that take into account individual mutation patterns could increase precision in the dosage of GPCR-targeting drugs.
Collapse
Affiliation(s)
- Marcus Conrad
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Christian A. Söldner
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
- Correspondence:
| |
Collapse
|
31
|
Spigoni V, Cinquegrani G, Iannozzi NT, Frigeri G, Maggiolo G, Maggi M, Parello V, Dei Cas A. Activation of G protein-coupled receptors by ketone bodies: Clinical implication of the ketogenic diet in metabolic disorders. Front Endocrinol (Lausanne) 2022; 13:972890. [PMID: 36339405 PMCID: PMC9631778 DOI: 10.3389/fendo.2022.972890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Ketogenesis takes place in hepatocyte mitochondria where acetyl-CoA derived from fatty acid catabolism is converted to ketone bodies (KB), namely β-hydroxybutyrate (β-OHB), acetoacetate and acetone. KB represent important alternative energy sources under metabolic stress conditions. Ketogenic diets (KDs) are low-carbohydrate, fat-rich eating strategies which have been widely proposed as valid nutritional interventions in several metabolic disorders due to its substantial efficacy in weight loss achievement. Carbohydrate restriction during KD forces the use of FFA, which are subsequently transformed into KB in hepatocytes to provide energy, leading to a significant increase in ketone levels known as "nutritional ketosis". The recent discovery of KB as ligands of G protein-coupled receptors (GPCR) - cellular transducers implicated in a wide range of body functions - has aroused a great interest in understanding whether some of the clinical effects associated to KD consumption might be mediated by the ketone/GPCR axis. Specifically, anti-inflammatory effects associated to KD regimen are presumably due to GPR109A-mediated inhibition of NLRP3 inflammasome by β-OHB, whilst lipid profile amelioration by KDs could be ascribed to the actions of acetoacetate via GPR43 and of β-OHB via GPR109A on lipolysis. Thus, this review will focus on the effects of KD-induced nutritional ketosis potentially mediated by specific GPCRs in metabolic and endocrinological disorders. To discriminate the effects of ketone bodies per se, independently of weight loss, only studies comparing ketogenic vs isocaloric non-ketogenic diets will be considered as well as short-term tolerability and safety of KDs.
Collapse
Affiliation(s)
- Valentina Spigoni
- Endocrinology and Metabolic Diseases, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gloria Cinquegrani
- Endocrinology and Metabolic Diseases, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Nicolas Thomas Iannozzi
- Endocrinology and Metabolic Diseases, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Giulia Frigeri
- Division of Nutritional and Metabolic Sciences, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Giulia Maggiolo
- Division of Nutritional and Metabolic Sciences, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Marta Maggi
- Division of Nutritional and Metabolic Sciences, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Vanessa Parello
- Endocrinology and Metabolic Diseases, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Alessandra Dei Cas
- Endocrinology and Metabolic Diseases, Department of Medicine and Surgery, University of Parma, Parma, Italy
- Division of Nutritional and Metabolic Sciences, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
- *Correspondence: Alessandra Dei Cas,
| |
Collapse
|
32
|
Root-Bernstein R, Churchill B. Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities. Life (Basel) 2021; 11:life11111217. [PMID: 34833093 PMCID: PMC8623292 DOI: 10.3390/life11111217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Cross-talk between opioid and adrenergic receptors is well-characterized and involves second messenger systems, the formation of receptor heterodimers, and the presence of extracellular allosteric binding regions for the complementary ligand; however, the evolutionary origins of these interactions have not been investigated. We propose that opioid and adrenergic ligands and receptors co-evolved from a common set of modular precursors so that they share binding functions. We demonstrate the plausibility of this hypothesis through a review of experimental evidence for molecularly complementary modules and report unexpected homologies between the two receptor types. Briefly, opioids form homodimers also bind adrenergic compounds; opioids bind to conserved extracellular regions of adrenergic receptors while adrenergic compounds bind to conserved extracellular regions of opioid receptors; opioid-like modules appear in both sets of receptors within key ligand-binding regions. Transmembrane regions associated with homodimerization of each class of receptors are also highly conserved across receptor types and implicated in heterodimerization. This conservation of multiple functional modules suggests opioid–adrenergic ligand and receptor co-evolution and provides mechanisms for explaining the evolution of their crosstalk. These modules also suggest the structure of a primordial receptor, providing clues for engineering receptor functions.
Collapse
|
33
|
Joseph MD, Tomas Bort E, Grose RP, McCormick PJ, Simoncelli S. Quantitative Super-Resolution Imaging for the Analysis of GPCR Oligomerization. Biomolecules 2021; 11:biom11101503. [PMID: 34680136 PMCID: PMC8533726 DOI: 10.3390/biom11101503] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/13/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are known to form homo- and hetero- oligomers which are considered critical to modulate their function. However, studying the existence and functional implication of these complexes is not straightforward as controversial results are obtained depending on the method of analysis employed. Here, we use a quantitative single molecule super-resolution imaging technique named qPAINT to quantify complex formation within an example GPCR. qPAINT, based upon DNA-PAINT, takes advantage of the binding kinetics between fluorescently labelled DNA imager strands to complementary DNA docking strands coupled to protein targeting antibodies to quantify the protein copy number in nanoscale dimensions. We demonstrate qPAINT analysis via a novel pipeline to study the oligomerization of the purinergic receptor Y2 (P2Y2), a rhodopsin-like GPCR, highly expressed in the pancreatic cancer cell line AsPC-1, under control, agonistic and antagonistic conditions. Results reveal that whilst the density of P2Y2 receptors remained unchanged, antagonistic conditions displayed reduced percentage of oligomers, and smaller numbers of receptors in complexes. Yet, the oligomeric state of the receptors was not affected by agonist treatment, in line with previous reports. Understanding P2Y2 oligomerization under agonistic and antagonistic conditions will contribute to unravelling P2Y2 mechanistic action and therapeutic targeting.
Collapse
Affiliation(s)
- Megan D. Joseph
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK;
| | - Elena Tomas Bort
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (E.T.B.); (R.P.G.)
- Centre for Endocrinology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (E.T.B.); (R.P.G.)
| | - Peter J. McCormick
- Centre for Endocrinology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Sabrina Simoncelli
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK;
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Correspondence:
| |
Collapse
|
34
|
Wüthrich K. Brownian motion, spin diffusion and protein structure determination in solution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 331:107031. [PMID: 34391647 DOI: 10.1016/j.jmr.2021.107031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
This paper presents my recollections on the development of protein structure determination by NMR in solution from 1968 to 1992. The key to success was to identify NMR-accessible parameters that unambiguously determine the spatial arrangement of polypeptide chains. Inspired by work with cyclopeptides, model considerations showed that enforcing short non-bonding interatomic distances imposes «ring closure conditions» on polypeptide chains. Given that distances are scalar parameters, this indicated an avenue for studies of proteins in solution, i.e., under the regime of stochastic rotational and translational motions at frequencies in the nanosecond range (Brownian motion), where sharp pictures could not be obtained by photography-related methods. Later-on, we used distance geometry calculations with sets of inter-atomic distances derived from protein crystal structures to confirm that measurements of short proton-proton distances could provide atomic-resolution structures of globular proteins. During the years 1976-1984 the following four lines of research then led to protein structure determination by NMR in solution. First, the development of NMR experiments enabling the use of the nuclear Overhauser effect (NOE) for measurements of interatomic distances between pairs of hydrogen atoms in proteins. Second, obtaining sequence-specific resonance assignment solved the "phase problem" for protein structure determination by NMR. Third, generating and programming novel distance geometry algorithms enabled the calculation of atomic-resolution protein structures from limited sets of distance constraints measured by NMR. Fourth, the introduction of two-dimensional NMR provided greatly improved spectral resolution of the complex spectra of proteins as well as efficient delineation of scalar and dipole-dipole 1H-1H connectivities, thus making protein structure determination in solution viable and attractive.
Collapse
Affiliation(s)
- Kurt Wüthrich
- ETH Zürich, Zürich Switzerland and Scripps Research, La Jolla, CA, USA
| |
Collapse
|
35
|
Pamula F, Tsai CJ. Biochemical Characterization of GPCR-G Protein Complex Formation. Methods Mol Biol 2021; 2302:37-48. [PMID: 33877621 DOI: 10.1007/978-1-0716-1394-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The complex of G protein-coupled receptors (GPCR) and G proteins is the core assembly in GPCR signaling in eukaryotes. With the recent development of cryo-electron microscopy, there has been a rapid growth in structures of GPCR-G protein complexes solved to near-atomic resolution, giving important insights into this signaling complex. Here we describe the biochemical protocol to study the interaction between GPCRs and G proteins before preparation of GPCR-G protein complexes for structural studies. We use gel filtration to analyze the binding properties between GPCR and G protein with the presence of agonist or antagonist, as well as the complex dissociation in the presence of GTP analogue. Methods used in the protocol are affinity purification and gel filtration, which are also commonly used in protein sample preparation for structural work. Therefore, the protocol can be easily adapted for large-scale sample preparation.
Collapse
Affiliation(s)
- Filip Pamula
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.
| |
Collapse
|
36
|
Kalinkovich A, Livshits G. Biased and allosteric modulation of bone cell-expressing G protein-coupled receptors as a novel approach to osteoporosis therapy. Pharmacol Res 2021; 171:105794. [PMID: 34329703 DOI: 10.1016/j.phrs.2021.105794] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 12/16/2022]
Abstract
On the cellular level, osteoporosis (OP) is a result of imbalanced bone remodeling, in which osteoclastic bone resorption outcompetes osteoblastic bone formation. Currently available OP medications include both antiresorptive and bone-forming drugs. However, their long-term use in OP patients, mainly in postmenopausal women, is accompanied by severe side effects. Notably, the fundamental coupling between bone resorption and formation processes underlies the existence of an undesirable secondary outcome that bone anabolic or anti-resorptive drugs also reduce bone formation. This drawback requires the development of anti-OP drugs capable of selectively stimulating osteoblastogenesis and concomitantly reducing osteoclastogenesis. We propose that the application of small synthetic biased and allosteric modulators of bone cell receptors, which belong to the G-protein coupled receptors (GPCR) family, could be the key to resolving the undesired anti-OP drug selectivity. This approach is based on the capacity of these GPCR modulators, unlike the natural ligands, to trigger signaling pathways that promote beneficial effects on bone remodeling while blocking potentially deleterious effects. Under the settings of OP, an optimal anti-OP drug should provide fine-tuned regulation of downstream effects, for example, intermittent cyclic AMP (cAMP) elevation, preservation of Ca2+ balance, stimulation of osteoprotegerin (OPG) and estrogen production, suppression of sclerostin secretion, and/or preserved/enhanced canonical β-catenin/Wnt signaling pathway. As such, selective modulation of GPCRs involved in bone remodeling presents a promising approach in OP treatment. This review focuses on the evidence for the validity of our hypothesis.
Collapse
Affiliation(s)
- Alexander Kalinkovich
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel
| | - Gregory Livshits
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel; Adelson School of Medicine, Ariel University, Ariel 4077625, Israel.
| |
Collapse
|
37
|
Jabeen A, Vijayram R, Ranganathan S. A two-stage computational approach to predict novel ligands for a chemosensory receptor. Curr Res Struct Biol 2021; 2:213-221. [PMID: 34235481 PMCID: PMC8244491 DOI: 10.1016/j.crstbi.2020.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 11/01/2022] Open
Abstract
Olfactory receptor (OR) 1A2 is the member of largest superfamily of G protein-coupled receptors (GPCRs). OR1A2 is an ectopically expressed receptor with only 13 known ligands, implicated in reducing hepatocellular carcinoma progression, with enormous therapeutic potential. We have developed a two-stage screening approach to identify novel putative ligands of OR1A2. We first used a pharmacophore model based on atomic property field (APF) to virtually screen a library of 5942 human metabolites. We then carried out structure-based virtual screening (SBVS) for predicting the potential agonists, based on a 3D homology model of OR1A2. This model was developed using a biophysical approach for template selection, based on multiple parameters including hydrophobicity correspondence, applied to the complete set of available GPCR structures to pick the most appropriate template. Finally, the membrane-embedded 3D model was refined by molecular dynamics (MD) simulations in both the apo and holo forms. The refined model in the apo form was selected for SBVS. Four novel small molecules were identified as strong binders to this olfactory receptor on the basis of computed binding energies.
Collapse
Key Words
- APF, Atomic property field
- Amber, Assisted model Building with Energy Refinement
- Atomic property field
- Binding free energy calculation
- CSF, Cerebrospinal fluid
- ECL, Extracellular loop
- GPCR, G protein coupled receptor
- HCMV, Human cytomegalovirus
- HMDB, Human metabolome database
- Hydrophobicity correspondence
- LBVS, Ligand based virtual screening
- LC, Lung carcinoids
- MD, Molecular dynamics
- MMGBSA, Molecular mechanics generalized born surface area
- MMPBSA, Molecular mechanics Poisson–Boltzmann surface area
- Molecular dynamics
- NAFLD, Non-alcoholic fatty liver disease
- NASH, Nonalcoholic steatohepatitis
- OR, olfactory receptor
- OR1A2
- Olfactory receptor
- PMEMD, Particle-Mesh Ewald Molecular Dynamics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero- 3-phosphatidylcholine
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuation
- SBVS, Structure based virtual screening
- SSD, Sum of squared difference
- TM, Transmembrane
- Virtual ligand screening
Collapse
Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ramya Vijayram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
38
|
Fernandez-Gonzalez P, Mas-Sanchez A, Garriga P. Polyphenols and Visual Health: Potential Effects on Degenerative Retinal Diseases. Molecules 2021; 26:3407. [PMID: 34199888 PMCID: PMC8200069 DOI: 10.3390/molecules26113407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/26/2022] Open
Abstract
Dietary polyphenols are a group of natural compounds that have been proposed to have beneficial effects on human health. They were first known for their antioxidant properties, but several studies over the years have shown that these compounds can exert protective effects against chronic diseases. Nonetheless, the mechanisms underlying these potential benefits are still uncertain and contradictory effects have been reported. In this review, we analyze the potential effects of polyphenol compounds on some visual diseases, with a special focus on retinal degenerative diseases. Current effective therapies for the treatment of such retinal diseases are lacking and new strategies need to be developed. For this reason, there is currently a renewed interest in finding novel ligands (or known ligands with previously unexpected features) that could bind to retinal photoreceptors and modulate their molecular properties. Some polyphenols, especially flavonoids (e.g., quercetin and tannic acid), could attenuate light-induced receptor damage and promote visual health benefits. Recent evidence suggests that certain flavonoids could help stabilize the correctly folded conformation of the visual photoreceptor protein rhodopsin and offset the deleterious effect of retinitis pigmentosa mutations. In this regard, certain polyphenols, like the flavonoids mentioned before, have been shown to improve the stability, expression, regeneration and folding of rhodopsin mutants in experimental in vitro studies. Moreover, these compounds appear to improve the integration of the receptor into the cell membrane while acting against oxidative stress at the same time. We anticipate that polyphenol compounds can be used to target visual photoreceptor proteins, such as rhodopsin, in a way that has only been recently proposed and that these can be used in novel approaches for the treatment of retinal degenerative diseases like retinitis pigmentosa; however, studies in this field are limited and further research is needed in order to properly characterize the effects of these compounds on retinal degenerative diseases through the proposed mechanisms.
Collapse
Affiliation(s)
| | | | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d’Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, 08222 Terrassa, Spain; (P.F.-G.); (A.M.-S.)
| |
Collapse
|
39
|
Stott LA, Brighton CA, Brown J, Mould R, Bennett KA, Newman R, Currinn H, Autore F, Higueruelo AP, Tehan BG, MacSweeney C, O'Brien MA, Watson SP. Characterisation of inverse agonism of the orphan-G protein-coupled receptor GPR52 by cannabinoid ligands Cannabidiol and O-1918. Heliyon 2021; 7:e07201. [PMID: 34189291 PMCID: PMC8219759 DOI: 10.1016/j.heliyon.2021.e07201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
The identification of cannabinoid ligands Cannabidiol and O-1918 as inverse agonists of the orphan receptor GPR52 is reported. Detailed characterisation of GPR52 pharmacology and modelling of the proposed receptor interaction is described. The identification of a novel and further CNS pharmacology for the polypharmacological agent and marketed drug Cannabidiol is noteworthy.
Collapse
Affiliation(s)
- Lisa A Stott
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Cheryl A Brighton
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Jason Brown
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Richard Mould
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Kirstie A Bennett
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Robert Newman
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Heather Currinn
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Flavia Autore
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Alicia P Higueruelo
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Benjamin G Tehan
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Cliona MacSweeney
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Michael A O'Brien
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| | - Steve P Watson
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom
| |
Collapse
|
40
|
Zhao J, Stephens T, Zhao Y. Molecular Regulation of Lysophosphatidic Acid Receptor 1 Maturation and Desensitization. Cell Biochem Biophys 2021; 79:477-483. [PMID: 34032994 DOI: 10.1007/s12013-021-00999-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2021] [Indexed: 10/21/2022]
Abstract
Lysophosphatidic acid receptor 1 (LPA1) belongs to the G protein-coupled receptor family. The ligand for LPA1 is LPA, the simplest lysophospholipid. LPA is considered a growth factor and induces cell proliferation, anti-apoptosis, and cell migration. The pro-inflammatory and pro-fibrotic roles of LPA have also been well-demonstrated. Most of the biological functions of LPA are mostly executed through LPA1. The mature form of LPA1 is glycosylated and localized on the plasma membrane. LPA1 is bound to heterotrimetric G proteins and transduces intracellular signaling in response to ligation to LPA. Desensitization of LPA1 negatively regulates LPA1-mediated signaling and the resulting biological functions. Phosphorylation and ubiquitination are well-demonstrated posttranslational modifications of GPCR. In this review, we will discuss our knowledge of LPA1 glycosylation, maturation, and trafficking from the endoplasmic reticulum (ER)/Golgi to the plasma membrane. Moreover, in light of recent findings, we will also discuss molecular regulation of LPA1 internalization and stability.
Collapse
Affiliation(s)
- Jing Zhao
- Department of Physiology and Cell Biology, the Ohio State University, Columbus, OH, USA
| | - Thomas Stephens
- Department of Physiology and Cell Biology, the Ohio State University, Columbus, OH, USA
| | - Yutong Zhao
- Department of Physiology and Cell Biology, the Ohio State University, Columbus, OH, USA.
| |
Collapse
|
41
|
Fine Sampling of Sequence Space for Membrane Protein Structural Biology. J Mol Biol 2021; 433:167055. [PMID: 34022208 DOI: 10.1016/j.jmb.2021.167055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
We describe an enhancement of traditional genomics-based approaches to improve the success of structure determination of membrane proteins. Following a broad screen of sequence space to identify initial expression-positive targets, we employ a second step to select orthologs with closely related sequences to these hits. We demonstrate that a greater percentage of these latter targets express well and are stable in detergent, increasing the likelihood of identifying candidates that will ultimately yield structural information.
Collapse
|
42
|
Liu N, Wang Y, Li T, Feng X. G-Protein Coupled Receptors (GPCRs): Signaling Pathways, Characterization, and Functions in Insect Physiology and Toxicology. Int J Mol Sci 2021; 22:ijms22105260. [PMID: 34067660 PMCID: PMC8156084 DOI: 10.3390/ijms22105260] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are known to play central roles in the physiology of many organisms. Members of this seven α-helical transmembrane protein family transduce the extracellular signals and regulate intracellular second messengers through coupling to heterotrimeric G-proteins, adenylate cyclase, cAMPs, and protein kinases. As a result of the critical function of GPCRs in cell physiology and biochemistry, they not only play important roles in cell biology and the medicines used to treat a wide range of human diseases but also in insects’ physiological functions. Recent studies have revealed the expression and function of GPCRs in insecticide resistance, improving our understanding of the molecular complexes governing the development of insecticide resistance. This article focuses on the review of G-protein coupled receptor (GPCR) signaling pathways in insect physiology, including insects’ reproduction, growth and development, stress responses, feeding, behaviors, and other physiological processes. Hormones and polypeptides that are involved in insect GPCR regulatory pathways are reviewed. The review also gives a brief introduction of GPCR pathways in organisms in general. At the end of the review, it provides the recent studies on the function of GPCRs in the development of insecticide resistance, focusing in particular on our current knowledge of the expression and function of GPCRs and their downstream regulation pathways and their roles in insecticide resistance and the regulation of resistance P450 gene expression. The latest insights into the exciting technological advances and new techniques for gene expression and functional characterization of the GPCRs in insects are provided.
Collapse
Affiliation(s)
- Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
- Correspondence: ; Tel.: +1-334-844-5076
| | - Yifan Wang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
| | - Ting Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
| | - Xuechun Feng
- Department of Biology Sciences, University of California, San Diego, CA 92093, USA;
| |
Collapse
|
43
|
Gerkin RC. Parsing Sage and Rosemary in Time: The Machine Learning Race to Crack Olfactory Perception. Chem Senses 2021; 46:6226923. [PMID: 33860304 DOI: 10.1093/chemse/bjab020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Color and pitch perception are largely understandable from characteristics of physical stimuli: the wavelengths of light and sound waves, respectively. By contrast, understanding olfactory percepts from odorous stimuli (volatile molecules) is much more challenging. No intuitive set of molecular features is up to the task. Here in Chemical Senses, the Ray lab reports using a predictive modeling framework-first breaking molecular structure into thousands of features and then using this to train a predictive statistical model on a wide range of perceptual descriptors-to create a tool for predicting the odor character of hundreds of thousands of available but previously uncharacterized molecules (Kowalewski et al. 2021). This will allow future investigators to representatively sample the space of odorous molecules as well as identify previously unknown odorants with a target odor character. Here, I put this work into the context of other modeling efforts and highlight the urgent need for large new datasets and transparent benchmarks for the field to make and evaluate modeling breakthroughs, respectively.
Collapse
Affiliation(s)
- Richard C Gerkin
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| |
Collapse
|
44
|
Nashiry A, Sarmin Sumi S, Islam S, Quinn JMW, Moni MA. Bioinformatics and system biology approach to identify the influences of COVID-19 on cardiovascular and hypertensive comorbidities. Brief Bioinform 2021; 22:1387-1401. [PMID: 33458761 PMCID: PMC7929376 DOI: 10.1093/bib/bbaa426] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/06/2020] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected individuals that have hypertension or cardiovascular comorbidities have an elevated risk of serious coronavirus disease 2019 (COVID-19) disease and high rates of mortality but how COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document} and cardiovascular diseases interact are unclear. We therefore sought to identify novel mechanisms of interaction by identifying genes with altered expression in SARS-CoV-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$2$\end{document} infection that are relevant to the pathogenesis of cardiovascular disease and hypertension. Some recent research shows the SARS-CoV-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$2$\end{document} uses the angiotensin converting enzyme-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$2$\end{document} (ACE-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$2$\end{document}) as a receptor to infect human susceptible cells. The ACE2 gene is expressed in many human tissues, including intestine, testis, kidneys, heart and lungs. ACE2 usually converts Angiotensin I in the renin–angiotensin-aldosterone system to Angiotensin II, which affects blood pressure levels. ACE inhibitors prescribed for cardiovascular disease and hypertension may increase the levels of ACE-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$2$\end{document}, although there are claims that such medications actually reduce lung injury caused by COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document}. We employed bioinformatics and systematic approaches to identify such genetic links, using messenger RNA data peripheral blood cells from COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document} patients and compared them with blood samples from patients with either chronic heart failure disease or hypertensive diseases. We have also considered the immune response genes with elevated expression in COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document} to those active in cardiovascular diseases and hypertension. Differentially expressed genes (DEGs) common to COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document} and chronic heart failure, and common to COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document} and hypertension, were identified; the involvement of these common genes in the signalling pathways and ontologies studied. COVID-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$19$\end{document} does not share a large number of differentially expressed genes with the conditions under consideration. However, those that were identified included genes playing roles in T cell functions, toll-like receptor pathways, cytokines, chemokines, cell stress, type 2 diabetes and gastric cancer. We also identified protein–protein interactions, gene regulatory networks and suggested drug and chemical compound interactions using the differentially expressed genes. The result of this study may help in identifying significant targets of treatment that can combat the ongoing pandemic due to SARS-CoV-\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{upgreek}
\usepackage{mathrsfs}
\setlength{\oddsidemargin}{-69pt}
\begin{document}
}{}$2$\end{document} infection.
Collapse
Affiliation(s)
- Asif Nashiry
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Bangladesh
| | - Shauli Sarmin Sumi
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Bangladesh
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Julian M W Quinn
- Healthy Ageing Theme, The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Mohammad Ali Moni
- Healthy Ageing Theme, The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.,WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia
| |
Collapse
|
45
|
Nagarajan SK, Babu S, Kulkarni SA, Vadivelu A, Devaraju P, Sohn H, Madhavan T. Understanding the influence of lipid bilayers and ligand molecules in determining the conformational dynamics of somatostatin receptor 2. Sci Rep 2021. [PMID: 33828200 DOI: 10.1038/s41598‐021‐87422‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Somatostatin receptor 2 (SSTR2) is a G-protein coupled receptor (GPCR) that controls numerous cellular processes including cell-to-cell signaling. In this study, we report how the lipid and ligand molecules influence the conformational dynamics of the membrane-bound SSTR2. Molecular simulations of different holo and apoenzyme complexes of SSTR2 in the presence and absence of a lipid bilayer were performed, observed, and correlated with previously reported studies. We identified the important SSTR2 residues that take part in the formation of the SSTR2-ligand complex. On analyzing the molecular simulation trajectories, we identified that the residue D3.32 is crucial in determining the bioactive conformation of SSTR2 ligands in the binding site. Based on the results, we suggest that designing a novel SSTR2 ligand with an H-bond donor group at the R1 position, and hydrophobic groups at R2 and R3 might have higher activity and SSTR2-selectivity. We analyzed the simulated systems to identify other important structural features involved in SSTR2-ligand binding and to observe the different conformational changes that occur in the protein after the ligand binding. Additionally, we studied the conformational dynamics of N- and C-terminal regions of SSTR2 in the presence and absence of the lipid bilayer. Both the systems were compared to understand the influence of lipid molecules in the formation of secondary structural domains by these extracellular regions. The comparative study revealed that the secondary structural elements formed by C-terminal residues in presence of lipid molecules is crucial for the functioning of SSTR2. Our study results highlight the structural complexities involved in the functioning of SSTR upon binding with the ligands in the presence and absence of lipid bilayer, which is essential for designing novel drug targets.
Collapse
Affiliation(s)
- Santhosh Kumar Nagarajan
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chennai, 603203, India
| | - Sathya Babu
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chennai, 603203, India
| | - Seema A Kulkarni
- Department of Food and Process Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chennai, 603203, India
| | - Aanand Vadivelu
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chennai, 603203, India
| | - Panneer Devaraju
- Unit of Vector Biology and Control, ICMR-Vector Control Research Centre, Indian Council of Medical Research (ICMR), Puducherry, India
| | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, South Korea.
| | - Thirumurthy Madhavan
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chennai, 603203, India.
| |
Collapse
|
46
|
Understanding the influence of lipid bilayers and ligand molecules in determining the conformational dynamics of somatostatin receptor 2. Sci Rep 2021; 11:7677. [PMID: 33828200 PMCID: PMC8027056 DOI: 10.1038/s41598-021-87422-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/26/2021] [Indexed: 11/11/2022] Open
Abstract
Somatostatin receptor 2 (SSTR2) is a G-protein coupled receptor (GPCR) that controls numerous cellular processes including cell-to-cell signaling. In this study, we report how the lipid and ligand molecules influence the conformational dynamics of the membrane-bound SSTR2. Molecular simulations of different holo and apoenzyme complexes of SSTR2 in the presence and absence of a lipid bilayer were performed, observed, and correlated with previously reported studies. We identified the important SSTR2 residues that take part in the formation of the SSTR2-ligand complex. On analyzing the molecular simulation trajectories, we identified that the residue D3.32 is crucial in determining the bioactive conformation of SSTR2 ligands in the binding site. Based on the results, we suggest that designing a novel SSTR2 ligand with an H-bond donor group at the R1 position, and hydrophobic groups at R2 and R3 might have higher activity and SSTR2-selectivity. We analyzed the simulated systems to identify other important structural features involved in SSTR2-ligand binding and to observe the different conformational changes that occur in the protein after the ligand binding. Additionally, we studied the conformational dynamics of N- and C-terminal regions of SSTR2 in the presence and absence of the lipid bilayer. Both the systems were compared to understand the influence of lipid molecules in the formation of secondary structural domains by these extracellular regions. The comparative study revealed that the secondary structural elements formed by C-terminal residues in presence of lipid molecules is crucial for the functioning of SSTR2. Our study results highlight the structural complexities involved in the functioning of SSTR upon binding with the ligands in the presence and absence of lipid bilayer, which is essential for designing novel drug targets.
Collapse
|
47
|
Heim B, Handrick R, Hartmann MD, Kiefer H. Refolding and characterization of two G protein-coupled receptors purified from E. coli inclusion bodies. PLoS One 2021; 16:e0247689. [PMID: 33626080 PMCID: PMC7904181 DOI: 10.1371/journal.pone.0247689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/10/2021] [Indexed: 11/18/2022] Open
Abstract
Aiming at streamlining GPCR production from E. coli inclusion bodies for structural analysis, we present a generic approach to assess and optimize refolding yield through thermostability analysis. Since commonly used hydrophobic dyes cannot be applied as probes for membrane protein unfolding, we adapted a technique based on reacting cysteins exposed upon thermal denaturation with fluorescent 7-Diethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). Successful expression, purification and refolding is shown for two G protein-coupled receptors (GPCR), the sphingosine-1-phosphate receptor S1P1, and the orphan receptor GPR3. Refolded receptors were subjected to lipidic cubic phase crystallization screening.
Collapse
Affiliation(s)
- Bastian Heim
- Institute of Applied Biotechnology, University of Applied Sciences, Biberach, Germany
- * E-mail:
| | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences, Biberach, Germany
| | | | - Hans Kiefer
- Institute of Applied Biotechnology, University of Applied Sciences, Biberach, Germany
| |
Collapse
|
48
|
Park S, Kang W, Choi D, Son B, Park T. Nonanal Stimulates Growth Factors via Cyclic Adenosine Monophosphate (cAMP) Signaling in Human Hair Follicle Dermal Papilla Cells. Int J Mol Sci 2020; 21:ijms21218054. [PMID: 33126774 PMCID: PMC7662673 DOI: 10.3390/ijms21218054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/30/2022] Open
Abstract
Human hair follicle dermal papilla cells (DPCs) are a specialized population of cells located in the hair follicles and regulate hair growth and development, particularly by releasing numerous growth factors in response to various physiological conditions. In the present study, we aimed to test whether nonanal, a scent compound from plants, stimulated growth factors in DPCs and to delineate the underlying mechanisms involved. We found that nonanal promoted DPC proliferation in a dose-dependent manner. Meanwhile, it also increased the intracellular cyclic adenosine monophosphate (cAMP) levels and the expression of various growth factor genes such as vascular endothelial growth factor, keratinocyte growth factor, and insulin-like growth factor 1. Furthermore, nonanal treatment stimulated DPC migration. Notably, the benefits of nonanal use were abrogated by cAMP inhibition. Our results reveal the potential of nonanal in preventing hair loss and suggest that its effects are cAMP-mediated in DPCs.
Collapse
Affiliation(s)
| | | | | | | | - Taesun Park
- Correspondence: ; Tel.: +82-2-2123-3123; Fax: +82-2-365-3118
| |
Collapse
|
49
|
Apostol CR, Hay M, Polt R. Glycopeptide drugs: A pharmacological dimension between "Small Molecules" and "Biologics". Peptides 2020; 131:170369. [PMID: 32673700 PMCID: PMC7448947 DOI: 10.1016/j.peptides.2020.170369] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Peptides are an important class of molecules with diverse biological activities. Many endogenous peptides, especially neuropeptides and peptide hormones, play critical roles in development and regulating homeostasis. Furthermore, as drug candidates their high receptor selectivity and potent binding leads to reduced off-target interactions and potential negative side effects. However, the therapeutic potential of peptides is severely hampered by their poor stability in vivo and low permeability across biological membranes. Several strategies have been successfully employed over the decades to address these concerns, and one of the most promising strategies is glycosylation. It has been demonstrated in numerous cases that glycosylation is an effective synthetic approach to improve the pharmacokinetic profiles and membrane permeability of peptides. The effects of glycosylation on peptide stability and peptide-membrane interactions in the context of blood-brain barrier penetration will be explored. Numerous examples of glycosylated analogues of endogenous peptides targeting class A and B G-protein coupled receptors (GPCRs) with an emphasis on O-linked glycopeptides will be reviewed. Notable examples of N-, S-, and C-linked glycopeptides will also be discussed. A small section is devoted to synthetic methods for the preparation of glycopeptides and requisite amino acid glycoside building blocks.
Collapse
Affiliation(s)
- Christopher R Apostol
- Dept. of Chemistry & Biochemistry, BIO5, The University of Arizona, Tucson, AZ 85721, USA.
| | - Meredith Hay
- Evelyn F. McKnight Brain Institute, Dept. of Physiology, The University of Arizona, Tucson, AZ 85724, USA
| | - Robin Polt
- Dept. of Chemistry & Biochemistry, BIO5, The University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
50
|
Poulie CBM, Liu N, Jensen AA, Bunch L. Design, Synthesis, and Pharmacological Characterization of Heterobivalent Ligands for the Putative 5-HT 2A/mGlu 2 Receptor Complex. J Med Chem 2020; 63:9928-9949. [PMID: 32815361 DOI: 10.1021/acs.jmedchem.0c01058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We report the synthesis of the first series of heterobivalent ligands targeting the putative heteromeric 5-HT2A/mGlu2 receptor complex, based on the 5-HT2A antagonist MDL-100,907 and the mGlu2 ago-PAM JNJ-42491293. The functional properties of monovalent and heterobivalent ligands were characterized in 5-HT2A-, mGlu2/Gqo5-, 5-HT2A/mGlu2-, and 5-HT2A/mGlu2/Gqo5-expressing HEK293 cells using a Ca2+ imaging assay and a [3H]ketanserin binding assay. Pronounced functional crosstalk was observed between the two receptors in 5-HT2A/mGlu2 and 5-HT2A/mGlu2/Gqo5 cells. While the synthesized monovalent ligands retained the 5-HT2A antagonist and mGlu2 ago-PAM functionalities, the seven bivalent ligands inhibited 5-HT-induced responses in 5-HT2A/mGlu2 cells and both 5-HT- and Glu-induced responses in 5-HT2A/mGlu2/Gqo5 cells. However, no definitive correlation between the functional potency and spacer length of the ligands was observed, an observation substantiated by the binding affinities exhibited by the compounds in 5-HT2A, 5-HT2A/mGlu2, and 5-HT2A/mGlu2/Gqo5 cells. In conclusion, while functional crosstalk between 5-HT2A and mGlu2 was demonstrated, it remains unclear how these heterobivalent ligands interact with the putative receptor complex.
Collapse
Affiliation(s)
- Christian B M Poulie
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen OE, Denmark
| | - Na Liu
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen OE, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen OE, Denmark
| | - Lennart Bunch
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen OE, Denmark
| |
Collapse
|