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Shen S, Deng Y, Shen C, Chen H, Cheng L, Wu C, Zhao C, Yang Z, Hou H, Wang K, Shao Z, Deng C, Ye F, Yan W. Structural basis of neuropeptide Y signaling through Y 1 and Y 2 receptors. MedComm (Beijing) 2024; 5:e565. [PMID: 38882210 PMCID: PMC11179954 DOI: 10.1002/mco2.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/20/2024] [Accepted: 03/02/2024] [Indexed: 06/18/2024] Open
Abstract
Neuropeptide Y (NPY), a 36-amino-acid peptide, functions as a neurotransmitter in both the central and peripheral nervous systems by activating the NPY receptor subfamily. Notably, NPY analogs display varying selectivity and exert diverse physiological effects through their interactions with this receptor family. [Pro34]-NPY and [Leu31, Pro34]-NPY, mainly acting on Y1R, reportedly increases blood pressure and postsynaptically potentiates the effect of other vasoactive substances above all, while N-terminal cleaved NPY variants in human body primary mediates angiogenesis and neurotransmitter release inhibition through Y2R. However, the recognition mechanisms of Y1R and Y2R with specific agonists remain elusive, thereby hindering subtype receptor-selective drug development. In this study, we report three cryo-electron microscopy (cryo-EM) structures of Gi2-coupled Y1R and Y2R in complexes with NPY, as well as Y1R bound to a selective agonist [Leu31, Pro34]-NPY. Combined with cell-based assays, our study not only reveals the conserved peptide-binding mode of NPY receptors but also identifies an additional sub-pocket that confers ligand selectivity. Moreover, our analysis of Y1R evolutionary dynamics suggests that this sub-pocket has undergone functional adaptive evolution across different species. Collectively, our findings shed light on the molecular underpinnings of neuropeptide recognition and receptor activation, and they present a promising avenue for the design of selective drugs targeting the NPY receptor family.
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Affiliation(s)
- Siyuan Shen
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
- Frontiers Medical Center Tianfu Jincheng Laboratory Chengdu China
| | - Yue Deng
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Chenglong Shen
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Haidi Chen
- Institutes for Systems Genetics Frontiers Science Centre for Disease‑Related Molecular Network West China Hospital Sichuan University Chengdu Sichuan China
| | - Lin Cheng
- Department of Otolaryngology Head and Neck Surgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu China
| | - Chao Wu
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Chang Zhao
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Zhiqian Yang
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Hanlin Hou
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Kexin Wang
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
- Frontiers Medical Center Tianfu Jincheng Laboratory Chengdu China
| | - Cheng Deng
- Institutes for Systems Genetics Frontiers Science Centre for Disease‑Related Molecular Network West China Hospital Sichuan University Chengdu Sichuan China
| | - Feng Ye
- Department of Pathology Institute of Clinical Pathology Frontiers Science Center for Disease-related Molecular Network West China Hospital of Sichuan University Chengdu China
| | - Wei Yan
- Division of Nephrology and Kidney Research Institute State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu Sichuan China
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2
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Szwabowski GL, Griffing M, Mugabe EJ, O'Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | - Makenzie Griffing
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Elijah J Mugabe
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Daniel O'Malley
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Lindsey N Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Daniel L Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Abby L Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
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3
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Xia X, Li Y. A new GRAB sensor reveals differences in the dynamics and molecular regulation between neuropeptide and neurotransmitter release. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595424. [PMID: 38826473 PMCID: PMC11142204 DOI: 10.1101/2024.05.22.595424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The co-existence and co-transmission of neuropeptides and small molecule neurotransmitters in the same neuron is a fundamental aspect of almost all neurons across various species. However, the differences regarding their in vivo spatiotemporal dynamics and underlying molecular regulation remain poorly understood. Here, we developed a GPCR-activation-based (GRAB) sensor for detecting short neuropeptide F (sNPF) with high sensitivity and spatiotemporal resolution. Furthermore, we explore the differences of in vivo dynamics and molecular regulation between sNPF and acetylcholine (ACh) from the same neurons. Interestingly, the release of sNPF and ACh shows different spatiotemporal dynamics. Notably, we found that distinct synaptotagmins (Syt) are involved in these two processes, as Syt7 and Sytα for sNPF release, while Syt1 for ACh release. Thus, this new GRAB sensor provides a powerful tool for studying neuropeptide release and providing new insights into the distinct release dynamics and molecular regulation between neuropeptides and small molecule neurotransmitters.
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Affiliation(s)
- Xiju Xia
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies (AAIS), and Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, Beijing, 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies (AAIS), and Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, Beijing, 100871, China
- Chinese Institute for Brain Research, Beijing 102206, China
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4
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Chen L, Su P, Wang Y, Liu Y, Chen LM, Gao S. CKR-1 orchestrates two motor states from a single motoneuron in C. elegans. iScience 2024; 27:109390. [PMID: 38510145 PMCID: PMC10952047 DOI: 10.1016/j.isci.2024.109390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/22/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Neuromodulation is pivotal in modifying neuronal properties and motor states. CKR-1, a homolog of the cholecystokinin receptor, modulates robust escape steering and undulation body bending in C. elegans. Nevertheless, the mechanisms through which CKR-1 governs these motor states remain elusive. We elucidate the head motoneuron SMD as the orchestrator of both motor states. This regulation involves two neuropeptides: NLP-12 from DVA enhances undulation body curvature, while NLP-18 from ASI amplifies Ω-turn head curvature. Moreover, synthetic NLP-12 and NLP-18 peptides elicit CKR-1-dependent currents in Xenopus oocytes and Ca2+ transients in SMD neurons. Notably, CKR-1 shows higher sensitivity to NLP-18 compared to NLP-12. In situ patch-clamp recordings reveal CKR-1, NLP-12, and NLP-18 are not essential for neurotransmission at C. elegans neuromuscular junction, suggesting that SMD independently regulates head and body bending. Our studies illustrate that a single motoneuron SMD utilizes a cholecystokinin receptor CKR-1 to integrate two motor states.
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Affiliation(s)
- Lili Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pan Su
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ya Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuting Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li-Ming Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shangbang Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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5
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Walrant A, Sachon E. Photoaffinity labeling coupled to MS to identify peptide biological partners: Secondary reactions, for better or for worse? MASS SPECTROMETRY REVIEWS 2024. [PMID: 38576378 DOI: 10.1002/mas.21880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/22/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Affinity photolabeling is a smart method to study noncovalent and transient interactions and provide a submolecular picture of the contacts between interacting partners. In this review, we will focus on the identification of peptide partners using photoaffinity labeling coupled to mass spectrometry in different contexts such as in vitro with a purified potential partner, in model systems such as model membranes, and with live cells using both targeted and nontargeted proteomics studies. Different biological partners will be described, among which glycoconjugates, oligonucleotides, peptides, proteins, and lipids, with the photoreactive label inserted either on the peptide of interest or on the potential partner. Particular attention will be paid to the observation and characterization of specific rearrangements following the photolabeling reaction, which can help characterize photoadducts and provide a better understanding of the interacting systems and environment.
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Affiliation(s)
- Astrid Walrant
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Emmanuelle Sachon
- Laboratoire des Biomolécules, LBM, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
- Sorbonne Université, Mass Spectrometry Sciences Sorbonne Université, MS3U platform, Fédération de Chimie moléculaire de Paris centre, Paris, France
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6
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Li MM, Yang Q, Chen LH, Li YY, Wu JX, Xu XL. Effect of short neuropeptide F signaling on larval feeding in Mythimna separata. INSECT SCIENCE 2024; 31:417-434. [PMID: 37464946 DOI: 10.1111/1744-7917.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 07/20/2023]
Abstract
Mythimna separata is a notorious phytophagous pest which poses serious threats to cereal crops owing to the gluttony of the larvae. Because short neuropeptide F (sNPF) and its receptor sNPFR are involved in a diversity of physiological functions, especially in functions related to feeding in insects, it is a molecular target for pest control. Herein, an sNPF and 2 sNPFRs were identified and cloned from M. separata. Bioinformatics analysis revealed that the sNPF and its receptors had a highly conserved RLRFamide C-terminus and 7 transmembrane domains, respectively. The sNPF and its receptor genes were distributed across larval periods and tissues, but 2 receptors had distinct expression patterns. The starvation-induced assay elucidated that sNPF and sNPFR expression levels were downregulated under food deprivation and recovered with subsequent re-feeding. RNA interference knockdown of sNPF, sNPFR1, and sNPFR2 by injection of double-stranded RNA into larvae not only suppressed food consumption and increased body size and weight, but also led to decrease of glycogen and total lipid contents, and increase of trehalose compared with double-stranded green fluorescent protein injection. Furthermore, molecular docking was performed on the interaction mode between sNPFR protein and its ligand sNPF based on the 3-dimensional models constructed by AlphaFold; the results indicated that both receptors were presumably activated by the mature peptide sNPF-2. These results revealed that sNPF signaling played a considerably vital role in the feeding regulation of M. separata and represents a potential control target for this pest.
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Affiliation(s)
- Mei-Mei Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Qi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Li-Hui Chen
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Yan-Ying Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Jun-Xiang Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Xiang-Li Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A & F University, Yangling, Shaanxi Province, China
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7
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Richardson JS, Williams CJ, Chen VB, Prisant MG, Richardson DC. The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions. Acta Crystallogr D Struct Biol 2023; 79:1071-1078. [PMID: 37921807 PMCID: PMC10833350 DOI: 10.1107/s2059798323008847] [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: 05/10/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedures and their validation break down and do not ensure reliably correct models. This is because in the broad density at lower resolution, critical features such as protein backbone carbonyl O atoms are not just less accurate but are not seen at all, and so peptide orientations are frequently wrongly fitted by 90-180°. This puts both backbone and side chains into the wrong local energy minimum, and they are then worsened rather than improved by further refinement into a valid but incorrect rotamer or Ramachandran region. On the positive side, new tools are being developed to locate this type of pernicious error in PDB depositions, such as CaBLAM, EMRinger, Pperp diagnosis of ribose puckers, and peptide flips in PDB-REDO, while interactive modeling in Coot or ISOLDE can help to fix many of them. Another positive trend is that artificial intelligence predictions such as those made by AlphaFold2 contribute additional evidence from large multiple sequence alignments, and in high-confidence parts they provide quite good starting models for loops, termini or whole domains with otherwise ambiguous density.
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Affiliation(s)
- Jane S. Richardson
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Vincent B. Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - Michael G. Prisant
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - David C. Richardson
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
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8
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Bale R, Doshi G. Cross talk about the role of Neuropeptide Y in CNS disorders and diseases. Neuropeptides 2023; 102:102388. [PMID: 37918268 DOI: 10.1016/j.npep.2023.102388] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
A peptide composed of a 36 amino acid called Neuropeptide Y (NPY) is employed in a variety of physiological processes to manage and treat conditions affecting the endocrine, circulatory, respiratory, digestive, and neurological systems. NPY naturally binds to G-protein coupled receptors, activating the Y-receptors (Y1-Y5 and y6). The findings on numerous therapeutic applications of NPY for CNS disease are presented in this review by the authors. New targets for treating diseases will be revealed by medication combinations that target NPY and its receptors. This review is mainly focused on disorders such as anxiety, Alzheimer's disease, Parkinson's disease, Huntington's disease, Machado Joseph disease, multiple sclerosis, schizophrenia, depression, migraine, alcohol use disorder, and substance use disorder. The findings from the preclinical studies and clinical studies covered in this article may help create efficient therapeutic plans to treat neurological conditions on the one hand and psychiatric disorders on the other. They may also open the door to the creation of novel NPY receptor ligands as medications to treat these conditions.
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Affiliation(s)
- Rajeshwari Bale
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V L M Road, Vile Parle (w), Mumbai 400056, India
| | - Gaurav Doshi
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, V L M Road, Vile Parle (w), Mumbai 400056, India.
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9
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Wygas MM, Laugwitz JM, Schmidt P, Elgeti M, Kaiser A. Dynamics of the Second Extracellular Loop Control Transducer Coupling of Peptide-Activated GPCRs. Int J Mol Sci 2023; 24:12197. [PMID: 37569573 PMCID: PMC10419011 DOI: 10.3390/ijms241512197] [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: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Many peptide-activated rhodopsin-like GPCRs share a β-hairpin folding motif in the extracellular loop 2 (ECL2), which interacts with the peptide ligand while at the same time being connected to transmembrane helix 3 (TM3) via a highly conserved disulfide bond. Currently, it remains unknown whether the coupling of the specifically shaped ECL2 to TM3 influences the activation of peptide-activated GPCRs. We investigated this possibility in a selection of peptide GPCRs with known structures. Most of the receptors with cysteine to alanine mutations folded like the respective wild-type and resided in the cell membrane, challenging pure folding stabilization by the disulfide bridge. G-protein signaling of the disulfide mutants was retained to a greater extent in secretin-like GPCRs than in rhodopsin-like GPCRs, while recruitment of arrestin was completely abolished in both groups, which may be linked to alterations in ligand residence time. We found a correlation between receptor activity of the neuropeptide Y2 receptor and alterations in ECL2 dynamics using engineered disulfide bridges or site-directed spin labeling and EPR spectroscopy. These data highlight the functional importance of the TM3-ECL2 link for the activation of specific signaling pathways in peptide-activated GPCRs, which might have implications for future drug discovery.
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Affiliation(s)
- Marcel M. Wygas
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Jeannette M. Laugwitz
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Peter Schmidt
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Matthias Elgeti
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
- Medical Faculty, Department of Anesthesiology and Intensive Care, Leipzig University, Liebigstrasse 19, 04103 Leipzig, Germany
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10
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Plut E, Calderón JC, Stanojlović V, Gattor AO, Höring C, Humphrys LJ, Konieczny A, Kerres S, Schubert M, Keller M, Cabrele C, Clark T, Reiser O. Stereochemistry-Driven Interactions of α,γ-Peptide Ligands with the Neuropeptide Y Y 4-Receptor. J Med Chem 2023. [PMID: 37440703 DOI: 10.1021/acs.jmedchem.3c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The G-protein-coupled Y4-receptor (Y4R) and its endogenous ligand, pancreatic polypeptide (PP), suppress appetite in response to food intake and, thus, are attractive drug targets for body-weight control. The C-terminus of human PP (hPP), T32-R33-P34-R35-Y36-NH2, penetrates deep into the binding pocket with its tyrosine-amide and di-arginine motif. Here, we present two C-terminally amidated α,γ-hexapeptides (1a/b) with sequence Ac-R31-γ-CBAA32-R33-L34-R35-Y36-NH2, where γ-CBAA is the (1R,2S,3R)-configured 2-(aminomethyl)-3-phenylcyclobutanecarboxyl moiety (1a) or its mirror image (1b). Both peptides bind the Y4R (Ki of 1a/b: 0.66/12 nM) and act as partial agonists (intrinsic activity of 1a/b: 50/39%). Their induced-fit binding poses in the Y4R pocket are unique and build ligand-receptor contacts distinct from those of the C-terminus of the endogenous ligand hPP. We conclude that energetically favorable interactions, although they do not match those of the native ligand hPP, still guarantee high binding affinity (with 1a rivaling hPP) but not the maximum receptor activation.
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Affiliation(s)
- Eva Plut
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Jacqueline C Calderón
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Vesna Stanojlović
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Carina Höring
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Laura J Humphrys
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Adam Konieczny
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Kerres
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Chiara Cabrele
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Oliver Reiser
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
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11
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Wong AR, Hung A, Yang AWH, Gill H, Lenon GB. Poria cocos compounds targeting neuropeptide Y1 receptor (Y1R) for weight management: A computational ligand- and structure-based study with molecular dynamics simulations identified beta-amyrin acetate as a putative Y1R inhibitor. PLoS One 2023; 18:e0277873. [PMID: 37390097 PMCID: PMC10313034 DOI: 10.1371/journal.pone.0277873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/09/2022] [Indexed: 07/02/2023] Open
Abstract
Poria cocos (PC) is a medicinal herb frequently used in weight-loss clinical trials, however the mechanisms by which its compounds target orexigenic receptors including the neuropeptide Y1 receptor (Y1R) remain largely unknown. This study aimed to screen PC compounds for favourable pharmacokinetics profiles and examine their molecular mechanisms targeting Y1R. Forty-three PC compounds were systematically sought from pharmacological databases and docked with Y1R (PDB: 5ZBQ). By comparing the relative binding affinities, pharmacokinetics and toxicity profiles, we hypothesised that compounds designated PC1 3,4-Dihydroxybenzoic acid, PC8 Vanillic acid, PC40 1-(alpha-L-Ribofuranosyl)uracil, could be potential antagonists as they contact major residues Asn283 and Asp287, similar to various potent Y1R antagonists. In addition, PC21 Poricoic acid B, PC22 Poricoic acid G and PC43 16alpha,25-Dihydroxy-24-methylene-3,4-secolanosta-4(28),7,9(11)-triene-3,21-dioic acid, contacting Asn299, Asp104 and Asp200 proximal to the extracellular surface could also interfere with agonist binding by stabilising the extracellular loop (ECL) 2 of Y1R in a closed position. Owing to their selective interaction with Phe302, an important residue in binding of selective Y1R antagonists, PC12 beta-Amyrin acetate, PC26 3-Epidehydrotumulosic acid and PC27 Cerevisterol were proposed as putative antagonists. Following the consensus approach, PC12 beta-Amyrin acetate, PC26 3-Epidehydrotumulosic acid and PC27 Cerevisterol were identified as candidate compounds due to their high affinities (-12.2, -11.0 and -10.8 kcal, respectively), high drug-likeness and low toxicity profiles. Trajectory analyses and energy contributions of PC12-Y1R complex further confirmed their structural stability and favourable binding free energies, highlighting the feasibility and possible development of PC12 beta-Amyrin acetate as a future Y1R inhibitor.
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Affiliation(s)
- Ann Rann Wong
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Andrew Hung
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Angela Wei Hong Yang
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Harsharn Gill
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - George Binh Lenon
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
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12
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Sánchez ML, Rodríguez FD, Coveñas R. Neuropeptide Y Peptide Family and Cancer: Antitumor Therapeutic Strategies. Int J Mol Sci 2023; 24:9962. [PMID: 37373115 DOI: 10.3390/ijms24129962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Currently available data on the involvement of neuropeptide Y (NPY), peptide YY (PYY), and pancreatic polypeptide (PP) and their receptors (YRs) in cancer are updated. The structure and dynamics of YRs and their intracellular signaling pathways are also studied. The roles played by these peptides in 22 different cancer types are reviewed (e.g., breast cancer, colorectal cancer, Ewing sarcoma, liver cancer, melanoma, neuroblastoma, pancreatic cancer, pheochromocytoma, and prostate cancer). YRs could be used as cancer diagnostic markers and therapeutic targets. A high Y1R expression has been correlated with lymph node metastasis, advanced stages, and perineural invasion; an increased Y5R expression with survival and tumor growth; and a high serum NPY level with relapse, metastasis, and poor survival. YRs mediate tumor cell proliferation, migration, invasion, metastasis, and angiogenesis; YR antagonists block the previous actions and promote the death of cancer cells. NPY favors tumor cell growth, migration, and metastasis and promotes angiogenesis in some tumors (e.g., breast cancer, colorectal cancer, neuroblastoma, pancreatic cancer), whereas in others it exerts an antitumor effect (e.g., cholangiocarcinoma, Ewing sarcoma, liver cancer). PYY or its fragments block tumor cell growth, migration, and invasion in breast, colorectal, esophageal, liver, pancreatic, and prostate cancer. Current data show the peptidergic system's high potential for cancer diagnosis, treatment, and support using Y2R/Y5R antagonists and NPY or PYY agonists as promising antitumor therapeutic strategies. Some important research lines to be developed in the future will also be suggested.
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Affiliation(s)
- Manuel Lisardo Sánchez
- Laboratory of Neuroanatomy of the Peptidergic Systems, Institute of Neurosciences of Castilla and León (INCYL), University of Salamanca, 37008 Salamanca, Spain
| | - Francisco D Rodríguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemical Sciences, University of Salamanca, 37008 Salamanca, Spain
- Group GIR-USAL: BMD (Bases Moleculares del Desarrollo), University of Salamanca, 37008 Salamanca, Spain
| | - Rafael Coveñas
- Laboratory of Neuroanatomy of the Peptidergic Systems, Institute of Neurosciences of Castilla and León (INCYL), University of Salamanca, 37008 Salamanca, Spain
- Group GIR-USAL: BMD (Bases Moleculares del Desarrollo), University of Salamanca, 37008 Salamanca, Spain
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13
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Liessmann F, Künze G, Meiler J. Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection. Int J Mol Sci 2023; 24:7788. [PMID: 37175495 PMCID: PMC10178219 DOI: 10.3390/ijms24097788] [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: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of Cα-Cα-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications.
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Affiliation(s)
- Fabian Liessmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Jens Meiler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105 Leipzig, Germany
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14
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Ball HL, Said H, Chapman K, Fu R, Xiong Y, Burk JA, Rosenbaum D, Veneziano R, Cotten ML. Orexin A, an amphipathic α-helical neuropeptide involved in pleiotropic functions in the nervous and immune systems: Synthetic approach and biophysical studies of the membrane-bound state. Biophys Chem 2023; 297:107007. [PMID: 37037119 DOI: 10.1016/j.bpc.2023.107007] [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: 02/06/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
This research reports on the membrane interactions of orexin A (OXA), an α-helical and amphipathic neuropeptide that contains 33 residues and two disulfide bonds in the N-terminal region. OXA, which activates the orexins 1 and 2 receptors in neural and immune cell membranes, has essential pleiotropic physiological effects, including at the levels of arousal, sleep/wakefulness, energy balance, neuroprotection, lipid signaling, the inflammatory response, and pain. As a result, the orexin system has become a prominent target to treat diseases such as sleep disorders, drug addiction, and inflammation. While the high-resolution structure of OXA has been investigated in water and bound to micelles, there is a lack of information about its conformation bound to phospholipid membranes and its receptors. NMR is a powerful method to investigate peptide structures in a membrane environment. To facilitate the NMR structural studies of OXA exposed to membranes, we present a novel synthetic scheme, leading to the production of isotopically-labeled material at high purity. A receptor activation assay shows that the 15N-labeled peptide is biologically active. Biophysical studies are performed using surface plasmon resonance, circular dichroism, and NMR to investigate the interactions of OXA with phospholipid bilayers. The results demonstrate a strong interaction between the peptide and phospholipids, an increase in α-helical content upon membrane binding, and an in-plane orientation of the C-terminal region critical to function. This new knowledge about structure-activity relationships in OXA could inspire the design of novel therapeutics that leverage the anti-inflammatory and neuro-protective functions of OXA, and therefore could help address neuroinflammation, a major issue associated with neurological disorders such as Alzheimer's disease.
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Affiliation(s)
- Haydn L Ball
- Department of Chemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hooda Said
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Karen Chapman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Joshua A Burk
- Department of Psychological Sciences, William & Mary, Williamsburg, VA 23185, USA
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Remi Veneziano
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA.
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15
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Ortiz C, Klein S, Reul WH, Magdaleno F, Gröschl S, Dietrich P, Schierwagen R, Uschner FE, Torres S, Hieber C, Meier C, Kraus N, Tyc O, Brol M, Zeuzem S, Welsch C, Poglitsch M, Hellerbrand C, Alfonso-Prieto M, Mira F, Keller UAD, Tetzner A, Moore A, Walther T, Trebicka J. Neprilysin-dependent neuropeptide Y cleavage in the liver promotes fibrosis by blocking NPY-receptor 1. Cell Rep 2023; 42:112059. [PMID: 36729833 PMCID: PMC9989826 DOI: 10.1016/j.celrep.2023.112059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/17/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
Development of liver fibrosis is paralleled by contraction of hepatic stellate cells (HSCs), the main profibrotic hepatic cells. Yet, little is known about the interplay of neprilysin (NEP) and its substrate neuropeptide Y (NPY), a potent enhancer of contraction, in liver fibrosis. We demonstrate that HSCs are the source of NEP. Importantly, NPY originates majorly from the splanchnic region and is cleaved by NEP in order to terminate contraction. Interestingly, NEP deficiency (Nep-/-) showed less fibrosis but portal hypertension upon liver injury in two different fibrosis models in mice. We demonstrate the incremental benefit of Nep-/- in addition to AT1R blocker (ARB) or ACE inhibitors for fibrosis and portal hypertension. Finally, oral administration of Entresto, a combination of ARB and NEP inhibitor, decreased hepatic fibrosis and portal pressure in mice. These results provide a mechanistic rationale for translation of NEP-AT1R-blockade in human liver fibrosis and portal hypertension.
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Affiliation(s)
- Cristina Ortiz
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sabine Klein
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany; Department of Internal Medicine B, University of Münster, Albert-Schweitzer Campus 1, 48149 Münster, Germany
| | - Winfried H Reul
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | | | - Stefanie Gröschl
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany; Department of Internal Medicine 1, FAU Erlangen-Nuremberg and Universitätsklinikum Erlangen, Ulmenweg 18, 91054 Erlangen, Germany
| | - Robert Schierwagen
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Frank E Uschner
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sandra Torres
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Hieber
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Caroline Meier
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Nico Kraus
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Olaf Tyc
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Maximilian Brol
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Welsch
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany
| | | | - Claus Hellerbrand
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Neuroscience and Medicine INM-9 and Institute for Advanced Simulations IAS-5, Forschungszentrum Jülich, Jülich, Germany; Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fabio Mira
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Anja Tetzner
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Andrew Moore
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Thomas Walther
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland; Department of Pediatric Surgery, Centre for Fetal Medicine, Division of Women and Child Health, University of Leipzig, Leipzig, Germany; Department of Obstetrics, Centre for Fetal Medicine, Division of Women and Child Health, University of Leipzig, Leipzig, Germany
| | - Jonel Trebicka
- Department of Internal Medicine I, University Hospital Frankfurt, Frankfurt am Main, Germany; Institute of Clinical Research, Odense University Hospital, University of Southern Denmark, Odense, Denmark; European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain; Institute for Bioengineering of Catalonia, Barcelona, Spain; Department of Internal Medicine B, University of Münster, Albert-Schweitzer Campus 1, 48149 Münster, Germany.
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16
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Grätz L, Müller C, Pegoli A, Schindler L, Bernhardt G, Littmann T. Insertion of Nanoluc into the Extracellular Loops as a Complementary Method To Establish BRET-Based Binding Assays for GPCRs. ACS Pharmacol Transl Sci 2022; 5:1142-1155. [PMID: 36407949 PMCID: PMC9667534 DOI: 10.1021/acsptsci.2c00162] [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: 08/15/2022] [Indexed: 11/13/2022]
Abstract
Luminescence-based techniques play an increasingly important role in all areas of biochemical research, including investigations on G protein-coupled receptors (GPCRs). One quite recent and popular addition has been made by introducing bioluminescence resonance energy transfer (BRET)-based binding assays for GPCRs, which are based on the fusion of nanoluciferase (Nluc) to the N-terminus of the receptor and the occurring energy transfer via BRET to a bound fluorescent ligand. However, being based on BRET, the technique is strongly dependent on the distance/orientation between the luciferase and the fluorescent ligand. Here we describe an alternative strategy to establish BRET-based binding assays for GPCRs, where the N-terminal fusion of Nluc did not result in functioning test systems with our fluorescent ligands (e.g., for the neuropeptide Y Y1 receptor (Y1R) and the neurotensin receptor type 1 (NTS1R)). Instead, we introduced Nluc into their second extracellular loop and we obtained binding data for the fluorescent ligands and reported standard ligands (in saturation and competition binding experiments, respectively) comparable to data from the literature. The strategy was transferred to the angiotensin II receptor type 1 (AT1R) and the M1 muscarinic acetylcholine receptor (M1R), which led to affinity estimates comparable to data from radioligand binding experiments. Additionally, an analysis of the binding kinetics of all fluorescent ligands at their respective target was performed using the newly described receptor/Nluc-constructs.
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Affiliation(s)
| | - Christoph Müller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | | | - Lisa Schindler
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Günther Bernhardt
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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17
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Puri S, Kenyon BM, Hamrah P. Immunomodulatory Role of Neuropeptides in the Cornea. Biomedicines 2022; 10:1985. [PMID: 36009532 PMCID: PMC9406019 DOI: 10.3390/biomedicines10081985] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 12/21/2022] Open
Abstract
The transparency of the cornea along with its dense sensory innervation and resident leukocyte populations make it an ideal tissue to study interactions between the nervous and immune systems. The cornea is the most densely innervated tissue of the body and possesses both immune and vascular privilege, in part due to its unique repertoire of resident immune cells. Corneal nerves produce various neuropeptides that have a wide range of functions on immune cells. As research in this area expands, further insights are made into the role of neuropeptides and their immunomodulatory functions in the healthy and diseased cornea. Much remains to be known regarding the details of neuropeptide signaling and how it contributes to pathophysiology, which is likely due to complex interactions among neuropeptides, receptor isoform-specific signaling events, and the inflammatory microenvironment in disease. However, progress in this area has led to an increase in studies that have begun modulating neuropeptide activity for the treatment of corneal diseases with promising results, necessitating the need for a comprehensive review of the literature. This review focuses on the role of neuropeptides in maintaining the homeostasis of the ocular surface, alterations in disease settings, and the possible therapeutic potential of targeting these systems.
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Affiliation(s)
- Sudan Puri
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
- Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Brendan M. Kenyon
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
- Program in Neuroscience, Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Pedram Hamrah
- Center for Translational Ocular Immunology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
- Department of Ophthalmology, Tufts Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
- Program in Neuroscience, Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
- Departments of Immunology and Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
- Cornea Service, Tufts New England Eye Center, Boston, MA 02111, USA
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18
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Chen Q, Liang Z, Yue Q, Wang X, Siu SWI, Pui-Man Hoi M, Lee SMY. A Neuropeptide Y/F-like Polypeptide Derived from the Transcriptome of Turbinaria peltata Suppresses LPS-Induced Astrocytic Inflammation. JOURNAL OF NATURAL PRODUCTS 2022; 85:1569-1580. [PMID: 35694811 DOI: 10.1021/acs.jnatprod.2c00158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Neuropeptides are a group of neuronal signaling molecules that regulate physiological and behavioral processes in animals. Here, we used in silico mining to predict the polypeptide composition of available transcriptomic data of Turbinaria peltata. In total, 118 transcripts encoding putative peptide precursors were discovered. One neuropeptide Y/F-like peptide, named TpNPY, was identified and selected for in silico structural, in silico binding, and pharmacological studies. In our study, the anti-inflammation effect of TpNPY was evaluated using an LPS-stimulated C8-D1A astrocyte cell model. Our results demonstrated that TpNPY, at 0.75-3 μM, inhibited LPS-induced NO production and reduced the expression of iNOS in a dose-dependent manner. Furthermore, TpNPY reduced the secretion of proinflammatory cytokines. Additionally, treatment with TpNPY reduced LPS-mediated elevation of ROS production and the intracellular calcium concentration. Further investigation revealed that TpNPY downregulated the IKK/IκB/NF-κB signaling pathway and inhibited expression of the NLRP3 inflammasome. Through molecular docking and using an NPY receptor antagonist, TpNPY was shown to have the ability to interact with the NPY Y1 receptor. On the basis of these findings, we concluded that TpNPY might prevent LPS-induced injury in astrocytes through activation of the NPY-Y1R.
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Affiliation(s)
- Qian Chen
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Zirong Liang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Qian Yue
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xiufen Wang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Shirley Weng In Siu
- Institute of Science and Environment, University of Saint Joseph, Macao, China
| | - Maggie Pui-Man Hoi
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Macao, China
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19
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Tang T, Tan Q, Han S, Diemar A, Löbner K, Wang H, Schüß C, Behr V, Mörl K, Wang M, Chu X, Yi C, Keller M, Kofoed J, Reedtz-Runge S, Kaiser A, Beck-Sickinger AG, Zhao Q, Wu B. Receptor-specific recognition of NPY peptides revealed by structures of NPY receptors. SCIENCE ADVANCES 2022; 8:eabm1232. [PMID: 35507650 PMCID: PMC9067930 DOI: 10.1126/sciadv.abm1232] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
In response to three highly conserved neuropeptides, neuropeptide Y (NPY), peptide YY, and pancreatic polypeptide (PP), four G protein-coupled receptors mediate multiple essential physiological processes, such as food intake, vasoconstriction, sedation, and memory retention. Here, we report the structures of the human Y1, Y2, and Y4 receptors in complex with NPY or PP, and the Gi1 protein. These structures reveal distinct binding poses of the peptide upon coupling to different receptors, reflecting the importance of the conformational plasticity of the peptide in recognizing the NPY receptors. The N terminus of the peptide forms extensive interactions with the Y1 receptor, but not with the Y2 and Y4 receptors. Supported by mutagenesis and functional studies, subtype-specific interactions between the receptors and peptides were further observed. These findings provide insight into key factors that govern NPY signal recognition and transduction, and would enable development of selective drugs.
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Affiliation(s)
- Tingting Tang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiuxiang Tan
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shuo Han
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Anne Diemar
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Kristin Löbner
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Hongyu Wang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Corinna Schüß
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Victoria Behr
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Karin Mörl
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Mu Wang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaojing Chu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Cuiying Yi
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Max Keller
- Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - Jacob Kofoed
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | | | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | | | - Qiang Zhao
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Beili Wu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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20
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Liolios C, Patsis C, Lambrinidis G, Tzortzini E, Roscher M, Bauder-Wüst U, Kolocouris A, Kopka K. Investigation of Tumor Cells and Receptor-Ligand Simulation Models for the Development of PET Imaging Probes Targeting PSMA and GRPR and a Possible Crosstalk between the Two Receptors. Mol Pharm 2022; 19:2231-2247. [PMID: 35467350 DOI: 10.1021/acs.molpharmaceut.2c00070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Prostate-specific membrane antigen (PSMA) and gastrin-releasing peptide receptor (GRPR) have both been used in nuclear medicine as targets for molecular imaging and therapy of prostate (PCa) and breast cancer (BCa). Three bioconjugate probes, the PSMA specific: [68Ga]Ga-1, ((HBED-CC)-Ahx-Lys-NH-CO-NH Glu or PSMA-11), the GRPR specific: [68Ga]Ga-2, ((HBED-CC)-4-amino-1-carboxymethyl piperidine-[D-Phe6, Sta13]BN(6-14), a bombesin (BN) analogue), and 3 (the BN analogue: 4-amino-1-carboxymethyl piperidine-[(R)-Phe6, Sta13]BN(6-14) connected with the fluorescent dye, BDP-FL), were synthesized and tested in vitro with PCa and BCa cell lines, more specifically, with PCa cells, PC-3 and LNCaP, with BCa cells, T47D, MDA-MB-231, and with the in-house created PSMA-overexpressing PC-3(PSMA), T47D(PSMA), and MDA-MB-231(PSMA). In addition, biomolecular simulations were conducted on the association of 1 and 2 with PSMA and GRPR. The PSMA overexpression resulted in an increase of cell-bound radioligand [68Ga]Ga-1 (PSMA) for PCa and BCa cells and also of [68Ga]Ga-2 (GRPR), especially in those cell lines already expressing GRPR. The results were confirmed by fluorescence-activated cell sorting with a PE-labeled PSMA-specific antibody and the fluorescence tracer 3. The docking calculations and molecular dynamics simulations showed how 1 enters the PSMA funnel region and how pharmacophore Glu-urea-Lys interacts with the arginine patch, the S1', and S1 subpockets by forming hydrogen and van der Waals bonds. The chelating moiety of 1, that is, HBED-CC, forms additional stabilizing hydrogen bonding and van der Waals interactions in the arene-binding site. Ligand 2 is diving into the GRPR transmembrane (TM) helical cavity, thereby forming hydrogen bonds through its amidated end, water-mediated hydrogen bonds, and π-π interactions. Our results provide valuable information regarding the molecular mechanisms involved in the interactions of 1 and 2 with PSMA and GRPR, which might be useful for the diagnostic imaging and therapy of PCa and BCa.
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Affiliation(s)
- Christos Liolios
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Radiochemical Studies Laboratory, INRASTES, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece.,Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Christos Patsis
- Division of Cell Plasticity and Epigenetic Remodelling, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Translational Oncology, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Mareike Roscher
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ulrike Bauder-Wüst
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Klaus Kopka
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, 01328 Dresden, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, Technical University Dresden, Lebensmittelchemie Chemiegebäude, Raum 413 Bergstr. 66, 01069 Dresden, Germany
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21
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Development of Neuropeptide Y and Cell-Penetrating Peptide MAP Adsorbed onto Lipid Nanoparticle Surface. Molecules 2022; 27:molecules27092734. [PMID: 35566093 PMCID: PMC9101637 DOI: 10.3390/molecules27092734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022] Open
Abstract
Functionalization of nanoparticles surfaces have been widely used to improve diagnostic and therapeutic biological outcome. Several methods can be applied to modify nanoparticle surface; however, in this article we focus toward a simple and less time-consuming method. We applied an adsorption method on already formulated nanostructured lipid carriers (NLC) to functionalize these nanoparticles with three distinct peptides sequences. We selected a cell-penetrating peptide (CPP), a lysine modified model amphipathic peptide (Lys(N3)-MAP), CPP/drug complex, and the neuropeptide Y. The aim of this work is to evaluate the effect of several parameters such as peptide concentration, different types of NLC, different types of peptides, and incubation medium on the physicochemical proprieties of NLC and determine if adsorption occurs. The preliminary results from zeta potential analysis indicate some evidence that this method was successful in adsorbing three types of peptides onto NLC. Several non-covalent interactions appear to be involved in peptide adsorption with the possibility of three adsorption peptide hypothesis that may occur with NLC in solution. Moreover, and for the first time, in silico docking analysis demonstrated strong interaction between CPP MAP and NPY Y1 receptor with high score values when compared to standard antagonist and NPY.
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22
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Langley DB, Schofield P, Jackson J, Herzog H, Christ D. Crystal structures of human neuropeptide Y (NPY) and peptide YY (PYY). Neuropeptides 2022; 92:102231. [PMID: 35180645 DOI: 10.1016/j.npep.2022.102231] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
Neuropeptide Y (NPY), peptide YY (PYY) and pancreatic polypeptide (PP) form the evolutionarily conserved pancreatic polypeptide family. While the fold is widely utilized in nature, crystal structures remain elusive, particularly for the human forms, with only the structure of a distant avian form of PP reported. Here we utilize a crystallization chaperone (antibody Fab fragment), specifically recognizing the amidated peptide termini, to solve the structures of human NPY and human PYY. Intriguingly, and despite limited sequence identity (~50%), the structure of human PYY closely resembles that of avian PP, highlighting the broad structural conservation of the fold throughout evolution. Specifically, the PYY structure is characterized by a C-terminal amidated α-helix, preceded by a backfolded poly-proline N-terminus, with the termini in close proximity to each other. In contrast, in the structure of human NPY the N-terminal component is disordered, while the helical component of the peptide is observed in a four-helix bundle type arrangement, consistent with a propensity for multimerization suggested by NMR studies.
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Affiliation(s)
- David B Langley
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Jenny Jackson
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Herbert Herzog
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia.
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23
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Müller C, Gleixner J, Tahk MJ, Kopanchuk S, Laasfeld T, Weinhart M, Schollmeyer D, Betschart MU, Lüdeke S, Koch P, Rinken A, Keller M. Structure-Based Design of High-Affinity Fluorescent Probes for the Neuropeptide Y Y 1 Receptor. J Med Chem 2022; 65:4832-4853. [PMID: 35263541 DOI: 10.1021/acs.jmedchem.1c02033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The recent crystallization of the neuropeptide Y Y1 receptor (Y1R) in complex with the argininamide-type Y1R selective antagonist UR-MK299 (2) opened up a new approach toward structure-based design of nonpeptidic Y1R ligands. We designed novel fluorescent probes showing excellent Y1R selectivity and, in contrast to previously described fluorescent Y1R ligands, considerably higher (∼100-fold) binding affinity. This was achieved through the attachment of different fluorescent dyes to the diphenylacetyl moiety in 2 via an amine-functionalized linker. The fluorescent ligands exhibited picomolar Y1R binding affinities (pKi values of 9.36-9.95) and proved to be Y1R antagonists, as validated in a Fura-2 calcium assay. The versatile applicability of the probes as tool compounds was demonstrated by flow cytometry- and fluorescence anisotropy-based Y1R binding studies (saturation and competition binding and association and dissociation kinetics) as well as by widefield and total internal reflection fluorescence (TIRF) microscopy of live tumor cells, revealing that fluorescence was mainly localized at the plasma membrane.
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Affiliation(s)
- Christoph Müller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Maris-Johanna Tahk
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Sergei Kopanchuk
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Tõnis Laasfeld
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Michael Weinhart
- Institute of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Dieter Schollmeyer
- Department of Chemistry, Johannes-Gutenberg-University Mainz, Düsbergweg 10-14, 55099 Mainz, Germany
| | - Martin U Betschart
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Pierre Koch
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Ago Rinken
- Institute of Chemistry, Faculty of Bioorganic Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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24
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Structural basis of neuropeptide Y signaling through Y1 receptor. Nat Commun 2022; 13:853. [PMID: 35165283 PMCID: PMC8844075 DOI: 10.1038/s41467-022-28510-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/26/2022] [Indexed: 01/07/2023] Open
Abstract
AbstractNeuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, the molecular details of the interactions between NPY and its receptors are poorly understood. Here, we report a cryo-electron microscopy structure of the NPY-bound neuropeptide Y1 receptor (Y1R) in complex with Gi1 protein. The NPY C-terminal segment forming the extended conformation binds deep into the Y1R transmembrane core, where the amidated C-terminal residue Y36 of NPY is located at the base of the ligand-binding pocket. Furthermore, the helical region and two N-terminal residues of NPY interact with Y1R extracellular loops, contributing to the high affinity of NPY for Y1R. The structural analysis of NPY-bound Y1R and mutagenesis studies provide molecular insights into the activation mechanism of Y1R upon NPY binding.
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25
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Chandler B, Todd L, Smith SO. Magic angle spinning NMR of G protein-coupled receptors. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:25-43. [PMID: 35282868 PMCID: PMC10718405 DOI: 10.1016/j.pnmrs.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) have a simple seven transmembrane helix architecture which has evolved to recognize a diverse number of chemical signals. The more than 800 GPCRs encoded in the human genome function as receptors for vision, smell and taste, and mediate key physiological processes. Consequently, these receptors are a major target for pharmaceuticals. Protein crystallography and electron cryo-microscopy have provided high resolution structures of many GPCRs in both active and inactive conformations. However, these structures have not sparked a surge in rational drug design, in part because GPCRs are inherently dynamic and the structural changes induced by ligand or drug binding to stabilize inactive or active conformations are often subtle rearrangements in packing or hydrogen-bonding interactions. NMR spectroscopy provides a sensitive probe of local structure and dynamics at specific sites within these receptors as well as global changes in receptor structure and dynamics. These methods can also capture intermediate states and conformations with low populations that provide insights into the activation pathways. We review the use of solid-state magic angle spinning NMR to address the structure and activation mechanisms of GPCRs. The focus is on the large and diverse class A family of receptors. We highlight three specific class A GPCRs in order to illustrate how solid-state, as well as solution-state, NMR spectroscopy can answer questions in the field involving how different GPCR classes and subfamilies are activated by their associated ligands, and how small molecule drugs can modulate GPCR activation.
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Affiliation(s)
- Bianca Chandler
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Lauren Todd
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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26
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Rudolf S, Kaempf K, Vu O, Meiler J, Beck‐Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y
5
Receptor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarina Rudolf
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
| | - Kerstin Kaempf
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
| | - Oanh Vu
- Chemistry Department Vanderbilt University Nashville TN 37212 USA
| | - Jens Meiler
- Chemistry Department Vanderbilt University Nashville TN 37212 USA
- Center for Structural Biology Department of Biological Sciences Vanderbilt University Nashville TN 37212 USA
- Institute of Drug Design Faculty of Medicine Leipzig University 04103 Leipzig Germany
| | | | - Irene Coin
- Institute of Biochemistry Faculty of Life Science Leipzig University 04103 Leipzig Germany
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27
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Rudolf S, Kaempf K, Vu O, Meiler J, Beck-Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y 5 Receptor. Angew Chem Int Ed Engl 2022; 61:e202108738. [PMID: 34822209 PMCID: PMC8766924 DOI: 10.1002/anie.202108738] [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: 07/19/2021] [Indexed: 01/28/2023]
Abstract
The binding mode of natural peptide ligands to the Y5 G protein-coupled receptor (Y5 R), an attractive therapeutic target for the treatment of obesity, is largely unknown. Here, we apply complementary biochemical and computational approaches, including scanning of the receptor surface with a genetically encoded crosslinker, Ala-scanning of the ligand and double-cycle mutagenesis, to map interactions in the ligand-receptor interface and build a structural model of the NPY-Y5 R complex guided by the experimental data. In the model, the carboxyl (C)-terminus of bound NPY is placed close to the extracellular loop (ECL) 3, whereas the characteristic α-helical segment of the ligand drapes over ECL1 and is tethered towards ECL2 by a hydrophobic cluster. We further show that the other two natural ligands of Y5 R, peptide YY (PYY) and pancreatic polypeptide (PP) dock to the receptor in a similar pose.
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Affiliation(s)
- Sarina Rudolf
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
| | - Kerstin Kaempf
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
| | - Oanh Vu
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
| | - Jens Meiler
- Chemistry Department, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
- Center for Structural Biology, Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37212, U.S.A
- Institute of Drug Design, Faculty of Medicine, Leipzig University, Leipzig 04103, Germany
| | | | - Irene Coin
- Institute of Biochemistry, Faculty of Life Science, Leipzig University, Leipzig 04103, Germany
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28
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Fischer TF, Beck-Sickinger AG. Chemerin - exploring a versatile adipokine. Biol Chem 2022; 403:625-642. [PMID: 35040613 DOI: 10.1515/hsz-2021-0409] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
Chemerin is a small chemotactic protein and a key player in initiating the early immune response. As an adipokine, chemerin is also involved in energy homeostasis and the regulation of reproductive functions. Secreted as inactive prochemerin, it relies on proteolytic activation by serine proteases to exert biological activity. Chemerin binds to three distinct G protein-coupled receptors (GPCR), namely chemokine-like receptor 1 (CMKLR1, recently named chemerin1), G protein-coupled receptor 1 (GPR1, recently named chemerin2), and CC-motif chemokine receptor-like 2 (CCRL2). Only CMKLR1 displays conventional G protein signaling, while GPR1 only recruits arrestin in response to ligand stimulation, and no CCRL2-mediated signaling events have been described to date. However, GPR1 undergoes constitutive endocytosis, making this receptor perfectly adapted as decoy receptor. Here, we discuss expression pattern, activation, and receptor binding of chemerin. Moreover, we review the current literature regarding the involvement of chemerin in cancer and several obesity-related diseases, as well as recent developments in therapeutic targeting of the chemerin system.
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Affiliation(s)
- Tobias F Fischer
- Institute of Biochemistry, University of Leipzig, Brüderstraße 34, D-04103 Leipzig, Germany
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29
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Sharma A, Ren X, Zhang H, Pandey GN. Effect of depression and suicidal behavior on neuropeptide Y (NPY) and its receptors in the adult human brain: A postmortem study. Prog Neuropsychopharmacol Biol Psychiatry 2022; 112:110428. [PMID: 34411658 PMCID: PMC8489679 DOI: 10.1016/j.pnpbp.2021.110428] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 01/12/2023]
Abstract
Neuropeptides are small proteinaceous molecules (3-100 amino acids) that are secreted by neurons and act on both neuronal and non-neuronal cells. Neuropeptide Y (NPY), a highly conserved and expressed neuropeptide in the central nervous system of mammals, plays a major role in stress response and resilience. Increasing evidence suggests that NPY and its receptors are altered in depression and suicide, pointing to their antidepressant-like nature. The objective of this study was to examine the role of NPY system in depression and suicidal behavior. Expression of NPY and its four receptors, NPY1R, NPY2R, NPY4R, and NPY5R was studied at the transcriptional and translational levels in the prefrontal cortex (PFC) and hippocampus regions of the postmortem brain of normal control (NC) (n = 24) and depressed suicide (DS) (n = 24) subjects. We observed a significant decrease in NPY mRNA and upregulation in NPY1R and NPY2R mRNA in both brain regions of DS subjects compared with NC subjects. We also observed a significant decrease in NPY protein expression in the PFC of subjects with DS. This study provides the first detailed evidence of alterations in the NPY system and the associated stress response in depression and suicidal behavior in humans. The outcomes of this study could be applied in the development of novel NPY system-targeted approaches for the treatment of depression.
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Affiliation(s)
| | | | | | - Ghanshyam N. Pandey
- Corresponding Author: Ghanshyam N. Pandey, Ph.D., University of Illinois at Chicago, 1601 West Taylor Street, Chicago, IL 60612, USA, Phone (312) 413-4540, Fax: (312) 413-4547,
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30
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Chen QC, Zhang Y. The Role of NPY in the Regulation of Bone Metabolism. Front Endocrinol (Lausanne) 2022; 13:833485. [PMID: 35273572 PMCID: PMC8902412 DOI: 10.3389/fendo.2022.833485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Bone diseases are the leading causes of disability and severely compromised quality of life. Neuropeptide Y (NPY) is a multifunctional neuropeptide that participates in various physiological and pathological processes and exists in both the nerve system and bone tissue. In bone tissue, it actively participates in bone metabolism and disease progression through its receptors. Previous studies have focused on the opposite effects of NPY on bone formation and resorption through paracrine modes. In this review, we present a brief overview of the progress made in this research field in recent times in order to provide reference for further understanding the regulatory mechanism of bone physiology and pathological metabolism.
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Affiliation(s)
- Qing-Chang Chen
- Department of Ultrasound Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Yan Zhang
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yan Zhang,
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31
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Vu O, Bender BJ, Pankewitz L, Huster D, Beck-Sickinger AG, Meiler J. The Structural Basis of Peptide Binding at Class A G Protein-Coupled Receptors. Molecules 2021; 27:molecules27010210. [PMID: 35011444 PMCID: PMC8746363 DOI: 10.3390/molecules27010210] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/16/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest membrane protein family and a significant target class for therapeutics. Receptors from GPCRs’ largest class, class A, influence virtually every aspect of human physiology. About 45% of the members of this family endogenously bind flexible peptides or peptides segments within larger protein ligands. While many of these peptides have been structurally characterized in their solution state, the few studies of peptides in their receptor-bound state suggest that these peptides interact with a shared set of residues and undergo significant conformational changes. For the purpose of understanding binding dynamics and the development of peptidomimetic drug compounds, further studies should investigate the peptide ligands that are complexed to their cognate receptor.
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Affiliation(s)
- Oanh Vu
- Deparment of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
| | - Brian Joseph Bender
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Lisa Pankewitz
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Medical Department, Leipzig University, Härtelstr. 16–18, D-04107 Leipzig, Germany;
| | - Annette G. Beck-Sickinger
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany;
| | - Jens Meiler
- Deparment of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; (B.J.B.); (L.P.)
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Leipzig University Medical Center, Institute for Drug Discovery, Departments of Chemistry and Computer Science, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
- Correspondence:
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32
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Xue K, Movellan KT, Zhang XC, Najbauer EE, Forster MC, Becker S, Andreas LB. Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR. Chem Sci 2021; 12:14332-14342. [PMID: 34880983 PMCID: PMC8580007 DOI: 10.1039/d1sc02813h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins. ssNMR can probe both the structure and dynamics of membrane proteins, revealing protein function in a near-native lipid bilayer environment. The main limitation of the method is spectral resolution and sensitivity, however recent developments in ssNMR hardware, including the commercialization of 28 T magnets (1.2 GHz proton frequency) and ultrafast MAS spinning (<100 kHz) promise to accelerate acquisition, while reducing sample requirement, both of which are critical to membrane protein studies. Here, we review recent advances in ssNMR methodology used for structure determination of membrane proteins in native and mimetic environments, as well as the study of protein functions such as protein dynamics, and interactions with ligands, lipids and cholesterol.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Kumar Tekwani Movellan
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Xizhou Cecily Zhang
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Eszter E Najbauer
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Marcel C Forster
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
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NPF activates a specific NPF receptor and regulates food intake in Pacific abalone Haliotis discus hannai. Sci Rep 2021; 11:20912. [PMID: 34686694 PMCID: PMC8536682 DOI: 10.1038/s41598-021-00238-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/07/2021] [Indexed: 01/13/2023] Open
Abstract
Neuropeptides function through G protein-coupled receptors (GPCRs) with high specificity, implying a significant degree of neuropeptide-GPCR coevolution. However, potential neuropeptide signaling systems in non-chordates are relatively elusive. We determined the specificity of the neuropeptide F (Hdh-NPF) signaling system with a cognate receptor (Hdh-NPFR) in the Pacific abalone, Haliotis discus hannai. Phylogenetic and exon–intron arrangement analyses of bilaterian NPF and the chordate ortholog NPY with their receptor sequences revealed a likely common ancestor, and Hdh-NPFR was similar to the NPYR2 subtype among the NPYR1, NPYR2, and NPYR5 subtypes. Among four Hdh-NPFR-related receptors, Hdh-NPFR specifically responded to Hdh-NPF peptide, supported by the dose–response luciferase reporter curve, intracellular Ca2+ mobilization, and phosphorylation of ERK1/2 and its inhibition with a protein kinase C inhibitor. Peptide fragmentations and shuffling of Hdh-NPF with human NPY could not activate the cellular response of Hdh-NPFR. Three-dimensional in silico modeling suggested that interaction of Hdh-NPF C-terminal amino acids with the extracellular loops of Hdh-NPFR is critical for Hdh-NPFR activation. In vivo injection of Hdh-NPF peptide increased food consumption, and knockdown of Hdh-NPF expression decreased food consumption in Pacific abalone. These findings provide evidence for co-evolution of the NPF/Y ligand-receptor system, enabling further research on mollusk orexigenic neuropeptides.
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De La Cruz DL, Prokai L, Prokai-Tatrai K. The Antagonist pGlu-βGlu-Pro-NH 2 Binds to an Allosteric Site of the Thyrotropin-Releasing Hormone Receptor. Molecules 2021; 26:5397. [PMID: 34500828 PMCID: PMC8433856 DOI: 10.3390/molecules26175397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
After we identified pGlu-βGlu-Pro-NH2 as the first functional antagonist of the cholinergic central actions of the thyrotropin-releasing hormone (TRH, pGlu-His-Pro-NH2), we became interested in finding the receptor-associated mechanism responsible for this antagonism. By utilizing a human TRH receptor (hTRH-R) homology model, we first refined the active binding site within the transmembrane bundle of this receptor to enhance TRH's binding affinity. However, this binding site did not accommodate the TRH antagonist. This directed us to consider a potential allosteric binding site in the extracellular domain (ECD). Searches for ECD binding pockets prompted the remodeling of the extracellular loops and the N-terminus. We found that different trajectories of ECDs produced novel binding cavities that were then systematically probed with TRH, as well as its antagonist. This led us to establish not only a surface-recognition binding site for TRH, but also an allosteric site that exhibited a selective and high-affinity binding for pGlu-βGlu-Pro-NH2. The allosteric binding of this TRH antagonist is more robust than TRH's binding to its own active site. The findings reported here may shed light on the mechanisms and the multimodal roles by which the ECD of a TRH receptor is involved in agonist and/or antagonist actions.
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Affiliation(s)
| | | | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (D.L.D.L.C.); (L.P.)
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Choong YS, Lim YY, Soong JX, Savoo N, Guida C, Rhyman L, Ramracheya R, Ramasami P. Theoretical study of the interactions between peptide tyrosine tyrosine [PYY (1-36)], a newly identified modulator in type 2 diabetes pathophysiology, with receptors NPY1R and NPY4R. Hormones (Athens) 2021; 20:557-569. [PMID: 33782920 DOI: 10.1007/s42000-021-00278-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/10/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE Diabetes mellitus is a common condition in the clinically obese. Bariatric surgery is one of the ways to put type 2 diabetes in remission. Recent findings propose the appetite-regulator peptide tyrosine tyrosine (PYY) as a therapeutic option for patients with type 2 diabetes. This novel gut hormone restores impaired insulin and glucagon secretion in pancreatic islets and is implicated in type 2 diabetes reversal after bariatric surgery. The current study elucidates the interactions between PYY and the NPY1R and NPY4R receptors using computational methods. METHODS Protein structure prediction, molecular docking simulation, and molecular dynamics (MD) simulation were performed to elucidate the interactions of PYY with NPY1R and NPY4R. RESULTS The predicted binding models of PYY-NPY receptors are in agreement with those described in the literature, although different interaction partners are presented for the C-terminal tail of PYY. Non-polar interactions are predicted to drive the formation of the protein complex. The calculated binding energies show that PYY has higher affinity for NPY4R (ΔGGBSA = -65.08 and ΔGPBSA = -87.62 kcal/mol) than for NPY1R (ΔGGBSA = -23.11 and ΔGPBSA = -50.56 kcal/mol). CONCLUSIONS Based on the constructed models, the binding conformations obtained from docking and MD simulation for both the PYY-NPY1R and PYY-NPY4R complexes provide a detailed map of possible interactions. The calculated binding energies show a higher affinity of PYY for NPY4R. These findings may help to understand the mechanisms behind the improvement of diabetes following bariatric surgery.
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Affiliation(s)
- Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Jia Xin Soong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Nandini Savoo
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Claudia Guida
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, OX3 7LJ, United Kingdom
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa
| | - Reshma Ramracheya
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, OX3 7LJ, United Kingdom.
- Pharmaceutical Operations, Centre International de Dévelopment Pharmaceutique, BioPark Mauritius, Socota Phoenicia, Phoenix 73408, Mauritius.
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius.
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa.
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36
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Lv X, Gao F, Li TP, Xue P, Wang X, Wan M, Hu B, Chen H, Jain A, Shao Z, Cao X. Skeleton interoception regulates bone and fat metabolism through hypothalamic neuroendocrine NPY. eLife 2021; 10:e70324. [PMID: 34468315 PMCID: PMC8439655 DOI: 10.7554/elife.70324] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 01/04/2023] Open
Abstract
The central nervous system regulates activity of peripheral organs through interoception. In our previous study, we have demonstrated that PGE2/EP4 skeleton interception regulate bone homeostasis. Here, we show that ascending skeleton interoceptive signaling downregulates expression of hypothalamic neuropeptide Y (NPY) and induce lipolysis of adipose tissue for osteoblastic bone formation. Specifically, the ascending skeleton interoceptive signaling induces expression of small heterodimer partner-interacting leucine zipper protein (SMILE) in the hypothalamus. SMILE binds to pCREB as a transcriptional heterodimer on Npy promoters to inhibit NPY expression. Knockout of EP4 in sensory nerve increases expression of NPY causing bone catabolism and fat anabolism. Importantly, inhibition of NPY Y1 receptor (Y1R) accelerated oxidation of free fatty acids in osteoblasts and rescued bone loss in AvilCre:Ptger4fl/fl mice. Thus, downregulation of hypothalamic NPY expression lipolyzes free fatty acids for anabolic bone formation through a neuroendocrine descending interoceptive regulation.
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Affiliation(s)
- Xiao Lv
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Feng Gao
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Tuo Peter Li
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Peng Xue
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Xiao Wang
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Mei Wan
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Bo Hu
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Hao Chen
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Amit Jain
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
| | - Zengwu Shao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Xu Cao
- Department of Orthopaedic Surgery, Institute of Cell Engineering, and Department of Biomedical Engineering, The Johns Hopkins UniversityBaltimoreUnited States
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37
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Tsutsumi N, Qu Q, Mavri M, Baggesen MS, Maeda S, Waghray D, Berg C, Kobilka BK, Rosenkilde MM, Skiniotis G, Garcia KC. Structural basis for the constitutive activity and immunomodulatory properties of the Epstein-Barr virus-encoded G protein-coupled receptor BILF1. Immunity 2021; 54:1405-1416.e7. [PMID: 34216564 DOI: 10.1016/j.immuni.2021.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/21/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022]
Abstract
Epstein-Barr virus (EBV) encodes a G protein-coupled receptor (GPCR) termed BILF1 that is essential for EBV-mediated immunosuppression and oncogenesis. BILF1 couples with inhibitory G protein (Gi), the major intracellular signaling effector for human chemokine receptors, and exhibits constitutive signaling activity; the ligand(s) for BILF1 are unknown. We studied the origins of BILF1's constitutive activity through structure determination of BILF1 bound to the inhibitory G protein (Gi) heterotrimer. The 3.2-Å resolution cryo-electron microscopy structure revealed an extracellular loop within BILF1 that blocked the typical chemokine binding site, suggesting ligand-autonomous receptor activation. Rather, amino acid substitutions within BILF1 transmembrane regions at hallmark ligand-activated class A GPCR "microswitches" stabilized a constitutively active BILF1 conformation for Gi coupling in a ligand-independent fashion. Thus, the constitutive activity of BILF1 promotes immunosuppression and virulence independent of ligand availability, with implications for the function of GPCRs encoded by related viruses and for therapeutic targeting of EBV.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maša Mavri
- Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maibritt S Baggesen
- Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian Berg
- Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mette M Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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38
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Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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39
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Montégut L, Lopez-Otin C, Magnan C, Kroemer G. Old Paradoxes and New Opportunities for Appetite Control in Obesity. Trends Endocrinol Metab 2021; 32:264-294. [PMID: 33707095 DOI: 10.1016/j.tem.2021.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
Human obesity is accompanied by alterations in the blood concentrations of multiple circulating appetite regulators. Paradoxically, most of the appetite-inhibitory hormones are elevated in nonsyndromic obesity, while most of the appetite stimulatory hormones are reduced, perhaps reflecting vain attempts of regulation by inefficient feedback circuitries. In this context, it is important to understand which appetite regulators exhibit a convergent rather than paradoxical behavior and hence are likely to contribute to the maintenance of the obese state. Pharmacological interventions in obesity should preferentially consist of the supplementation of deficient appetite inhibitors or the neutralization of excessive appetite stimulators. Here, we critically analyze the current literature on appetite-regulatory peptide hormones. We propose a short-list of appetite modulators that may constitute the best candidates for therapeutic interventions.
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Affiliation(s)
- Léa Montégut
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | | | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France; Unité de Biologie Fonctionnelle et Adaptative, Sorbonne Paris Cité, CNRS UMR8251, Université Paris Diderot, Paris, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-, HP, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
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40
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Künze G, Huster D, Samsonov SA. Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship. Biol Chem 2021; 402:1337-1355. [PMID: 33882203 DOI: 10.1515/hsz-2021-0119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/09/2021] [Indexed: 11/15/2022]
Abstract
The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.
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Affiliation(s)
- Georg Künze
- Center for Structural Biology, Vanderbilt University, 465 21st Ave S, 5140 MRB3, Nashville, TN37240, USA.,Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN37235, USA.,Institute for Drug Discovery, University of Leipzig, Brüderstr. 34, D-04103Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107Leipzig, Germany
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308Gdańsk, Poland
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41
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Gershkovich MM, Groß VE, Vu O, Schoeder CT, Meiler J, Prömel S, Kaiser A. Structural Perspective on Ancient Neuropeptide Y-like System reveals Hallmark Features for Peptide Recognition and Receptor Activation. J Mol Biol 2021; 433:166992. [PMID: 33865871 PMCID: PMC8380825 DOI: 10.1016/j.jmb.2021.166992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 11/30/2022]
Abstract
The neuropeptide Y (NPY) family is a peptide-activated G protein-coupled receptor system conserved across all bilaterians, and is involved in food intake, learning, and behavior. We hypothesized that comparing the NPY system in evolutionarily ancient organisms can reveal structural determinants of peptide recognition and receptor activation conserved in evolution. To test this hypothesis, we investigated the homologous FLP/NPR system of the protostome C.elegans. For three prototypic peptide-receptor complexes representing different ligand types, we integrate extensive functional data into structural models of the receptors. Common features include acidic patches in the extracellular loops (ECLs) of the receptors that cooperatively 'draw' the peptide into the binding pocket, which was functionally validated in vivo. A structurally conserved glutamate in the ECL2 anchors the peptides by a conserved salt bridge to the arginine of the RFamide motif. Beyond this conserved interaction, peptide binding show variability enabled by receptor-specific interactions. The family-conserved residue Q3.32 is a key player for peptide binding and receptor activation. Altered interaction patterns at Q3.32 may drastically increase the efficacy to activate the receptor.
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Affiliation(s)
- Miron Mikhailowitsch Gershkovich
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany; Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA
| | - Victoria Elisabeth Groß
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Oanh Vu
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA
| | - Clara Tabea Schoeder
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA; Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, 465 21st Ave South, BIOSCI/MRBIII, Nashville, TN 37235, USA; Institute for Drug Discovery, Medical Faculty, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Simone Prömel
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany.
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42
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Albanese V, Ruzza C, Marzola E, Bernardi T, Fabbri M, Fantinati A, Trapella C, Reinscheid RK, Ferrari F, Sturaro C, Calò G, Amendola G, Cosconati S, Pacifico S, Guerrini R, Preti D. Structure-Activity Relationship Studies on Oxazolo[3,4- a]pyrazine Derivatives Leading to the Discovery of a Novel Neuropeptide S Receptor Antagonist with Potent In Vivo Activity. J Med Chem 2021; 64:4089-4108. [PMID: 33733768 PMCID: PMC8041306 DOI: 10.1021/acs.jmedchem.0c02223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neuropeptide S modulates important neurobiological functions including locomotion, anxiety, and drug abuse through interaction with its G protein-coupled receptor known as neuropeptide S receptor (NPSR). NPSR antagonists are potentially useful for the treatment of substance abuse disorders against which there is an urgent need for new effective therapeutic approaches. Potent NPSR antagonists in vitro have been discovered which, however, require further optimization of their in vivo pharmacological profile. This work describes a new series of NPSR antagonists of the oxazolo[3,4-a]pyrazine class. The guanidine derivative 16 exhibited nanomolar activity in vitro and 5-fold improved potency in vivo compared to SHA-68, a reference pharmacological tool in this field. Compound 16 can be considered a new tool for research studies on the translational potential of the NPSergic system. An in-depth molecular modeling investigation was also performed to gain new insights into the observed structure-activity relationships and provide an updated model of ligand/NPSR interactions.
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Affiliation(s)
- Valentina Albanese
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Chiara Ruzza
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Erika Marzola
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Tatiana Bernardi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Martina Fabbri
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Anna Fantinati
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Claudio Trapella
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Rainer K Reinscheid
- Institute of Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
- Institute of Physiology I, University Hospital Münster, University of Münster, 48149 Münster, Germany
| | - Federica Ferrari
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
| | - Chiara Sturaro
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
| | - Girolamo Calò
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti, 2, 35131 Padova, Italy
| | - Giorgio Amendola
- "DiSTABiF", Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Sandro Cosconati
- "DiSTABiF", Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Salvatore Pacifico
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Delia Preti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
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43
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Fischer TF, Schoeder CT, Zellmann T, Stichel J, Meiler J, Beck-Sickinger AG. Cyclic Analogues of the Chemerin C-Terminus Mimic a Loop Conformation Essential for Activating the Chemokine-like Receptor 1. J Med Chem 2021; 64:3048-3058. [PMID: 33705662 DOI: 10.1021/acs.jmedchem.0c01804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chemokine-like receptor 1 (CMKLR1) is a promising target for treating autoinflammatory diseases, cancer, and reproductive disorders. However, the interaction between CMKLR1 and its protein-ligand chemerin remains uncharacterized, and no drugs targeting this interaction have passed clinical trials. Here, we identify the binding mode of chemerin-9, the C-terminus of chemerin, at the receptor by combining complementary mutagenesis with structure-based modeling. Incorporating our experimental data, we present a detailed model of this binding site, including experimentally confirmed pairwise interactions for the most critical ligand residues: Chemerin-9 residue F8 binds to a hydrophobic pocket in CMKLR1 formed by the extracellular loop (ECL) 2, while F6 interacts with Y2.68, suggesting a turn-like structure. On the basis of this model, we created the first cyclic peptide with nanomolar activity, confirming the overall binding conformation. This constrained agonist mimics the loop conformation adopted by the natural ligand and can serve as a lead compound for future drug design.
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Affiliation(s)
- Tobias F Fischer
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Clara T Schoeder
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee37212, United States
| | - Tristan Zellmann
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee37212, United States.,Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany
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44
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Schüß C, Vu O, Schubert M, Du Y, Mishra NM, Tough IR, Stichel J, Weaver CD, Emmitte KA, Cox HM, Meiler J, Beck-Sickinger AG. Highly Selective Y 4 Receptor Antagonist Binds in an Allosteric Binding Pocket. J Med Chem 2021; 64:2801-2814. [PMID: 33595306 DOI: 10.1021/acs.jmedchem.0c02000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human neuropeptide Y receptors (Y1R, Y2R, Y4R, and Y5R) belong to the superfamily of G protein-coupled receptors and play an important role in the regulation of food intake and energy metabolism. We identified and characterized the first selective Y4R allosteric antagonist (S)-VU0637120, an important step toward validating Y receptors as therapeutic targets for metabolic diseases. To obtain insight into the antagonistic mechanism of (S)-VU0637120, we conducted a variety of in vitro, ex vivo, and in silico studies. These studies revealed that (S)-VU0637120 selectively inhibits native Y4R function and binds in an allosteric site located below the binding pocket of the endogenous ligand pancreatic polypeptide in the core of the Y4R transmembrane domains. Taken together, our studies provide a first-of-its-kind tool for probing Y4R function and improve the general understanding of allosteric modulation, ultimately contributing to the rational development of allosteric modulators for peptide-activated G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Corinna Schüß
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - Oanh Vu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mario Schubert
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - Yu Du
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Nigam M Mishra
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Iain R Tough
- King's College London, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, London SE1 1UL, U.K
| | - Jan Stichel
- Institute of Biochemistry, Leipzig University, Leipzig 04103, Germany
| | - C David Weaver
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kyle A Emmitte
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Helen M Cox
- King's College London, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, London SE1 1UL, U.K
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Institute for Drug Discovery, Leipzig University, Leipzig 04103, Germany
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45
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Zheng YL, Wang WD, Li MM, Lin S, Lin HL. Updated Role of Neuropeptide Y in Nicotine-Induced Endothelial Dysfunction and Atherosclerosis. Front Cardiovasc Med 2021; 8:630968. [PMID: 33708805 PMCID: PMC7940677 DOI: 10.3389/fcvm.2021.630968] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease is the leading cause of death worldwide. Endothelial dysfunction of the arterial vasculature plays a pivotal role in cardiovascular pathogenesis. Nicotine-induced endothelial dysfunction substantially contributes to the development of arteriosclerotic cardiovascular disease. Nicotine promotes oxidative inflammation, thrombosis, pathological angiogenesis, and vasoconstriction, and induces insulin resistance. However, the exact mechanism through which nicotine induces endothelial dysfunction remains unclear. Neuropeptide Y (NPY) is widely distributed in the central nervous system and peripheral tissues, and it participates in the pathogenesis of atherosclerosis by regulating vasoconstriction, energy metabolism, local plaque inflammatory response, activation and aggregation of platelets, and stress and anxiety-related emotion. Nicotine can increase the expression of NPY, suggesting that NPY is involved in nicotine-induced endothelial dysfunction. Herein, we present an updated review of the possible mechanisms of nicotine-induced atherosclerosis, with a focus on endothelial cell dysfunction associated with nicotine and NPY.
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Affiliation(s)
- Yan-Li Zheng
- Department of Cardiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Wan-da Wang
- Department of Cardiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Mei-Mei Li
- Department of Cardiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Shu Lin
- Department of Cardiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.,Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.,Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Hui-Li Lin
- Department of Cardiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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46
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Structural basis for ligand recognition of the neuropeptide Y Y 2 receptor. Nat Commun 2021; 12:737. [PMID: 33531491 PMCID: PMC7854658 DOI: 10.1038/s41467-021-21030-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/08/2021] [Indexed: 12/02/2022] Open
Abstract
The human neuropeptide Y (NPY) Y2 receptor (Y2R) plays essential roles in food intake, bone formation and mood regulation, and has been considered an important drug target for obesity and anxiety. However, development of drugs targeting Y2R remains challenging with no success in clinical application yet. Here, we report the crystal structure of Y2R bound to a selective antagonist JNJ-31020028 at 2.8 Å resolution. The structure reveals molecular details of the ligand-binding mode of Y2R. Combined with mutagenesis studies, the Y2R structure provides insights into key factors that define antagonistic activity of diverse antagonists. Comparison with the previously determined antagonist-bound Y1R structures identified receptor-ligand interactions that play different roles in modulating receptor activation and mediating ligand selectivity. These findings deepen our understanding about molecular mechanisms of ligand recognition and subtype specificity of NPY receptors, and would enable structure-based drug design. The human neuropeptide Y receptor Y2 (Y2R) is a drug target for the treatment of obesity and anxiety. Crystal structure of Y2R bound to a selective antagonist and accompanying mutagenesis provide insights into ligand recognition and subtype specificity of NPY receptors.
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47
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Cattaneo S, Verlengia G, Marino P, Simonato M, Bettegazzi B. NPY and Gene Therapy for Epilepsy: How, When,... and Y. Front Mol Neurosci 2021; 13:608001. [PMID: 33551745 PMCID: PMC7862707 DOI: 10.3389/fnmol.2020.608001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Neuropeptide Y (NPY) is a neuropeptide abundantly expressed in the mammalian central and peripheral nervous system. NPY is a pleiotropic molecule, which influences cell proliferation, cardiovascular and metabolic function, pain and neuronal excitability. In the central nervous system, NPY acts as a neuromodulator, affecting pathways that range from cellular (excitability, neurogenesis) to circuit level (food intake, stress response, pain perception). NPY has a broad repertoire of receptor subtypes, each activating specific signaling pathways in different tissues and cellular sub-regions. In the context of epilepsy, NPY is thought to act as an endogenous anticonvulsant that performs its action through Y2 and Y5 receptors. In fact, its overexpression in the brain with the aid of viral vectors can suppress seizures in animal models of epilepsy. Therefore, NPY-based gene therapy may represent a novel approach for the treatment of epilepsy patients, particularly for pharmaco-resistant and genetic forms of the disease. Nonetheless, considering all the aforementioned aspects of NPY signaling, the study of possible NPY applications as a therapeutic molecule is not devoid of critical aspects. The present review will summarize data related to NPY biology, focusing on its anti-epileptic effects, with a critical appraisal of key elements that could be exploited to improve the already existing NPY-based gene therapy approaches for epilepsy.
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Affiliation(s)
- Stefano Cattaneo
- Vita-Salute San Raffaele University, Milan, Italy.,San Raffaele Scientific Institute, Milan, Italy
| | - Gianluca Verlengia
- San Raffaele Scientific Institute, Milan, Italy.,Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Ferrara, Italy
| | - Pietro Marino
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Ferrara, Italy.,Department of Medical Sciences, Section of Pediatrics, University of Ferrara, Ferrara, Italy
| | - Michele Simonato
- Vita-Salute San Raffaele University, Milan, Italy.,San Raffaele Scientific Institute, Milan, Italy.,Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Ferrara, Italy
| | - Barbara Bettegazzi
- Vita-Salute San Raffaele University, Milan, Italy.,San Raffaele Scientific Institute, Milan, Italy
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48
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Quadruple Bond Forming Multicomponent Approach to 5-(3-chromenyl)-5H-chromeno[2,3-b]pyridines and Its Interaction with the Neuropeptide Y1 Receptor. Chem Heterocycl Compd (N Y) 2021. [DOI: 10.1007/s10593-020-02850-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. The Conformational Equilibrium of the Neuropeptide Y2 Receptor in Bilayer Membranes. Angew Chem Int Ed Engl 2020; 59:23854-23861. [PMID: 32790043 PMCID: PMC7736470 DOI: 10.1002/anie.202006075] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Indexed: 12/23/2022]
Abstract
Dynamic structural transitions within the seven-transmembrane bundle represent the mechanism by which G-protein-coupled receptors convert an extracellular chemical signal into an intracellular biological function. Here, the conformational dynamics of the neuropeptide Y receptor type 2 (Y2R) during activation was investigated. The apo, full agonist-, and arrestin-bound states of Y2R were prepared by cell-free expression, functional refolding, and reconstitution into lipid membranes. To study conformational transitions between these states, all six tryptophans of Y2R were 13 C-labeled. NMR-signal assignment was achieved by dynamic-nuclear-polarization enhancement and the individual functional states of the receptor were characterized by monitoring 13 C NMR chemical shifts. Activation of Y2R is mediated by molecular switches involving the toggle switch residue Trp2816.48 of the highly conserved SWLP motif and Trp3277.55 adjacent to the NPxxY motif. Furthermore, a conformationally preserved "cysteine lock"-Trp11623.50 was identified.
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Affiliation(s)
- Ulrike Krug
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Anika Gloge
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Peter Schmidt
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Johanna Becker‐Baldus
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Frank Bernhard
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Anette Kaiser
- Institute of BiochemistryUniversity of LeipzigLeipzigGermany
| | - Cindy Montag
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Marcel Gauglitz
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
- Berlin Joint Electron Paramagnetic Resonance LaboratoryFree University BerlinGermany
| | | | | | | | - Clemens Glaubitz
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Daniel Huster
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
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50
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. Das Konformationsgleichgewicht des Neuropeptid‐Y2‐Rezeptors in Lipidmembranen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ulrike Krug
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Anika Gloge
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Peter Schmidt
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Johanna Becker‐Baldus
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Frank Bernhard
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Anette Kaiser
- Institut für Biochemie Universität Leipzig Deutschland
| | - Cindy Montag
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Marcel Gauglitz
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
- Berlin Joint Electron Paramagnetic Resonance Laboratory Freie Universität Berlin Deutschland
| | | | | | | | - Clemens Glaubitz
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
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