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Pedroni L, Perugino F, Magnaghi F, Dall’Asta C, Galaverna G, Dellafiora L. Free fatty acid receptors beyond fatty acids: A computational journey to explore peptides as possible binders of GPR120. Curr Res Food Sci 2024; 8:100710. [PMID: 38496766 PMCID: PMC10940776 DOI: 10.1016/j.crfs.2024.100710] [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: 01/29/2024] [Revised: 02/07/2024] [Accepted: 03/01/2024] [Indexed: 03/19/2024] Open
Abstract
Free fatty acids receptors, with members among G protein-coupled receptors (GPCRs), are crucial for biological signaling, including the perception of the so called "fatty taste". In recent years, GPR120, a protein belonging to the GPCR family, drew attention as an interesting pharmacological target to cope with obesity, satiety and diabetes. Apart from long chain fatty acids, which are GPR120 natural agonists, other synthetic molecules were identified as agonists expanding the chemical space of GPR120's ligands. In this scenario, we unveiled peptides as possible GPR120 binders toward a better understanding of this multifaceted and relevant target. This study analyzed a virtual library collecting 531 441 low-polar hexapeptides, providing mechanistic insights on the GPR120 activation and further extending the possible chemical space of GPR120 agonists. The computational pipeline started with a narrow filtering of hexapeptides based on their chemical similarity with known GPR120 agonists. The best hits were tested through docking studies, molecular dynamics and umbrella sampling simulations, which pointed to G[I,L]FGGG as a promising GPR120 agonist sequence. The presence of both peptides in food-related proteins was thoroughly assessed, revealing they may occur in mushrooms, food-grade bacteria and rice. Simulations on the counterparts with D-amino acids were also performed. Umbrella sampling simulations described that GdIFGGG may have a better interaction compared to its all-L counterpart (-13 kCal/mol ΔG and -6 kCal/mol ΔG, respectively). Overall, we obtained a predictive model to better understand the underpinning mechanism of GPR120-hexapeptides interaction, hierarchizing novel potential agonist peptides for further analysis and describing promising food sources worth of further dedicated investigations.
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Affiliation(s)
- Lorenzo Pedroni
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Florinda Perugino
- Department of Food and Drug, University of Parma, Parma, Italy
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Fabio Magnaghi
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Parma, Italy
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2
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Catalani V, Botha M, Corkery JM, Guirguis A, Vento A, Schifano F. Designer Benzodiazepines' Activity on Opioid Receptors: A Docking Study. Curr Pharm Des 2022; 28:2639-2652. [PMID: 35538798 DOI: 10.2174/1381612828666220510153319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/21/2022] [Indexed: 12/16/2022]
Abstract
BACKGROUND Previous studies have reported that benzodiazepines (BZDs) seem to enhance euphoric and reinforcing properties of opioids in opioid users so that a direct effect on opioid receptors has been postulated, together with a possible synergistic induction of severe side effects due to co use of BDZs and opioids. This is particularly worrisome given the appearance on the market of designer benzodiazepines (DBZDs), whose activity/toxicity profiles are scarcely known. OBJECTIVES This study aimed to evaluate, through computational studies, the binding affinity (or lack thereof) of 101 DBZDs identified online on the kappa, mu, and delta opioid receptors (K, M, DOR); and to assess whether their mechanism of action could include activation of the latter. METHODS MOE® was used for the computational studies. Pharmacophore mapping based on strong opioids agonist binders' 3D chemical features was used to filter the DBZDs. Resultant DBZDs were docked into the crystallised 3D active conformation of KOR (PDB6B73), DOR (PDB6PT3) and MOR (PDB5C1M). Co-crystallised ligands and four strong agonists were used as reference compounds. A score (S, Kcal/mol) representative of the predicted binding affinity, and a description of ligand interactions were obtained from MOE®. RESULTS The docking results, filtered for S < -8.0 and the interaction with the Asp residue, identified five DBZDs as putative binders of the three ORs : ciclotizolam, fluloprazolam, JQ1, Ro 48-6791, and Ro 48-8684. CONCLUSION It may be inferred that at least some DBZDs may have the potential to activate opioid receptors. This could mediate/increase their anxiolytic, analgesic, and addiction potentials, as well as worsen the side effects associated with opioid co-use.
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Affiliation(s)
- Valeria Catalani
- Psychopharmacology, Drug Misuse & Novel Psychoactive Substances Research Unit, School of Life & Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield, United Kingdom
| | - Michelle Botha
- Psychopharmacology, Drug Misuse & Novel Psychoactive Substances Research Unit, School of Life & Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield, United Kingdom
| | - John Martin Corkery
- Psychopharmacology, Drug Misuse & Novel Psychoactive Substances Research Unit, School of Life & Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield, United Kingdom
| | - Amira Guirguis
- Psychopharmacology, Drug Misuse & Novel Psychoactive Substances Research Unit, School of Life & Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield, United Kingdom.,Swansea University Medical School, The Grove, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Alessandro Vento
- Department of Mental Health, ASL Roma 2, Rome, Italy.,Addictions\' Observatory (ODDPSS), Rome, Italy.,Guglielmo Marconi' University, Rome, Italy
| | - Fabrizio Schifano
- Psychopharmacology, Drug Misuse & Novel Psychoactive Substances Research Unit, School of Life & Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield, United Kingdom
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Lee B, Shin MK, Yoo JS, Jang W, Sung JS. Identifying novel antimicrobial peptides from venom gland of spider Pardosa astrigera by deep multi-task learning. Front Microbiol 2022; 13:971503. [PMID: 36090084 PMCID: PMC9449525 DOI: 10.3389/fmicb.2022.971503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022] Open
Abstract
Antimicrobial peptides (AMPs) show promises as valuable compounds for developing therapeutic agents to control the worldwide health threat posed by the increasing prevalence of antibiotic-resistant bacteria. Animal venom can be a useful source for screening AMPs due to its various bioactive components. Here, the deep learning model was developed to predict species-specific antimicrobial activity. To overcome the data deficiency, a multi-task learning method was implemented, achieving F1 scores of 0.818, 0.696, 0.814, 0.787, and 0.719 for Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus epidermidis, respectively. Peptides PA-Full and PA-Win were identified from the model using different inputs of full and partial sequences, broadening the application of transcriptome data of the spider Pardosa astrigera. Two peptides exhibited strong antimicrobial activity against all five strains along with cytocompatibility. Our approach enables excavating AMPs with high potency, which can be expanded into the fields of biology to address data insufficiency.
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Affiliation(s)
- Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang-si, South Korea
| | - Min Kyoung Shin
- Department of Life Science, Dongguk University-Seoul, Goyang-si, South Korea
| | - Jung Sun Yoo
- Animal Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang-si, South Korea
- Wonhee Jang,
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University-Seoul, Goyang-si, South Korea
- *Correspondence: Jung-Suk Sung,
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Abdin O, Nim S, Wen H, Kim PM. PepNN: a deep attention model for the identification of peptide binding sites. Commun Biol 2022; 5:503. [PMID: 35618814 PMCID: PMC9135736 DOI: 10.1038/s42003-022-03445-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/03/2022] [Indexed: 11/09/2022] Open
Abstract
Protein-peptide interactions play a fundamental role in many cellular processes, but remain underexplored experimentally and difficult to model computationally. Here, we present PepNN-Struct and PepNN-Seq, structure and sequence-based approaches for the prediction of peptide binding sites on a protein. A main difficulty for the prediction of peptide-protein interactions is the flexibility of peptides and their tendency to undergo conformational changes upon binding. Motivated by this, we developed reciprocal attention to simultaneously update the encodings of peptide and protein residues while enforcing symmetry, allowing for information flow between the two inputs. PepNN integrates this module with modern graph neural network layers and a series of transfer learning steps are used during training to compensate for the scarcity of peptide-protein complex information. We show that PepNN-Struct achieves consistently high performance across different benchmark datasets. We also show that PepNN makes reasonable peptide-agnostic predictions, allowing for the identification of novel peptide binding proteins.
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Affiliation(s)
- Osama Abdin
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Han Wen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Philip M Kim
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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5
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Wang X, Bushra N, Muschol M, Madsen JJ, Ye L. An in-membrane NMR spectroscopic approach probing native ligand-GPCR interaction. Int J Biol Macromol 2022; 206:911-916. [PMID: 35318080 DOI: 10.1016/j.ijbiomac.2022.03.099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 01/02/2023]
Abstract
Conventional approaches to study ligand-receptor interactions using solution-state NMR often involve laborious sample preparation, isotopic labeling, and receptor reconstitution. Each of these steps remains challenging for membrane proteins such as G protein-coupled receptors (GPCRs). Here we introduce a combinational approach integrating NMR and homogenized membrane nano-discs preparation to characterize the ligand-GPCR interactions. The approach will have a great potential for drug screening as it benefits from minimal receptor preparation, minimizing non-specific binding. In addition, the approach maintains receptor structural heterogeneity essential for functional diversity, making it feasible for probing a more reliable ligand-GPCR interaction that is vital for faithful ligand discovery.
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Affiliation(s)
- Xudong Wang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Nabila Bushra
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Libin Ye
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA.
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6
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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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Lyapina I, Ivanov V, Fesenko I. Peptidome: Chaos or Inevitability. Int J Mol Sci 2021; 22:13128. [PMID: 34884929 PMCID: PMC8658490 DOI: 10.3390/ijms222313128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.
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Affiliation(s)
| | | | - Igor Fesenko
- Department of Functional Genomics and Proteomics of Plants, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (I.L.); (V.I.)
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8
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Wu F, Jin X, Guan Z, Lin J, Cai C, Wang L, Li Y, Lin S, Xu P, Gao L. Membrane Nanopores Induced by Nanotoroids via an Insertion and Pore-Forming Pathway. NANO LETTERS 2021; 21:8545-8553. [PMID: 34623162 DOI: 10.1021/acs.nanolett.1c01331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of membrane nanopores is one of the crucial activities of cells and has attracted considerable attention. However, the understanding of their types and mechanisms is still limited. Herein, we report a novel nanopore formation phenomenon achieved through the insertion of polymeric nanotoroids into the cellular membrane. As revealed by theoretical simulations, the nanotoroid can embed in the membrane, leaving a nanopore on the cell. The through-the-cavity wrapping of lipids is critical for the retention of the nanotoroid in the membrane, which is attributed to both a relatively large inner cavity of the nanotoroid and a moderate attraction between the nanotoroid and membrane lipids. Under the guidance of the simulation predictions, experiments using polypeptide toroids as pore-forming agents were performed, confirming the unique biophysical phenomenon. This work demonstrates a distinctive pore-forming pathway, deepens the understanding of the membrane nanopore phenomenon, and assists in the design of advanced pore-forming materials.
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Affiliation(s)
- Fangsheng Wu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xiao Jin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhou Guan
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Chunhua Cai
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Liquan Wang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Yongsheng Li
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Shaoliang Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Pengfei Xu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Liang Gao
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
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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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Abstract
Biological processes are often mediated by complexes formed between proteins and various biomolecules. The 3D structures of such protein-biomolecule complexes provide insights into the molecular mechanism of their action. The structure of these complexes can be predicted by various computational methods. Choosing an appropriate method for modelling depends on the category of biomolecule that a protein interacts with and the availability of structural information about the protein and its interacting partner. We intend for the contents of this chapter to serve as a guide as to what software would be the most appropriate for the type of data at hand and the kind of 3D complex structure required. Particularly, we have dealt with protein-small molecule ligand, protein-peptide, protein-protein, and protein-nucleic acid interactions.Most, if not all, model building protocols perform some sampling and scoring. Typically, several alternate conformations and configurations of the interactors are sampled. Each such sample is then scored for optimization. To boost the confidence in these predicted models, their assessment using other independent scoring schemes besides the inbuilt/default ones would prove to be helpful. This chapter also lists such software and serves as a guide to gauge the fidelity of modelled structures of biomolecular complexes.
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Usman S, Khawer M, Rafique S, Naz Z, Saleem K. The current status of anti-GPCR drugs against different cancers. J Pharm Anal 2020; 10:517-521. [PMID: 33425448 PMCID: PMC7775845 DOI: 10.1016/j.jpha.2020.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/23/2022] Open
Abstract
G protein coupled receptors (GPCRs) have emerged as the most potential target for a number of drug discovery programs ranging from control of blood pressure, diabetes, cure for genetic diseases to treatment of cancer. A panel of different ligands including hormones, peptides, ions and small molecules is responsible for activation of these receptors. Molecular genetics has identified key GPCRs, whose mutations or altered expressions are linked with tumorgenicity. In this review, we discussed recent advances regarding the involvement of GPCRs in the development of cancers and approaches to manipulating the mechanism behind GPCRs involved tumor growth and metastasis to treat different types of human cancer. This review provides an insight into the current scenario of GPCR-targeted therapy, progress to date and the challenges in the development of anticancer drugs.
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Affiliation(s)
- Sana Usman
- Centre for Applied Molecular Biology, 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Maria Khawer
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Zara Naz
- Centre for Applied Molecular Biology, 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Komal Saleem
- Centre for Applied Molecular Biology, 87-West Canal Bank Road Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
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Pharmacological and functional similarities of the human neuropeptide Y system in C. elegans challenges phylogenetic views on the FLP/NPR system. Cell Commun Signal 2019; 17:123. [PMID: 31533726 PMCID: PMC6751662 DOI: 10.1186/s12964-019-0436-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/02/2019] [Indexed: 11/14/2022] Open
Abstract
Background The neuropeptide Y system affects various processes, among others food intake, and is frequently discussed in the context of targeting obesity. Studies in model organisms are indispensable to enable molecular studies in a physiological context. Although the NPY system is evolutionarily conserved in all bilaterians, in the widely used model Caenorhabditis elegans there is controversy on the existence of NPY orthologous molecules. While the FMRFamide-like peptide (FLP)/Neuropeptide receptor-Resemblance (NPR) system in the nematode was initially suggested to be orthologous to the mammalian NPY system, later global phylogenetic studies indicate that FLP/NPR is protostome-specific. Methods We performed a comprehensive pharmacological study of the FLP/NPR system in transfected cells in vitro, and tested for functional substitution in C. elegans knockout strains. Further, we phenotypically compared different flp loss-of-function strains. Differences between groups were compared by ANOVA and post-hoc testing (Dunnett, Bonferroni). Results Our pharmacological analysis of the FLP/NPR system including formerly functionally uncharacterized NPY-like peptides from C. elegans demonstrates that G protein-coupling and ligand requirements for receptor activation are similar to the human NPY system. In vitro and in vivo analyses show cross-reactivity of NPY with the FLP/NPR system manifesting in the ability of the human GPCRs to functionally substitute FLP/NPR signaling in vivo. The high pharmacological/functional similarities enabled us to identify C. elegans FLP-14 as a key molecule in avoidance behavior. Conclusions Our data demonstrate the pharmacological and functional similarities of human NPY and C. elegans NPR systems. This adds a novel perspective to current phylogenetic reconstructions of the neuropeptide Y system. NPY and NPR receptors are pharmacologically so similar that the human receptors can functionally compensate for the C. elegans ones, suggesting orthologous relationships. This is also underlined by the presence of NPY-like peptides and parallels in peptide requirements for receptor activation. Further, the results presented here highlight the potential of this knowledge for physiological as well as molecular studies on neuropeptide GPCRs such as the NPY system in the future.
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Ritler A, Shoshan MS, Deupi X, Wilhelm P, Schibli R, Wennemers H, Béhé M. Elucidating the Structure-Activity Relationship of the Pentaglutamic Acid Sequence of Minigastrin with Cholecystokinin Receptor Subtype 2. Bioconjug Chem 2019; 30:657-666. [PMID: 30608664 DOI: 10.1021/acs.bioconjchem.8b00849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Derivatized minigastrin analogues make up a promising class of candidates for targeting cholecystokinin receptor subtype 2 (CCK2R), which is overexpressed on cancer cells of various neuroendocrine tumors. The pentaglutamic acid sequence of minigastrin influences its biological properties. In particular, it plays a crucial role in the kidney reuptake mechanism. However, the importance of the binding affinity and interaction of this region with the receptor on a molecular level remains unclear. To elucidate its structure-activity relationship with CCK2R, we replaced this sequence with various linkers differing in their amount of anionic charge, structural characteristics, and flexibility. Specifically, a flexible aliphatic linker, a linker with only three d-Glu residues, and a structured linker with four adjacent β3-glutamic acid residues were evaluated and compared to the lead compound PP-F11N (DOTA-[d-Glu1-6,Nle11]gastrin-13). 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) was conjugated to the minigastrin derivatives, which allowed radiolabeling with Lutetium-177. The levels of In vitro internalization into MZ-CRC1 cells and in vivo tumor uptake as well as human blood plasma stability increased in the following order: aliphatic linker < three d-Glu < (β3-Glu)4 < (d-Glu)6. The in vitro and in vivo behavior was therefore significantly improved with anionic charges. Computational modeling of a CCK2 receptor-ligand complex revealed ionic interactions between cationic residues (Arg and His) of the receptor and anionic residues of the ligand in the linker.
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Affiliation(s)
- Andreas Ritler
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland.,Department of Chemistry and Applied Biosciences (D-CHAB), Institute of Pharmaceutical Sciences (IPW) , ETH , CH-8093 Zurich , Switzerland.,Research Department of Biology and Chemistry, Center for Radiopharmaceutical Sciences (CRS) , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| | - Michal S Shoshan
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research and Condensed Matter Theory Group , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| | - Patrick Wilhelm
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland
| | - Roger Schibli
- Department of Chemistry and Applied Biosciences (D-CHAB), Institute of Pharmaceutical Sciences (IPW) , ETH , CH-8093 Zurich , Switzerland.,Research Department of Biology and Chemistry, Center for Radiopharmaceutical Sciences (CRS) , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| | - Helma Wennemers
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland
| | - Martin Béhé
- Research Department of Biology and Chemistry, Center for Radiopharmaceutical Sciences (CRS) , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
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14
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Do TD, Checco JW, Tro M, Shea JE, Bowers MT, Sweedler JV. Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit. Phys Chem Chem Phys 2018; 20:22047-22057. [PMID: 30112548 DOI: 10.1039/c8cp03661f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins and peptides in nature are almost exclusively made from l-amino acids, and this is even more absolute in the metazoan. With the advent of modern bioanalytical techniques, however, previously unappreciated roles for d-amino acids in biological processes have been revealed. Over 30 d-amino acid containing peptides (DAACPs) have been discovered in animals where at least one l-residue has been isomerized to the d-form via an enzyme-catalyzed process. In Aplysia californica, GdFFD and GdYFD (the lower-case letter "d" indicates a d-amino acid residue) modulate the feeding behavior by activating the Aplysia achatin-like neuropeptide receptor (apALNR). However, little is known about how the three-dimensional conformation of DAACPs influences activity at the receptor, and the role that d-residues play in these peptide conformations. Here, we use a combination of computational modeling, drift-tube ion-mobility mass spectrometry, and receptor activation assays to create a simple model that predicts bioactivities for a series of GdFFD analogs. Our results suggest that the active conformations of GdFFD and GdYFD are similar to their lowest energy conformations in solution. Our model helps connect the predicted structures of GdFFD analogs to their activities, and highlights a steric effect on peptide activity at position 1 on the GdFFD receptor apALNR. Overall, these methods allow us to understand ligand-receptor interactions in the absence of high-resolution structural data.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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15
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Kang SW, Jayanthi S, Nagarajan G, Suresh Kumar TK, Kuenzel WJ. Identification of avian vasotocin receptor subtype-specific antagonists involved in the stress response of the chicken, Gallus gallus. J Biomol Struct Dyn 2018; 37:1685-1699. [PMID: 29658387 DOI: 10.1080/07391102.2018.1464957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Vasotocin 1a and 1b receptors (V1aR and V1bR) have been shown to play important roles in the neuroendocrine regulation of stress responses via the anterior pituitary (AP) of birds. To identify effective subtype-specific antagonists for the chicken V1aR (cV1aR) and cV1bR, potential antagonists to the mammalian V1R were screened against the cV1aR and cV1bR 3D structural models by molecular docking analysis with determination of binding pocket/amino acid residues involved in the interaction. The antagonistic effects of the selected ligands were examined by measuring pro-opiomelanocortin (POMC) heteronuclear RNA (hnPOMC) levels following the in vitro stress administration to primary chicken AP cells. Results of in silico analysis showed that the Manning compound and several other antagonists were bound to cV1bR with higher affinity than the natural agonist, arginine vasotocin (AVT). Similarities and differences in the antagonist-receptor binding interface with receptors were characterized for each ligand. Non-peptide mammalian V1bR antagonists, SSR-149415 and L-368899, were shown to be effective and had an additive effect in blocking POMC hnRNA expression in pituitary cell culture studies. SR-49059 antagonized the effect(s) of AVT/CRH on the downregulation of the cV1aR and the upregulation of the cCRH-R2 expression but not the cV1bR and cCRH-R1. The Manning compound antagonized the downregulation of cV1aR, cV1bR and cCRH-R1 and the upregulation of cCRH-R2 expression. The specificity of antagonists apparently resulted from unique differences in the interacting residues and their binding affinities. Collectively, these results provide valuable leads for future development of novel compounds capable of blocking or attenuating the AP stress response of avian species and perhaps other non-mammalian vertebrates as well.
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Affiliation(s)
- Seong W Kang
- a Department of Poultry Sciences , University of Arkansas , Fayetteville , AR , USA
| | - Srinivas Jayanthi
- b Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , AR , USA
| | - Gurueswar Nagarajan
- a Department of Poultry Sciences , University of Arkansas , Fayetteville , AR , USA
| | | | - Wayne J Kuenzel
- a Department of Poultry Sciences , University of Arkansas , Fayetteville , AR , USA
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16
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Abstract
Neuropeptides are the largest class of intercellular signaling molecules, contributing to a wide variety of physiological processes. Neuropeptide receptors are therapeutic targets for a broad range of drugs, including medications to treat pain, addiction, sleep disorders, and nausea. In addition to >100 peptides with known functions, many peptides have been identified in mammalian brain for which the cognate receptors have not been identified. Similarly, dozens of "orphan" G protein-coupled receptors have been identified in the mammalian genome. While it would seem straightforward to match the orphan peptides and receptors, this is not always easily accomplished. In this review we focus on peptides named PEN and big LEN, which are among the most abundant neuropeptides in mouse brain, and their recently identified receptors: GPR83 and GPR171. These receptors are co-expressed in some brain regions and are able to interact. Because PEN and big LEN are produced from the same precursor protein and co-secreted, the interaction of GPR83 and GPR171 is physiologically relevant. In addition to interactions of these two peptides/receptors, PEN and LEN are co-localized with neuropeptide Y and Agouti-related peptide in neurons that regulate feeding. In this review, using these peptide receptors as an example, we highlight the multiple modes of regulation of receptors and present the emerging view that neuropeptides function combinatorially to generate a network of signaling messages. The complexity of neuropeptides, receptors, and their signaling pathways is important to consider both in the initial deorphanization of peptides and receptors, and in the subsequent development of therapeutic applications.
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Affiliation(s)
- Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States
| | - Lakshmi A Devi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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17
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Brancaccio D, Diana D, Di Maro S, Di Leva FS, Tomassi S, Fattorusso R, Russo L, Scala S, Trotta AM, Portella L, Novellino E, Marinelli L, Carotenuto A. Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)–Ligand Interactions on Living Cancer Cells. J Med Chem 2018. [DOI: 10.1021/acs.jmedchem.7b01830] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Diego Brancaccio
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, C.N.R., 80134 Naples, Italy
| | - Salvatore Di Maro
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | | | - Stefano Tomassi
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy
| | - Anna Maria Trotta
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy
| | - Luigi Portella
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Dipartimento di Farmacia, Università di Napoli Federico II, 80131 Naples, Italy
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18
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Kaiser A, Hempel C, Wanka L, Schubert M, Hamm HE, Beck-Sickinger AG. G Protein Preassembly Rescues Efficacy of W6.48 Toggle Mutations in Neuropeptide Y2 Receptor. Mol Pharmacol 2018; 93:387-401. [DOI: 10.1124/mol.117.110544] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/02/2018] [Indexed: 12/19/2022] Open
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19
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Ge X, Yang H, Bednarek MA, Galon-Tilleman H, Chen P, Chen M, Lichtman JS, Wang Y, Dalmas O, Yin Y, Tian H, Jermutus L, Grimsby J, Rondinone CM, Konkar A, Kaplan DD. LEAP2 Is an Endogenous Antagonist of the Ghrelin Receptor. Cell Metab 2018; 27:461-469.e6. [PMID: 29233536 DOI: 10.1016/j.cmet.2017.10.016] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/13/2017] [Accepted: 10/30/2017] [Indexed: 01/04/2023]
Abstract
Ghrelin, an appetite-stimulatory hormone secreted by the stomach, was discovered as a ligand for the growth hormone secretagogue receptor (GHSR). Through GHSR, ghrelin stimulates growth hormone (GH) secretion, a function that evolved to protect against starvation-induced hypoglycemia. Though the biology mediated by ghrelin has been described in great detail, regulation of ghrelin action is poorly understood. Here, we report the discovery of liver-expressed antimicrobial peptide 2 (LEAP2) as an endogenous antagonist of GHSR. LEAP2 is produced in the liver and small intestine, and its secretion is suppressed by fasting. LEAP2 fully inhibits GHSR activation by ghrelin and blocks the major effects of ghrelin in vivo, including food intake, GH release, and maintenance of viable glucose levels during chronic caloric restriction. In contrast, neutralizing antibodies that block endogenous LEAP2 function enhance ghrelin action in vivo. Our findings reveal a mechanism for fine-tuning ghrelin action in response to changing environmental conditions.
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Affiliation(s)
- Xuecai Ge
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA.
| | - Hong Yang
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, MedImmune Ltd, Cambridge CB21 6GH, UK
| | | | - Peirong Chen
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Michael Chen
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | | | - Yan Wang
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Olivier Dalmas
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Yiyuan Yin
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Hui Tian
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
| | - Lutz Jermutus
- Department of Antibody Discovery & Protein Engineering, MedImmune Ltd, Cambridge CB21 6GH, UK; Department of Cardiovascular and Metabolic Disease Research, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - Joseph Grimsby
- Department of Cardiovascular and Metabolic Disease Research, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - Cristina M Rondinone
- Department of Cardiovascular and Metabolic Disease Research, MedImmune LLC, Gaithersburg, MD 20878, USA
| | - Anish Konkar
- Department of Cardiovascular and Metabolic Disease Research, MedImmune LLC, Gaithersburg, MD 20878, USA
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20
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Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. Structure 2018; 26:7-19.e5. [DOI: 10.1016/j.str.2017.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/02/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022]
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21
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Sojka AC, Brennan KM, Maizels ET, Young CD. The Science Behind G Protein-Coupled Receptors (GPCRs) and Their Accurate Visual Representation in Scientific Research. THE JOURNAL OF BIOCOMMUNICATION 2017; 41:e6. [PMID: 36405408 PMCID: PMC9140105 DOI: 10.5210/jbc.v41i1.7309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
G Protein-Coupled Receptors (GPCRs) are transmembrane (TM) proteins that span the cell membrane seven times, and contain intracellular and extracellular domains, comprised of connecting loops, as well as terminal extension sequences. GPCRs bind ligands within their transmembrane and/or extracellular domains. Ligand binding elicits conformational changes that initiate downstream intracellular signaling events through arrestins and G proteins. GPCRs play central roles in many physiological processes, from sensory to neurological, cardiovascular, endocrine, and reproductive functions. This paper strives to provide an entry point to current GPCR science, and to identify visual approaches to communicate select aspects of GPCR structure and function with clarity and accuracy. The overall GPCR structure, primary sequence and the implications of sequence for membrane topology, ligand binding and helical rearrangements accompanying activation are considered and discussed in the context of visualization strategies, including two-dimensional topological diagrams, three-dimensional representations, and common errors that arise from these representations.
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22
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Ranganathan A, Heine P, Rudling A, Plückthun A, Kummer L, Carlsson J. Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries. ACS Chem Biol 2017; 12:735-745. [PMID: 28032980 DOI: 10.1021/acschembio.6b00646] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptide-recognizing G protein-coupled receptors (GPCRs) are promising therapeutic targets but often resist drug discovery efforts. Determination of crystal structures for peptide-binding GPCRs has provided opportunities to explore structure-based methods in lead development. Molecular docking screens of two chemical libraries, containing either fragment- or lead-like compounds, against a neurotensin receptor 1 crystal structure allowed for a comparison between different drug development strategies for peptide-binding GPCRs. A total of 2.3 million molecules were screened computationally, and 25 fragments and 27 leads that were top-ranked in each library were selected for experimental evaluation. Of these, eight fragments and five leads were confirmed as ligands by surface plasmon resonance. The hit rate for the fragment screen (32%) was thus higher than for the lead-like library (19%), but the affinities of the fragments were ∼100-fold lower. Both screens returned unique scaffolds and demonstrated that a crystal structure of a stabilized peptide-binding GPCR can guide the discovery of small-molecule agonists. The complementary advantages of exploring fragment- and lead-like chemical space suggest that these strategies should be applied synergistically in structure-based screens against challenging GPCR targets.
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Affiliation(s)
- Anirudh Ranganathan
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Philipp Heine
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Axel Rudling
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Andreas Plückthun
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lutz Kummer
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- G7 Therapeutics AG, Grabenstrasse
11a, 8952 Schlieren, Switzerland
| | - Jens Carlsson
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC,
Box 596, SE-751 24 Uppsala, Sweden
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23
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Moschonas IC, Kellici TF, Mavromoustakos T, Stathopoulos P, Tsikaris V, Magafa V, Tzakos AG, Tselepis AD. Molecular requirements involving the human platelet protease-activated receptor-4 mechanism of activation by peptide analogues of its tethered-ligand. Platelets 2017; 28:812-821. [DOI: 10.1080/09537104.2017.1282607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- I. C. Moschonas
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - T. F. Kellici
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
| | - T. Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
- Department of Chemistry, York College and the Graduate Center of the City University of New York, Jamaica, NY, USA
| | - P. Stathopoulos
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - V. Tsikaris
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - V. Magafa
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Patras, Patras, Greece
| | - A. G. Tzakos
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - A. D. Tselepis
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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Cordomí A, Fourmy D, Tikhonova IG. Gut hormone GPCRs: structure, function, drug discovery. Curr Opin Pharmacol 2016; 31:63-67. [DOI: 10.1016/j.coph.2016.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/24/2016] [Accepted: 09/01/2016] [Indexed: 01/08/2023]
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25
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Saier MH, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G. The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res 2015; 44:D372-9. [PMID: 26546518 PMCID: PMC4702804 DOI: 10.1093/nar/gkv1103] [Citation(s) in RCA: 460] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/11/2015] [Indexed: 11/16/2022] Open
Abstract
The Transporter Classification Database (TCDB; http://www.tcdb.org) is a freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness. Here we present a comprehensive update of the database contents and features and summarize recent discoveries recorded in TCDB.
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Affiliation(s)
- Milton H Saier
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Vamsee S Reddy
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA Department of Medical Sciences, Boston University School of Medicine, 72 E Concord St., Boston, MA 02118, USA
| | - Brian V Tsu
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Muhammad Saad Ahmed
- Department of Biological Engineering, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Chun Li
- Department of Biological Engineering, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Gabriel Moreno-Hagelsieb
- Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, Canada N2L 3C5
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