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Kumari N, Pullaguri N, Rath SN, Bajaj A, Sahu V, Ealla KKR. Dysregulation of calcium homeostasis in cancer and its role in chemoresistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:11. [PMID: 38510751 PMCID: PMC10951838 DOI: 10.20517/cdr.2023.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/03/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
Globally, cancer, as a major public health concern, poses a severe threat to people's well-being. Advanced and specialized therapies can now cure the majority of people with early-stage cancer. However, emerging resistance to traditional and novel chemotherapeutic drugs remains a serious issue in clinical medicine. Chemoresistance often leads to cancer recurrence, metastasis, and increased mortality, accounting for 90% of chemotherapy failures. Thus, it is important to understand the molecular mechanisms of chemoresistance and find novel therapeutic approaches for cancer treatment. Among the several factors responsible for chemoresistance, calcium (Ca2+) dysregulation plays a significant role in cancer progression and chemoresistance. Therefore, targeting this derailed Ca2+ signalling for cancer therapy has become an emerging research area. Of note, the Ca2+ signal and its proteins are a multifaceted and potent tool by which cells achieve specific outcomes. Depending on cell survival needs, Ca2+ is either upregulated or downregulated in both chemosensitive and chemoresistant cancer cells. Consequently, the appropriate treatment should be selected based on Ca2+ signalling dysregulation. This review discusses the role of Ca2+ in cancer cells and the targeting of Ca2+ channels, pumps, and exchangers. Furthermore, we have emphasised the role of Ca2+ in chemoresistance and therapeutic strategies. In conclusion, targeting Ca2+ signalling is a multifaceted process. Methods such as site-specific drug delivery, target-based drug-designing, and targeting two or more Ca2+ proteins simultaneously may be explored; however, further clinical studies are essential to validate Ca2+ blockers' anti-cancer efficacy.
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Affiliation(s)
- Neema Kumari
- Department of Microbiology, Malla Reddy Institute of Medical Sciences, Hyderabad 500055, India
- Authors contributed equally
| | - Narasimha Pullaguri
- Research & Development division, Hetero Biopharma Limited, Jadcherla 509301, India
- Authors contributed equally
| | - Subha Narayan Rath
- Department of Biomedical Engineering, Indian Institute of Technology, Hyderabad 502284, India
| | - Ashish Bajaj
- National Reference Laboratory, Oncquest Laboratories Ltd., Gurugram 122001, India
| | - Vikas Sahu
- Department of Oral and Maxillofacial Pathology, Malla Reddy Institute of Dental Sciences, Hyderabad 500055, India
| | - Kranti Kiran Reddy Ealla
- Department of Oral and Maxillofacial Pathology, Malla Reddy Institute of Dental Sciences, Hyderabad 500055, India
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2
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Wang Y, Weng S, Tang Y, Lin S, Liu X, Zhang W, Liu G, Pandi B, Wu Y, Ma L, Wang L. A transmembrane scaffold from CD20 helps recombinant expression of a chimeric claudin 18.2 in an in vitro coupled transcription and translation system. Protein Expr Purif 2024; 215:106392. [PMID: 37952787 DOI: 10.1016/j.pep.2023.106392] [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: 09/14/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023]
Abstract
Cluster of differentiation 20 (CD20) is a nonglycosylated, multispanning transmembrane protein specifically integrated by B lymphocytes. Similar to CD20, another four-pass transmembrane protein, claudin 18.2, has attracted attention as an emerging therapeutic target for cancer. However, their poor solubility and toxic nature often hinder downstream applications, such as antibody drug development. Therefore, developing a cost-effective method for producing drug targets with multiple membrane-spanning domains is crucial. In this study, a high yield of recombinant CD20 was achieved through an E. coli-based in vitro coupled transcription-translation system. Surface plasmon resonance results showed that rituximab (an antileukemia drug) has nanomolar affinity with the CD20 protein, which aligns with published results. Notably, a previously hard-to-express claudin 18.2 recombinant protein was successfully expressed in the same reaction system by replacing its membrane-spanning domains with the transmembrane domains of CD20. The folding of the extracellular domain of the chimeric protein was verified using a commercial anti-claudin 18 antibody. This study provides a novel concept for promoting the expression of four-pass transmembrane proteins and lays the foundation for the large-scale industrial production of membrane-associated drug targets, similar to claudin 18.2.
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Affiliation(s)
- Yao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Shaoting Weng
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Yajie Tang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Sen Lin
- Anyang Kindstar Global Medical Laboratory Ltd, Anyang, Henan province, 455000, China
| | - Xiayue Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Wenhui Zhang
- Henan Panran Medical Equipment Co., Ltd, Anyang, Henan province, 455000, China
| | - Gang Liu
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Boomi Pandi
- Department of bioinformatics, Alagappa University, Karaikudi, India
| | - Yinrong Wu
- Henan Panran Medical Equipment Co., Ltd, Anyang, Henan province, 455000, China
| | - Lei Ma
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Lin Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China.
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3
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Kumar V, Chunchagatta Lakshman PK, Prasad TK, Manjunath K, Bairy S, Vasu AS, Ganavi B, Jasti S, Kamariah N. Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening. Heliyon 2024; 10:e23864. [PMID: 38226204 PMCID: PMC10788520 DOI: 10.1016/j.heliyon.2023.e23864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of in-vitro activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), Förster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target's role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.
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Affiliation(s)
| | | | - Thazhe Kootteri Prasad
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Sneha Bairy
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Akshaya S. Vasu
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - B. Ganavi
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Subbarao Jasti
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Neelagandan Kamariah
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
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Kunioku Y, Kimura M, Ouchi T, Fukuda K, Shibukawa Y. Intracellular cAMP Signaling Pathway via G s Protein-Coupled Receptor Activation in Rat Primary Cultured Trigeminal Ganglion Cells. Biomedicines 2023; 11:2347. [PMID: 37760789 PMCID: PMC10525138 DOI: 10.3390/biomedicines11092347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/29/2023] Open
Abstract
G protein-coupled receptors in trigeminal ganglion (TG) neurons are often associated with sensory mechanisms, including nociception. We have previously reported the expression of P2Y12 receptors, which are Gi protein-coupled receptors, in TG cells. Activating P2Y12 receptors decreased the intracellular free Ca2+ concentration ([Ca2+]i). This indicated that intracellular adenosine 3',5'-cyclic monophosphate (cAMP) levels can mediate Ca2+ signaling in TG cells. Here, we report more extensive-expression patterns of Gs protein-coupled receptors in primary cultured TG neurons isolated from 7-day-old newborn Wistar rats and further examine the roles of these receptors in cAMP signaling using the BacMam sensor in these neurons. To identify TG neurons, we also measured [Ca2+]i using fura-2 in TG cells and measured intracellular cAMP levels. TG neurons were positive for Gαs protein-coupled receptors, beta-2 adrenergic (β2), calcitonin gene-related peptide (CGRP), adenosine A2A (A2A), dopamine 1 (D1), prostaglandin I2 (IP), and 5-hydroxytriptamine 4 (5-HT4) receptor. Application of forskolin (FSK), an activator of adenylyl cyclase, transiently increased intracellular cAMP levels in TG neurons. The application of a phosphodiesterase inhibitor augmented the FSK-elicited intracellular cAMP level increase. These increases were significantly suppressed by the application of SQ22536, an adenylyl cyclase inhibitor, in TG neurons. Application of agonists for β2, CGRP, A2A, D1-like, IP, and 5-HT4 receptors increased intracellular cAMP levels. These increases were SQ22536-sensitive. These results suggested that TG neurons express β2, CGRP, A2A, D1, IP, and 5-HT4 receptors, and the activations of these Gαs protein-coupled receptors increase intracellular cAMP levels by activating adenylyl cyclase.
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Affiliation(s)
- Yuki Kunioku
- Department of Physiology, Tokyo Dental College, 2-9-18, Kanda-Misaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (Y.K.); (T.O.); (Y.S.)
- Division of Special Needs Dentistry and Orofacial Pain, Department of Oral Health and Clinical Science, Tokyo Dental College, 2-9-18, Kanda-Misaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan;
| | - Maki Kimura
- Department of Physiology, Tokyo Dental College, 2-9-18, Kanda-Misaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (Y.K.); (T.O.); (Y.S.)
| | - Takehito Ouchi
- Department of Physiology, Tokyo Dental College, 2-9-18, Kanda-Misaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (Y.K.); (T.O.); (Y.S.)
| | - Kenichi Fukuda
- Division of Special Needs Dentistry and Orofacial Pain, Department of Oral Health and Clinical Science, Tokyo Dental College, 2-9-18, Kanda-Misaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan;
| | - Yoshiyuki Shibukawa
- Department of Physiology, Tokyo Dental College, 2-9-18, Kanda-Misaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (Y.K.); (T.O.); (Y.S.)
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Akbarzadeh R, Müller A, Humrich JY, Riemekasten G. When natural antibodies become pathogenic: autoantibodies targeted against G protein-coupled receptors in the pathogenesis of systemic sclerosis. Front Immunol 2023; 14:1213804. [PMID: 37359516 PMCID: PMC10285309 DOI: 10.3389/fimmu.2023.1213804] [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: 04/28/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Systemic sclerosis (SSc) is a chronic, multisystem connective tissue, and autoimmune disease with the highest case-specific mortality and complications among rheumatic diseases. It is characterized by complex and variable features such as autoimmunity and inflammation, vasculopathy, and fibrosis, which pose challenges in understanding the pathogenesis of the disease. Among the large variety of autoantibodies (Abs) present in the sera of patients suffering from SSc, functionally active Abs against G protein-coupled receptors (GPCRs), the most abundant integral membrane proteins, have drawn much attention over the last decades. These Abs play an essential role in regulating the immune system, and their functions are dysregulated in diverse pathological conditions. Emerging evidence indicates that functional Abs targeting GPCRs, such as angiotensin II type 1 receptor (AT1R) and the endothelin-1 type A receptor (ETAR), are altered in SSc. These Abs are part of a network with several GPCR Abs, such as those directed to the chemokine receptors or coagulative thrombin receptors. In this review, we summarize the effects of Abs against GPCRs in SSc pathologies. Extending the knowledge on pathophysiological roles of Abs against GPCRs could provide insights into a better understanding of GPCR contribution to SSc pathogenesis and therefore help in developing potential therapeutic strategies that intervene with pathological functions of these receptors.
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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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7
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Two-step structural changes in M3 muscarinic receptor activation rely on the coupled G q protein cycle. Nat Commun 2023; 14:1276. [PMID: 36882424 PMCID: PMC9992711 DOI: 10.1038/s41467-023-36911-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
G protein-coupled receptors (GPCRs) regulate diverse intracellular signaling pathways through the activation of heterotrimeric G proteins. However, the effects of the sequential activation-deactivation cycle of G protein on the conformational changes of GPCRs remains unknown. By developing a Förster resonance energy transfer (FRET) tool for human M3 muscarinic receptor (hM3R), we find that a single-receptor FRET probe can display the consecutive structural conversion of a receptor by G protein cycle. Our results reveal that the G protein activation evokes a two-step change in the hM3R structure, including the fast step mediated by Gq protein binding and the subsequent slower step mediated by the physical separation of the Gαq and Gβγ subunits. We also find that the separated Gαq-GTP forms a stable complex with the ligand-activated hM3R and phospholipase Cβ. In sum, the present study uncovers the real-time conformational dynamics of innate hM3R during the downstream Gq protein cycle.
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8
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Heterogeneous Nucleation in Protein Crystallization. Biomimetics (Basel) 2023; 8:biomimetics8010068. [PMID: 36810399 PMCID: PMC9944892 DOI: 10.3390/biomimetics8010068] [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: 01/05/2023] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Protein crystallization was first discovered in the nineteenth century and has been studied for nearly 200 years. Protein crystallization technology has recently been widely used in many fields, such as drug purification and protein structure analysis. The key to successful crystallization of proteins is the nucleation in the protein solution, which can be influenced by many factors, such as the precipitating agent, temperature, solution concentration, pH, etc., among which the role of the precipitating agent is extremely important. In this regard, we summarize the nucleation theory of protein crystallization, including classical nucleation theory, two-step nucleation theory, and heterogeneous nucleation theory. We focus on a variety of efficient heterogeneous nucleating agents and crystallization methods as well. The application of protein crystals in crystallography and biopharmaceutical fields is further discussed. Finally, the bottleneck of protein crystallization and the prospect of future technology development are reviewed.
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Haueis L, Stech M, Schneider E, Lanz T, Hebel N, Zemella A, Kubick S. Rapid One-Step Capturing of Native, Cell-Free Synthesized and Membrane-Embedded GLP-1R. Int J Mol Sci 2023; 24:ijms24032808. [PMID: 36769142 PMCID: PMC9917595 DOI: 10.3390/ijms24032808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are of outstanding pharmacological interest as they are abundant in cell membranes where they perform diverse functions that are closely related to the vitality of cells. The analysis of GPCRs in natural membranes is laborious, as established methods are almost exclusively cell culture-based and only a few methods for immobilization in a natural membrane outside the cell are known. Within this study, we present a one-step, fast and robust immobilization strategy of the GPCR glucagon-like peptide 1 receptor (GLP-1R). GLP-1R was synthesized in eukaryotic lysates harboring endogenous endoplasmic reticulum-derived microsomes enabling the embedment of GLP-1R in a natural membrane. Interestingly, we found that these microsomes spontaneously adsorbed to magnetic Neutravidin beads thus providing immobilized membrane protein preparations which required no additional manipulation of the target receptor or its supporting membrane. The accessibility of the extracellular domain of membrane-embedded and bead-immobilized GLP-1R was demonstrated by bead-based enzyme-linked immunosorbent assay (ELISA) using GLP-1R-specific monoclonal antibodies. In addition, ligand binding of immobilized GLP-1R was verified in a radioligand binding assay. In summary, we present an easy and straightforward synthesis and immobilization methodology of an active GPCR which can be beneficial for studying membrane proteins in general.
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Affiliation(s)
- Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Correspondence:
| | | | - Thorsten Lanz
- 3B Pharmaceuticals GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Nicole Hebel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus–Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
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Poulie CBM, Pottie E, Simon IA, Harpsøe K, D'Andrea L, Komarov IV, Gloriam DE, Jensen AA, Stove CP, Kristensen JL. Discovery of β-Arrestin-Biased 25CN-NBOH-Derived 5-HT 2A Receptor Agonists. J Med Chem 2022; 65:12031-12043. [PMID: 36099411 PMCID: PMC9511481 DOI: 10.1021/acs.jmedchem.2c00702] [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] [Indexed: 11/29/2022]
Abstract
The serotonin 2A receptor (5-HT2AR) is the mediator of the psychedelic effects of serotonergic psychedelics, which have shown promising results in clinical studies for several neuropsychiatric indications. The 5-HT2AR is able to signal through the Gαq and β-arrestin effector proteins, but it is currently not known how the different signaling pathways contribute to the therapeutic effects mediated by serotonergic psychedelics. In the present work, we have evaluated the subtype-selective 5-HT2AR agonist 25CN-NBOH and a series of close analogues for biased signaling at this receptor. These ligands were designed to evaluate the role of interactions with Ser1593×36. The lack of interaction between this hydroxyl moiety and Ser1593×36 resulted in detrimental effects on potency and efficacy in both βarr2 and miniGαq recruitment assays. Remarkably, Gαq-mediated signaling was considerably more affected. This led to the development of the first efficacious βarr2-biased 5-HT2AR agonists 4a-b and 6e-f, βarr2 preferring, relative to lysergic acid diethylamide (LSD).
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Affiliation(s)
- Christian B M Poulie
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
| | - Eline Pottie
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Icaro A Simon
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
| | - Laura D'Andrea
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
| | | | - David E Gloriam
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Jesper L Kristensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK─2100 Copenhagen, Denmark
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11
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Joshi B, Gaur H, Hui SP, Patra C. Celsr family genes are dynamically expressed in embryonic and juvenile zebrafish. Dev Neurobiol 2022; 82:192-213. [PMID: 35213071 DOI: 10.1002/dneu.22868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/06/2022]
Abstract
The Cadherin EGF LAG seven-pass G-type receptor (Celsr) family belongs to the adhesion G-protein coupled receptor superfamily. In most vertebrates, the Celsr family has three members (CELSR1-3), whereas zebrafish display four paralogues (celsr1a, 1b, 2, 3). Although studies have shown the importance of the Celsr family in planar cell polarity, axonal guidance, and dendritic growth, the molecular mechanisms of the Celsr family regulating these cellular processes in vertebrates remain elusive. Zebrafish is an experimentally more amenable model to study vertebrate development, as zebrafish embryos develop externally, optically transparent, remain alive with malformed organs, and zebrafish is genetically similar to humans. Understanding the detailed expression pattern is the first step of exploring the functional mechanisms of the genes involved in development. Thus, we report the spatiotemporal expression pattern of Celsr family members in zebrafish nervous tissues. Our analysis shows that celsr1b and celsr2 are expressed maternally. In embryos, celsr1a, celsr1b, and celsr2 are expressed in the neural progenitors, and celsr3 is expressed in all five primary neural clusters of the brain and mantle layer of the spinal cord. In juvenile zebrafish, celsr1a, celsr1b, and celsr2 are presumably expressed in the neural progenitor enriched regions of the CNS. Therefore, the expression pattern of zebrafish Celsr family members is reminiscent of patterns described in other vertebrates or mammalian speciate. This indicates the conserved role of Celsr family genes in nervous system development and suggests zebrafish as an excellent model to explore the cellular and molecular mechanisms of Celsr family genes in vertebrate neurogenesis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bhagyashri Joshi
- Agharkar Research Institute, Developmental Biology, Pune, 411004, India.,Also affiliated to SP Pune University, Pune, 411007, India
| | - Himanshu Gaur
- Agharkar Research Institute, Developmental Biology, Pune, 411004, India
| | - Subhra Prakash Hui
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata, 700019, India
| | - Chinmoy Patra
- Agharkar Research Institute, Developmental Biology, Pune, 411004, India.,Also affiliated to SP Pune University, Pune, 411007, India
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12
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Rombouts FJR, Hsiao CC, Bache S, De Cleyn M, Heckmann P, Leenaerts J, Martinéz-Lamenca C, Van Brandt S, Peschiulli A, Vos A, Gijsen HJM. Modulating physicochemical properties of tetrahydropyridine-2-amine BACE1 inhibitors with electron-withdrawing groups: A systematic study. Eur J Med Chem 2022; 228:114028. [PMID: 34920170 DOI: 10.1016/j.ejmech.2021.114028] [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: 09/03/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022]
Abstract
A common challenge for medicinal chemists is to reduce the pKa of strongly basic groups' conjugate acids into a range that preserves the desired effects, usually potency and/or solubility, but avoids undesired effects like high volume of distribution (Vd), limited membrane permeation, and off-target binding to, notably, the hERG channel and monoamine receptors. We faced this challenge with a 3,4,5,6-tetrahydropyridine-2-amine scaffold harboring an amidine, a key structural component of potential inhibitors of BACE1, the rate-limiting enzyme in the production of Aβ species that make up amyloid plaques in Alzheimer's disease. In our endeavor to balance potency with desirable properties to achieve brain penetration, we introduced a diverse set of groups in beta position of the amidine that modulate logD, PSA and pKa. Given the synthetic challenge to prepare these highly functionalized warheads, we first developed a design flow including predicted physicochemical parameters which allowed us to select only the most promising candidates for synthesis. For this we evaluated a set of commercial packages to predict physicochemical properties, which can guide medicinal chemists in their endeavors to modulate pKa values of amidine and amine bases.
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Affiliation(s)
| | - Chien-Chi Hsiao
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Solène Bache
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Michel De Cleyn
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Pauline Heckmann
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Jos Leenaerts
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | | | - Sven Van Brandt
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Aldo Peschiulli
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Ann Vos
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
| | - Harrie J M Gijsen
- Janssen Research & Development, Turnhoutseweg 30, B-2340, Beerse, Belgium
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13
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Ling C, Wei X, Shen Y, Zhang H. Development and validation of multiple machine learning algorithms for the classification of G-protein-coupled receptors using molecular evolution model-based feature extraction strategy. Amino Acids 2021; 53:1705-1714. [PMID: 34562175 DOI: 10.1007/s00726-021-03080-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022]
Abstract
Machine learning is one of the most potential ways to realize the function prediction of the incremental large-scale G-protein-coupled receptors (GPCR). Prior research reveals that the key to determining the overall classification accuracy of GPCR is extracting valuable features and filtering out redundancy. To achieve a more efficient classification model, we put the feature synonym problem into consideration and create a new method based on functional word clustering and integration. Through evaluating the evolution correlation between features using the transition scores in mature molecular substitution matrices, candidate features are clustered into synonym groups. Each group of the clustered features is then integrated and represented by a unique key functional word. These retained key functional words are used to form a feature knowledge base. The original GPCR sequences are then transferred into feature vectors based on a feature re-extraction strategy according to the features in the knowledge base before the training and testing stage. We create multiple machine learning models based on Naïve Bayesian (NB), random forest (RF), support vector machine (SVM), and multi-layer perceptron (MLP) algorithms. The established model is applied to classify two public data sets containing 8354 and 12,731 GPCRs, respectively. These models achieve significant performance in almost all evaluation criteria in comparison with state-of-the art. This work demonstrated the potential of the novel feature extraction strategy and provided an effective theoretical design for the hierarchical classification of GPCRs.
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Affiliation(s)
- Cheng Ling
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaolin Wei
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yitian Shen
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Haoyu Zhang
- School of Information Engineering, Zhejiang Ocean University, Zhoushan, China.
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14
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Zhou Y, Meng J, Xu C, Liu J. Multiple GPCR Functional Assays Based on Resonance Energy Transfer Sensors. Front Cell Dev Biol 2021; 9:611443. [PMID: 34041234 PMCID: PMC8141573 DOI: 10.3389/fcell.2021.611443] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent one of the largest membrane protein families that participate in various physiological and pathological activities. Accumulating structural evidences have revealed how GPCR activation induces conformational changes to accommodate the downstream G protein or β-arrestin. Multiple GPCR functional assays have been developed based on Förster resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) sensors to monitor the conformational changes in GPCRs, GPCR/G proteins, or GPCR/β-arrestin, especially over the past two decades. Here, we will summarize how these sensors have been optimized to increase the sensitivity and compatibility for application in different GPCR classes using various labeling strategies, meanwhile provide multiple solutions in functional assays for high-throughput drug screening.
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Affiliation(s)
- Yiwei Zhou
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiyong Meng
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chanjuan Xu
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jianfeng Liu
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
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15
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Mulry E, Ray AP, Eddy MT. Production of a Human Histamine Receptor for NMR Spectroscopy in Aqueous Solutions. Biomolecules 2021; 11:632. [PMID: 33923140 PMCID: PMC8146376 DOI: 10.3390/biom11050632] [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: 03/15/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
G protein-coupled receptors (GPCRs) bind a broad array of extracellular molecules and transmit intracellular signals that initiate physiological responses. The signal transduction functions of GPCRs are inherently related to their structural plasticity, which can be experimentally observed by spectroscopic techniques. Nuclear magnetic resonance (NMR) spectroscopy in particular is an especially advantageous method to study the dynamic behavior of GPCRs. The success of NMR studies critically relies on the production of functional GPCRs containing stable-isotope labeled probes, which remains a challenging endeavor for most human GPCRs. We report a protocol for the production of the human histamine H1 receptor (H1R) in the methylotrophic yeast Pichia pastoris for NMR experiments. Systematic evaluation of multiple expression parameters resulted in a ten-fold increase in the yield of expressed H1R over initial efforts in defined media. The expressed receptor could be purified to homogeneity and was found to respond to the addition of known H1R ligands. Two-dimensional transverse relaxation-optimized spectroscopy (TROSY) NMR spectra of stable-isotope labeled H1R show well-dispersed and resolved signals consistent with a properly folded protein, and 19F-NMR data register a response of the protein to differences in efficacies of bound ligands.
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MESH Headings
- Gene Expression
- Humans
- Ligands
- Magnetic Resonance Spectroscopy/methods
- Nuclear Magnetic Resonance, Biomolecular/methods
- Protein Binding
- Protein Conformation
- Protein Engineering/methods
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/isolation & purification
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Histamine/chemistry
- Receptors, Histamine/isolation & purification
- Receptors, Histamine/metabolism
- Receptors, Histamine H1/chemistry
- Receptors, Histamine H1/isolation & purification
- Receptors, Histamine H1/metabolism
- Saccharomycetales/metabolism
- Signal Transduction
- Structure-Activity Relationship
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Affiliation(s)
| | | | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; (E.M.); (A.P.R.)
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16
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He S, Lyu F, Lou L, Liu L, Li S, Jakowitsch J, Ma Y. Anti-tumor activities of Panax quinquefolius saponins and potential biomarkers in prostate cancer. J Ginseng Res 2021; 45:273-286. [PMID: 33841008 PMCID: PMC8020356 DOI: 10.1016/j.jgr.2019.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 10/28/2019] [Accepted: 12/30/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Prostate carcinoma is the second most common cancer among men worldwide. Developing new therapeutic approaches and diagnostic biomarkers for prostate cancer (PC) is a significant need. The Chinese herbal medicine Panax quinquefolius saponins (PQS) have been reported to show anti-tumor effects. We hypothesized that PQS exhibits anti-cancer activity in human PC cells and we aimed to search for novel biomarkers allowing early diagnosis of PC. METHODS We used the human PC cell line DU145 and the prostate epithelial cell line PNT2 to perform cell viability assays, flow cytometric analysis of the cell cycle, and FACS-based apoptosis assays. Microarray-based gene expression analysis was used to display specific gene expression patterns and to search for novel biomarkers. Western blot and quantitative real-time PCR were performed to demonstrate the expression levels of multiple cancer-related genes. RESULTS Our data showed that PQS inhibited the viability of DU145 cells and induced cell cycle arrest at the G1 phase. A significant decrease in DU145 cell invasion and migration were observed after 24 h treatment by PQS. PQS up-regulated the expression levels of p21, p53, TMEM79, ACOXL, ETV5, and SPINT1 while it down-regulated the expression levels of bcl2, STAT3, FANCD2, DRD2, and TMPRSS2. CONCLUSION PQS promoted cells apoptosis and inhibited the proliferation of DU145 cells, which suggests that PQS may be effective for treating PC. TMEM79 and ACOXL were expressed significantly higher in PNT2 than in DU145 cells and could be novel biomarker candidates for PC diagnosis.
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Key Words
- ACOXL, Acyl-CoA oxidase-like protein
- Chinese medicinal herbs
- DRD2, dopamine receptor D2
- ETV5, ETS variant 5
- FACS, fluorescence-activated cell sorting
- FANCD2, fanconi anemia group D2
- PC, prostate cancer
- PQS, Panax quinquefolius saponins
- Panax quinquefolius
- Potential biomarkers
- Prostate cancer cells
- SPINT1, serine peptidase inhibitor Kunitz type 1
- STAT3, signal transducer and activator of transcription 3
- TCM, Traditional Chinese Medicine
- TMEM79, transmembrane protein 79
- TMPRSS2, transmembrane protease serine 2
- bcl2, B-cell lymphoma 2
- p21, cyclin-dependent kinase inhibitor p21
- p53, tumor suppressor p53
- qRT-PCR, quantitative real-time PCR
- saponins
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Affiliation(s)
- Shan He
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology & Immunology, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Fangqiao Lyu
- Department of Cell Biology, School of Basic Medicine, Capital Medical University, Beijing, China
| | - Lixia Lou
- The Key Laboratory of Chinese Internal Medicine of Ministry of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lu Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Songlin Li
- Department of Pharmaceutical Analysis and Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine and Jiangsu Branch of China Academy of Chinese Medical Sciences, Nanjing, China
| | - Johannes Jakowitsch
- Department of Internal Medicine, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Yan Ma
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology & Immunology, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
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17
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Longwell CK, Hanna S, Hartrampf N, Sperberg RAP, Huang PS, Pentelute BL, Cochran JR. Identification of N-Terminally Diversified GLP-1R Agonists Using Saturation Mutagenesis and Chemical Design. ACS Chem Biol 2021; 16:58-66. [PMID: 33307682 DOI: 10.1021/acschembio.0c00722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The glucagon-like peptide 1 receptor (GLP-1R) is a class B G-protein coupled receptor (GPCR) and diabetes drug target expressed mainly in pancreatic β-cells that, when activated by its agonist glucagon-like peptide 1 (GLP-1) after a meal, stimulates insulin secretion and β-cell survival and proliferation. The N-terminal region of GLP-1 interacts with membrane-proximal residues of GLP-1R, stabilizing its active conformation to trigger intracellular signaling. The best-studied agonist peptides, GLP-1 and exendin-4, share sequence homology at their N-terminal region; however, modifications that can be tolerated here are not fully understood. In this work, a functional screen of GLP-1 variants with randomized N-terminal domains reveals new GLP-1R agonists and uncovers a pattern whereby a negative charge is preferred at the third position in various sequence contexts. We further tested this sequence-structure-activity principle by synthesizing peptide analogues where this position was mutated to both canonical and noncanonical amino acids. We discovered a highly active GLP-1 analogue in which the native glutamate residue three positions from the N-terminus was replaced with the sulfo-containing amino acid cysteic acid (GLP-1-CYA). The receptor binding and downstream signaling properties elicited by GLP-1-CYA were similar to the wild type GLP-1 peptide. Computational modeling identified a likely mode of interaction of the negatively charged side chain in GLP-1-CYA with an arginine on GLP-1R. This work highlights a strategy of combinatorial peptide screening coupled with chemical exploration that could be used to generate novel agonists for other receptors with peptide ligands.
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Affiliation(s)
- Chelsea K. Longwell
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, California 94305, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - R. Andres Parra Sperberg
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jennifer R. Cochran
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Shriram Center, 443 Via Ortega, Stanford, California 94305, United States
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18
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Corin K, Tegler LT, Koutsopoulos S. G-Protein-Coupled Receptor Expression and Purification. Methods Mol Biol 2021; 2178:439-467. [PMID: 33128765 DOI: 10.1007/978-1-0716-0775-6_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
G-protein-coupled receptors (GPCRs) are integral proteins of the cell membrane and are directly involved in the regulation of many biological functions and in drug targeting. However, our knowledge of GPCRs' structure and function remains limited. The first bottleneck in GPCR studies is producing sufficient quantities of soluble, functional, and stable receptors. Currently, GPCR production largely depends on the choice of the host system and the type of detergent used to extract the GPCR from the cell membrane and stabilize the protein outside the membrane bilayer. Here, we present three protocols that we employ in our lab to produce and solubilize stable GPCRs: (1) cell-free in vitro translation, (2) HEK cells, and (3) Escherichia coli. Stable receptors can be purified using immunoaffinity chromatography and gel filtration, and can be analyzed with standard biophysical techniques and biochemical assays.
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Affiliation(s)
- Karolina Corin
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Lotta T Tegler
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sotirios Koutsopoulos
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Rajda K, Podlewska S. Similar, or dissimilar, that is the question. How different are methods for comparison of compounds similarity? Comput Biol Chem 2020; 88:107367. [PMID: 32956952 DOI: 10.1016/j.compbiolchem.2020.107367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/13/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Comparison of compounds similarity is one of the main strategies of virtual screening protocols. Both similarity and dissimilarity concepts are of great importance during the search for new active compounds. Similarity is important due to the assumption that underlies the process of searching for new drug candidates: structurally similar compounds should induce similar biological response. On the other hand, we are also interested in dissimilarity, as we usually aim to find structurally novel ligands. In the study, we compared several approaches of evaluating compound similarity. Various representations and metrics were applied and we indicated the rate of variation of the results that can occur when shifting from one strategy to another. We compared both general similarity of datasets using different approaches, as well as examined the changes in the set of nearest neighbors when changing one compound representation into another, and the influence of representation/metric settings on the clustering outcome. We hope that the study will be of great help during the preparation of virtual screening experiments, stressing the need for careful selection of the way, the compound similarity is assessed. The differences in the results that can be obtained via the application of particular strategy can significantly influence the outcome of comparison studies; therefore, its settings should be carefully selected beforerunning the comparison.
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Affiliation(s)
- Krzysztof Rajda
- Wroclaw University of Science and Technology, Faculty of Computer Science and Management, 50-371 Wrocław, I. Łukasiewicza Street 5, Poland
| | - Sabina Podlewska
- Jagiellonian University Medical College, Department of Technology and Biotechnology of Drugs, 30-688 Kraków, 9 Medyczna Street, Poland; Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 31-343 Kraków, Smętna Street 12, Poland.
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20
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Parisi D, Adasme MF, Sveshnikova A, Bolz SN, Moreau Y, Schroeder M. Drug repositioning or target repositioning: A structural perspective of drug-target-indication relationship for available repurposed drugs. Comput Struct Biotechnol J 2020; 18:1043-1055. [PMID: 32419905 PMCID: PMC7215100 DOI: 10.1016/j.csbj.2020.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 12/18/2022] Open
Abstract
Drug repositioning aims to find new indications for existing drugs in order to reduce drug development cost and time. Currently,there are numerous stories of successful drug repositioning that have been reported and many repurposed drugs are already available on the market. Although drug repositioning is often a product of serendipity, repositioning opportunities can be uncovered systematically. There are three systematic approaches to drug repositioning: disease-centric approach, target-centric and drug-centric. Disease-centric approaches identify close relationships between an old and a new indication. A target-centric approach links a known target and its established drug to a new indication. Lastly, a drug-centric approach connects a known drug to a new target and its associated indication. These three approaches differ in their potential and their limitations, but above all else, in the required start information and computing power. This raises the question of which approach prevails in current drug discovery and what that implies for future developments. To address this question, we systematically evaluated over 100 drugs, 200 target structures and over 300 indications from the Drug Repositioning Database. Each analyzed case was classified as one of the three repositioning approaches. For the majority of cases (more than 60%) the disease-centric definition was assigned. Almost 30% of the cases were classified as target-centric and less than 10% as drug-centric approaches. We concluded that, despite the use of umbrella term “drug” repositioning, disease- and target-centric approaches have dominated the field until now. We propose the use of drug-centric approaches while discussing reasons, such as structure-based repositioning techniques, to exploit the full potential of drug-target-disease connections.
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Affiliation(s)
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Anastasia Sveshnikova
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | | | - Yves Moreau
- ESAT-STADIUS, KU Leuven, B-3001 Heverlee, Belgium
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
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21
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Abstract
The privileged substructure (PS) and activity cliff (AC) concepts are popular in pharmaceutical research. PSs have been empirically identified as preferred building blocks for target-class-directed generation of active compounds. Although some PSs are controversially viewed, they continue to receive much attention in drug discovery. ACs are formed by structurally similar active compounds with large potency differences and thus capture structure-activity relationship (SAR) discontinuity and reveal SAR determinants. So far, the PS and AC concepts have not been investigated in context. We have systematically explored ACs formed by compounds containing different PSs (PS-ACs). Such ACs were frequently identified in different series of compounds. PS-ACs were thoroughly characterized and compared to ACs formed by other compounds. The analysis revealed differences in AC formation between PSs. For example, individual PSs with an unusually high proportion of AC-forming compounds were identified. Furthermore, PS-AC network analysis identified clusters of ACs containing the same PS in different compound structure contexts with activity against different targets. From such PS-AC clusters, target-specific SAR information for PSs in different structural environments can be extracted.
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Affiliation(s)
- Huabin Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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22
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Chahal V, Nirwan S, Kakkar R. Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2019-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.
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23
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Cao C, Sun L, Du H, Moural TW, Bai H, Liu P, Zhu F. Physiological functions of a methuselah-like G protein coupled receptor in Lymantria dispar Linnaeus. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 160:1-10. [PMID: 31519242 DOI: 10.1016/j.pestbp.2019.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/13/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Insect G protein coupled receptors (GPCRs) have been identified as a highly attractive target for new generation insecticides discovery due to their critical physiological functions. However, few insect GPCRs have been functionally characterized. Here, we cloned the full length of a methuselah-like GPCR gene (Ldmthl1) from the Asian gypsy moth, Lymantria dispar. We then characterized the secondary and tertiary structures of Ldmthl1. We also predicted the global structure of this insect GPCR protein which is composed of three major domains. RNA interference of Ldmthl1 resulted in a reduction of gypsy moths' resistance to deltamethrin and suppressed expression of downstream stress-associated genes, such as P450s, glutathione S transferases, and heat shock proteins. The function of Ldmthl1 was further investigated using transgenic lines of Drosophila melanogaster. Drosophila with overexpression of Ldmthl1 showed significantly longer lifespan than control flies. Taken together, our studies revealed that the physiological functions of Ldmthl1 in L. dispar are associated with longevity and resistance to insecticide stresses. Potentially, Ldmthl1 can be used as a target for new insecticide discovery in order to manage this notorious forest pest.
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Affiliation(s)
- Chuanwang Cao
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Lili Sun
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Hui Du
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Timothy W Moural
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Peng Liu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
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Mohamed R, Janke R, Guo W, Cao Y, Zhou Y, Zheng W, Babaahmadi-Rezaei H, Xu S, Kamato D, Little PJ. GPCR transactivation signalling in vascular smooth muscle cells: role of NADPH oxidases and reactive oxygen species. VASCULAR BIOLOGY (BRISTOL, ENGLAND) 2019; 1:R1-R11. [PMID: 32923966 PMCID: PMC7439842 DOI: 10.1530/vb-18-0004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 07/23/2019] [Indexed: 02/02/2023]
Abstract
The discovery and extension of G-protein-coupled receptor (GPCR) transactivation-dependent signalling has enormously broadened the GPCR signalling paradigm. GPCRs can transactivate protein tyrosine kinase receptors (PTKRs) and serine/threonine kinase receptors (S/TKRs), notably the epidermal growth factor receptor (EGFR) and transforming growth factor-β type 1 receptor (TGFBR1), respectively. Initial comprehensive mechanistic studies suggest that these two transactivation pathways are distinct. Currently, there is a focus on GPCR inhibitors as drug targets, and they have proven to be efficacious in vascular diseases. With the broadening of GPCR transactivation signalling, it is therefore important from a therapeutic perspective to find a common transactivation pathway of EGFR and TGFBR1 that can be targeted to inhibit complex pathologies activated by the combined action of these receptors. Reactive oxygen species (ROS) are highly reactive molecules and they act as second messengers, thus modulating cellular signal transduction pathways. ROS are involved in different mechanisms of GPCR transactivation of EGFR. However, the role of ROS in GPCR transactivation of TGFBR1 has not yet been studied. In this review, we will discuss the involvement of ROS in GPCR transactivation-dependent signalling.
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Affiliation(s)
- Raafat Mohamed
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland, Australia
- Department of Basic Sciences, College of Dentistry, University of Mosul, Mosul, Iraq
| | - Reearna Janke
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Wanru Guo
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Yingnan Cao
- Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou, China
| | - Ying Zhou
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Wenhua Zheng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Hossein Babaahmadi-Rezaei
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Atherosclerosis Research Center, Ahvaz, Iran
| | - Suowen Xu
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Danielle Kamato
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland, Australia
- Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou, China
| | - Peter J Little
- School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Woolloongabba, Queensland, Australia
- Department of Pharmacy, Xinhua College of Sun Yat-sen University, Guangzhou, China
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Kroon T, Dawitz J, Kramvis I, Anink J, Obermayer J, Verhoog MB, Wilbers R, Goriounova NA, Idema S, Baayen JC, Aronica E, Mansvelder HD, Meredith RM. Group I mGluR-Mediated Activation of Martinotti Cells Inhibits Local Cortical Circuitry in Human Cortex. Front Cell Neurosci 2019; 13:315. [PMID: 31354435 PMCID: PMC6637283 DOI: 10.3389/fncel.2019.00315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/27/2019] [Indexed: 11/13/2022] Open
Abstract
Group I metabotropic glutamate receptors (mGluRs) mediate a range of signaling and plasticity processes in the brain and are of growing importance as potential therapeutic targets in clinical trials for neuropsychiatric and neurodevelopmental disorders (NDDs). Fundamental knowledge regarding the functional effects of mGluRs upon pyramidal neurons and interneurons is derived largely from rodent brain, and their effects upon human neurons are predominantly untested. We therefore addressed how group I mGluRs affect microcircuits in human neocortex. We show that activation of group I mGluRs elicits action potential firing in Martinotti cells, which leads to increased synaptic inhibition onto neighboring neurons. Some other interneurons, including fast-spiking interneurons, are depolarized but do not fire action potentials in response to group I mGluR activation. Furthermore, we confirm the existence of group I mGluR-mediated depression of excitatory synapses in human pyramidal neurons. We propose that the strong increase in inhibition and depression of excitatory synapses onto layer 2/3 pyramidal neurons upon group I mGluR activation likely results in a shift in the balance between excitation and inhibition in the human cortical network.
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Affiliation(s)
- Tim Kroon
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Julia Dawitz
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Ioannis Kramvis
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Jasper Anink
- Department of Neuropathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Stichting Epilepsie Instellingen Nederland, Heemstede, Netherlands
| | - Joshua Obermayer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Matthijs B. Verhoog
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Natalia A. Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Sander Idema
- Department of Neurosurgery, VU University Medical Center, Amsterdam, Netherlands
| | - Johannes C. Baayen
- Department of Neurosurgery, VU University Medical Center, Amsterdam, Netherlands
| | - Eleonora Aronica
- Department of Neuropathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Stichting Epilepsie Instellingen Nederland, Heemstede, Netherlands
| | - Huibert D. Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
| | - Rhiannon M. Meredith
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, Netherlands
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26
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Sun L, Liu P, Zhang C, Du H, Wang Z, Moural TW, Zhu F, Cao C. Ocular Albinism Type 1 Regulates Deltamethrin Tolerance in Lymantria dispar and Drosophila melanogaster. Front Physiol 2019; 10:766. [PMID: 31275171 PMCID: PMC6594220 DOI: 10.3389/fphys.2019.00766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 02/04/2023] Open
Abstract
The ocular albinism type 1 (OA1), a pigment cell-specific integral membrane glycoprotein, is a member of the G-protein-coupled receptor (GPCR) superfamily that binds to heterotrimeric G proteins in mammalian cells. We aimed to characterize the physiological functions an insect OA1 from Lymantria dispar (LdOA1) employs in the regulation of insecticide tolerance. In the present study, we investigated the roles of LdOA1 in response to deltamethrin exposure in both L. dispar and Drosophila melanogaster. LdOA1 was expressed at the lowest level during the 4th instar stage, while LdOA1 was significantly upregulated in the 5th instar and male stages. Knockdown of LdOA1 by injecting dsRNA of LdOA1 into gypsy moth larvae caused a 4.80-fold higher mortality than in control larvae microinjected with dsRNA of GFP under deltamethrin stress. Nine out of 11 L. dispar CYP genes were significantly downregulated under deltamethrin stress in LdOA1 silenced larvae as compared to control larvae. Moreover, the LdOA1 gene was successfully overexpressed in D. melanogaster using transgenic technique. The deltamethrin contact assay showed that the LdOA1 overexpression in flies significantly enhanced the tolerance to deltamethrin compared to the control flies. Furthermore, the downstream Drosophila CYP genes were upregulated in the LdOA1 overexpression flies, suggesting LdOA1 may play a master switch role in P450-mediated metabolic detoxification. This study is the first report of an insect OA1 gene regulating insecticide tolerance and potentially playing a role in the regulation of downstream cytochrome P450 expression. These results contribute to the future development of novel insecticides targeting insect GPCRs.
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Affiliation(s)
- Lili Sun
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Peng Liu
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Chenshu Zhang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Hui Du
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Zhiying Wang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
| | - Timothy W Moural
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Chuanwang Cao
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin, China
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Acúrcio RC, Scomparin A, Satchi‐Fainaro R, Florindo HF, Guedes RC. Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rita C. Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Anna Scomparin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Helena F. Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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Raschka S. Automated discovery of GPCR bioactive ligands. Curr Opin Struct Biol 2019; 55:17-24. [PMID: 30909105 DOI: 10.1016/j.sbi.2019.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
Abstract
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Because of the involvement of GPCRs in various signaling pathways and physiological roles, the identification of endogenous ligands as well as designing novel drugs is of high interest to the research and medical communities. Along with highlighting the recent advances in structure-based ligand discovery, including docking and molecular dynamics, this article focuses on the latest advances for automating the discovery of bioactive ligands using machine learning. Machine learning is centered around the development and applications of algorithms that can learn from data automatically. Such an approach offers immense opportunities for bioactivity prediction as well as quantitative structure-activity relationship studies. This review describes the most recent and successful applications of machine learning for bioactive ligand discovery, concluding with an outlook on deep learning methods that are capable of automatically extracting salient information from structural data as a promising future direction for rapid and efficient bioactive ligand discovery.
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Affiliation(s)
- Sebastian Raschka
- Department of Statistics, University of Wisconsin-Madison, 1300 Medical Sciences Center, Madison, WI 53706, USA.
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29
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Prediction of drug-target interaction by integrating diverse heterogeneous information source with multiple kernel learning and clustering methods. Comput Biol Chem 2019; 78:460-467. [DOI: 10.1016/j.compbiolchem.2018.11.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 02/08/2023]
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Affiliation(s)
- Oliver Plettenburg
- Institute of Medicinal ChemistryHelmholtz Zentrum München Ingolstädter Landstr. 1 D-85764 Neuherberg Germany
- Institute of Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ)Leibniz Universität Hannover Schneiderberg 1b D-30167 Hannover Germany
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31
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McPherson A, Larson SB. The X-ray crystal structure of human endothelin 1, a polypeptide hormone regulator of blood pressure. Acta Crystallogr F Struct Biol Commun 2019; 75:47-53. [PMID: 30605125 PMCID: PMC6317455 DOI: 10.1107/s2053230x18016011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/12/2018] [Indexed: 11/10/2022] Open
Abstract
Human endothelin is a 21-amino-acid polypeptide, constrained by two intra-chain disulfide bridges, that is made by endothelial cells. It is the most potent vasoconstrictor in the body and is crucially important in the regulation of blood pressure. It plays a major role in a host of medical conditions, including hypertension, diabetes, stroke and cancer. Endothelin was crystallized 28 years ago in the putative space group P6122, but the structure was never successfully solved by X-ray diffraction. Using X-ray diffraction data from 1992, the structure has now been solved. Assuming a unit cell belonging to space group P61 and a twin fraction of 0.28, a solution emerged with two, almost identical, closely associated molecules in the asymmetric unit. Although the data extended to beyond 1.8 Å resolution, a model containing 25 waters was refined to 1.85 Å resolution with an R of 0.216 and an Rfree of 0.284. The disulfide-constrained `core' of the molecule, amino-acid residues 1-15, has a main-chain conformation that is essentially the same as endothelin when bound to its receptor, but many side-chain rotamers are different. The carboxy-terminal `tail' comprising amino-acid residues 16-21 is extended as when receptor-bound, but it exhibits a different conformation with respect to the `core'. The dimer that comprises the asymmetric unit is maintained almost exclusively by hydrophobic interactions and may be stable in an aqueous medium.
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Affiliation(s)
- Alexander McPherson
- Molecular Biology and Biochemistry, University of California Irvine, McGaugh Hall, Irvine, CA 92697-3900, USA
| | - Steven B. Larson
- Molecular Biology and Biochemistry, University of California Irvine, McGaugh Hall, Irvine, CA 92697-3900, USA
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32
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Zhang AC, Gu Y, Han Y, Mei Z, Chiu YJ, Geng L, Cho SH, Lo YH. Computational cell analysis for label-free detection of cell properties in a microfluidic laminar flow. Analyst 2018; 141:4142-50. [PMID: 27163941 DOI: 10.1039/c6an00295a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although a flow cytometer, being one of the most popular research and clinical tools for biomedicine, can analyze cells based on the cell size, internal structures such as granularity, and molecular markers, it provides little information about the physical properties of cells such as cell stiffness and physical interactions between the cell membrane and fluid. In this paper, we propose a computational cell analysis technique using cells' different equilibrium positions in a laminar flow. This method utilizes a spatial coding technique to acquire the spatial position of the cell in a microfluidic channel and then uses mathematical algorithms to calculate the ratio of cell mixtures. Most uniquely, the invented computational cell analysis technique can unequivocally detect the subpopulation of each cell type without labeling even when the cell type shows a substantial overlap in the distribution plot with other cell types, a scenario limiting the use of conventional flow cytometers and machine learning techniques. To prove this concept, we have applied the computation method to distinguish live and fixed cancer cells without labeling, count neutrophils from human blood, and distinguish drug treated cells from untreated cells. Our work paves the way for using computation algorithms and fluidic dynamic properties for cell classification, a label-free method that can potentially classify over 200 types of human cells. Being a highly cost-effective cell analysis method complementary to flow cytometers, our method can offer orthogonal tests in companion with flow cytometers to provide crucial information for biomedical samples.
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Affiliation(s)
- Alex Ce Zhang
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, California 92093-0407, USA.
| | - Yi Gu
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, California 92093-0407, USA.
| | - Yuanyuan Han
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, California 92093-0407, USA.
| | - Zhe Mei
- Nanocellect Biomedical, Inc., San Diego, CA 92121, USA
| | - Yu-Jui Chiu
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0418, USA
| | - Lina Geng
- School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China
| | - Sung Hwan Cho
- Nanocellect Biomedical, Inc., San Diego, CA 92121, USA
| | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, California 92093-0407, USA. and Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0418, USA
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Yue Y, Xu Y, Huang L, Pan D, Bai Z, Wang L, Yang R, Yan J, Song H, Li X, Yang M. Evaluation of A Novel GLP-1R Ligand for PET Imaging of Prostate Cancer. Anticancer Agents Med Chem 2018; 19:509-514. [PMID: 30068284 DOI: 10.2174/1871520618666180801101730] [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] [Received: 10/15/2017] [Revised: 07/20/2018] [Accepted: 07/21/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glucagon-like peptide 1 receptor (GLP-1R) is an important biomarker for diagnosis and therapy of the endocrine cancers due to overexpression. Recently, in human prostate cancer cell lines the receptor was also observed, therefore it may be a potential target for the disease. 18F-Al-NOTA-MAL-Cys39- exendin-4 holds great promise for GLP-1R. Therefore, the feasibility of the 18F-labeled exendin-4 analog for prostate cancer imaging was investigated. METHODS New probe 18F-Al-NOTA-MAL-Cys39-exendin-4 was made through one-step fluorination. Prostate cancer PC3 cell xenograft model mice were established to primarily evaluate the imaging properties of the tracer via small animal PET studies in vivo. Pathological studies and Western Blots were also performed. RESULTS PC-3 prostate xenografts were clearly imaged under baseline conditions. At 30 and 60 min postinjection, the tumor uptakes were 2.90±0.41%ID/g and 2.26±0.32 %ID/g respectively. The presence of cys39-exendin-4 significantly reduced the tumor uptake to 0.82±0.10 %ID/g at 60 min p.i. Findings of ex vivo biodistribution studies were similar to those of in vivo PET imaging. The tumors to blood and muscles were significantly improved with the increase of time due to rapid clearance of the tracer from normal organs. Low levels of radioactivity were also detected in the GLP-1R positive tumor and normal organs after coinjection with excessive unlabeled peptides. Immunohistochemistry and Western Blots results confirmed that GLP-1R was widely expressed in PC-3 prostate cancers. CONCLUSION 18F-Al labeled exendin-4 analog might be a promising tracer for in vivo detecting GLP-1R positive prostate cancer with the advantage of facile synthesis and favorable pharmacokinetics. It may be useful in differential diagnosis, molecularly targeted therapy and prognosis of the cancers.
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Affiliation(s)
- Yuanyuan Yue
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Yuping Xu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Lirong Huang
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Donghui Pan
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Zhicheng Bai
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Lizhen Wang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Runlin Yang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Junjie Yan
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Huizhu Song
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, 214023, China
| | - Xiaotian Li
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450000, China
| | - Min Yang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
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Kim Y, Kim H, Lee J, Lee JK, Min SJ, Seong J, Rhim H, Tae J, Lee HJ, Choo H. Discovery of β-Arrestin Biased Ligands of 5-HT 7R. J Med Chem 2018; 61:7218-7233. [PMID: 30028132 DOI: 10.1021/acs.jmedchem.8b00642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Though many studies have been published about therapeutic potentials of selective 5-HT7R ligands, there have been few biased ligands of 5-HT7R. The development of potent and selective biased ligands of 5-HT7R would be of great help in understanding the relationship between pharmacological effects and G protein/β-arrestin signaling pathways of 5-HT7R. In order to identify 5-HT7R ligands with biased agonism, we designed and synthesized a series of tetrahydroazepine derivatives 1 and 2 with arylpyrazolo moiety or arylisoxazolo moiety. Through several biological evaluations such as binding affinity, selectivity profile, and functions in G protein and β-arrestin signaling pathways, 3-(4-chlorophenyl)-1,4,5,6,7,8-hexahydropyrazolo[3,4- d]azepine 1g was discovered as the β-arrestin biased ligand of 5-HT7R. In an electroencephalogram (EEG) test, 1g increased total non-rapid eye movement (NREM) sleep time and decreased total rapid eye movement (REM) sleep time.
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Affiliation(s)
- Youngjae Kim
- Center for Neuro-Medicine , Brain Research Institute, Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea.,Department of Chemistry , Yonsei University , Seoul 03722 , Republic of Korea
| | - Hyunguk Kim
- School of Electrical Engineering , Korea Advanced Institute of Science and Technology , Daejeon 34141 , Republic of Korea
| | - Jieon Lee
- Center for Neuro-Medicine , Brain Research Institute, Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Republic of Korea
| | - Jae Kyun Lee
- Center for Neuro-Medicine , Brain Research Institute, Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea
| | - Sun-Joon Min
- Department of Chemical & Molecular Engineering/Applied Chemistry , Hanyang University , Ansan , Gyeonggi-do 15588 , Republic of Korea
| | - Jihye Seong
- Center for Neuro-Medicine , Brain Research Institute, Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Republic of Korea.,Convergence Research Center for Diagnosis Treatment Care of Dementia , Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea
| | - Hyewhon Rhim
- Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Republic of Korea.,Center for Neuroscience , Brain Research Institute, Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea
| | - Jinsung Tae
- Department of Chemistry , Yonsei University , Seoul 03722 , Republic of Korea
| | - Hyunjoo Jenny Lee
- School of Electrical Engineering , Korea Advanced Institute of Science and Technology , Daejeon 34141 , Republic of Korea
| | - Hyunah Choo
- Center for Neuro-Medicine , Brain Research Institute, Korea Institute of Science and Technology , Seoul 02792 , Republic of Korea.,Division of Bio-Medical Science & Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Republic of Korea
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Che J, Wang Z, Sheng H, Huang F, Dong X, Hu Y, Xie X, Hu Y. Ligand-based pharmacophore model for the discovery of novel CXCR2 antagonists as anti-cancer metastatic agents. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180176. [PMID: 30109074 PMCID: PMC6083693 DOI: 10.1098/rsos.180176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/25/2018] [Indexed: 05/05/2023]
Abstract
Metastatic cancer is considered a fatal progression of cancer worldwide. It has been shown that a key player in this scenario is the CXC chemokine receptor 2 (CXCR2). To identify novel CXCR2 antagonists, a pharmacophore model was built with the HipHop program by screening a database containing compounds which were designed based on the known structure-activity relationship (SAR) of the diarylurea series CXCR2 antagonists. Compound 1a bearing the novel skeleton was selected from database screening and subjected to the in vitro biological test which showed a moderate CXCR2 antagonist potential. With further modification and exploration of SAR, compound 1e demonstrated improved CXCR2 antagonist activity with an IC50 value of 14.8 µM. Furthermore, wound healing assay using the NCI-H1299 cell line indicated that 1e showed an excellent anti-cancer metastatic effect (72% inhibition in cell migration at 50 µg ml-1).
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Affiliation(s)
- Jinxin Che
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhilong Wang
- Chinese Academy of Sciences, State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
| | - Haichao Sheng
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Feng Huang
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaowu Dong
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Youhong Hu
- Chinese Academy of Sciences, State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
| | - Xin Xie
- Chinese Academy of Sciences, State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
- Chinese Academy of Sciences, CAS Key Laboratory of Receptor Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai, People's Republic of China
- Authors for correspondence: Xin Xie e-mail:
| | - Yongzhou Hu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Authors for correspondence: Yongzhou Hu e-mail:
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Wang H, Wang J, Zhang L, Sun P, Du N, Li Y. A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method. Int J Biol Sci 2018; 14:901-906. [PMID: 29989071 PMCID: PMC6036746 DOI: 10.7150/ijbs.24327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/02/2018] [Indexed: 11/29/2022] Open
Abstract
Alpha-helical transmembrane protein (αTMP) is one of the two major categories of transmembrane protein (TMP). They are abundant existing in eukaryotic cells and involved in many biological processes. The special physicochemical properties, the structures of αTMP are hard to be experimentally solved, but αTMP's sequential segments are important to determine their conformations, so that TM-specific alignment is necessary to benefit their structure prediction. We used segment information extracted from topology structure and evolutionary information as features to implement a αTMP Segment Alignment method (TMSA). The method was trained using one non-redundant dataset and tested using another non-redundant dataset. Comparing the results to a general alignment method HHalign, TMSA achieved higher alignment accuracy, and easier to recognize the fold of αTMPs.
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Affiliation(s)
- Han Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
| | - Jingru Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
| | - Ning Du
- School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, China
| | - Yanwen Li
- School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.,Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China
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37
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Ge Y, Gu Y, Wang J, Zhang Z. Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1460-1469. [PMID: 29678469 DOI: 10.1016/j.bbamem.2018.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/24/2018] [Accepted: 04/15/2018] [Indexed: 11/19/2022]
Abstract
Sodium-coupled neutral amino acid transporter 2 (SNAT2) is a subtype of the amino acid transport system A that is widely expressed in mammalian tissues. It plays critical roles in glutamic acid-glutamine circulation, liver gluconeogenesis and other biological pathway. However, the topology of the SNAT2 amino acid transporter is unknown. Here we identified the topological structure of SNAT2 using bioinformatics analysis, Methoxy-polyethylene glycol maleimide (mPEG-Mal) chemical modification, protease cleavage assays, immunofluorescence and examination of glycosylation. Our results show that SNAT2 contains 11 transmembrane domains (TMDs) with an intracellular N terminus and an extracellular C terminus. Three N-glycosylation sites were verified at the largest extracellular loop. This model is consistent with the previous model of SNAT2 with the exception of a difference in number of glycosylation sites. This is the first time to confirm the SNAT2 membrane topology using experimental methods. Our study on SNAT2 topology provides valuable structural information of one of the solute carrier family 38 (SLC38) members.
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Affiliation(s)
- Yudan Ge
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Yanting Gu
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Jiahong Wang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Zhou Zhang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China.
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38
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Mani T, Bourguinat C, Prichard RK. G-protein-coupled receptor genes of Dirofilaria immitis. Mol Biochem Parasitol 2018; 222:6-13. [PMID: 29625152 DOI: 10.1016/j.molbiopara.2018.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/28/2018] [Accepted: 04/02/2018] [Indexed: 12/27/2022]
Abstract
The diversity and uniqueness of nematode heterotrimeric G-protein-coupled receptors (GPCRs) provides impetus for identifying ligands that can be used as therapeutics for treating diseases caused by parasitic nematode infections. In human medicine, GPCRs have represented the largest group of 'drugable' targets exploited in the market today. In the filarial nematode Dirofilaria immitis, which causes heartworm disease, the macrocyclic lactones (ML) have been used as the sole preventatives for more than 25 years and now there is confirmed ML resistance in this parasite. A novel anthelmintic emodepside, with antifilarial activity, can act on a GPCR. In view of the ML resistance, there is an urgent need to identify new drug targets and GPCRs of D. immitis may be promising receptors. Knowledge of polymorphism within the GPCR superfamily is of interest. A total of 127 GPCR genes have been identified, so far, in the genome of D. immitis. Whole genome sequencing data from four ML susceptible and four ML loss of efficacy populations was used to identify 393 polymorphic loci in 35 D. immitis GPCR genes. Out of 57 SNPs in exonic regions, 36 of them caused a change in an amino acid, out of which 2 changed the predicted secondary structure of the protein. Knowledge about GPCR genes and their polymorphism is valuable information for drug design processes. Further studies need to be carried out to more fully understand the implications of each of the SNPs identified by this study.
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Affiliation(s)
- Thangadurai Mani
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Catherine Bourguinat
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Roger K Prichard
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
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39
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Mella RM, Kortazar D, Roura-Ferrer M, Salado C, Valcárcel M, Castilla A, Villacé P. Nomad Biosensors: A New Multiplexed Technology for the Screening of GPCR Ligands. SLAS Technol 2018; 23:207-216. [PMID: 29412765 DOI: 10.1177/2472630318754828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Nomad Technology (Innoprot [Innovative Technologies in Biological Systems], Derio, Spain), a novel tool for multiplexing high-throughput cell-based G protein-coupled receptor (GPCR) assays, is described in this work. This new technology comprises a family of fluorescent biosensors called Nomad Biosensors that allow for the measurement of responses mediated by G proteins through their interactions with second-messenger transduction proteins. GPCRs are one of the largest protein families of receptors in eukaryotes, and their signaling mediates important physiological processes within cells. Thus, GPCRs are associated with a wide variety of diseases, and considered major targets in therapeutic research. Nomad constitutes a novel tool for unraveling the mechanism of GPCR signal transduction by simultaneously tracing different pathways. GPCR activation changes the structural folding of the biosensor and promotes its vesicularization, as well as an increase in the fluorescence intensity. Based on this technology, the MPXNomad cellular model was developed to discriminate between the Ca2+-mediated pathway and the cyclic adenosine monophosphate (cAMP)-mediated pathway. To validate this model, endothelin receptor B (ETBR) was coexpressed into the MPXNomad cell line and assessed with a specific agonist, an antagonist, and a chemical library of compounds. Nomad Technology optimizes the identification of novel GPCR ligands and enables the testing of large numbers of compounds.
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Affiliation(s)
- Rosa M Mella
- 1 Innoprot (Innovative Technologies in Biological Systems), Derio, Spain
| | - Danel Kortazar
- 1 Innoprot (Innovative Technologies in Biological Systems), Derio, Spain
| | | | - Clarisa Salado
- 1 Innoprot (Innovative Technologies in Biological Systems), Derio, Spain
| | - María Valcárcel
- 1 Innoprot (Innovative Technologies in Biological Systems), Derio, Spain
| | - Amaia Castilla
- 1 Innoprot (Innovative Technologies in Biological Systems), Derio, Spain
| | - Patricia Villacé
- 1 Innoprot (Innovative Technologies in Biological Systems), Derio, Spain
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40
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Xu X, Huang M, Zou X. Docking-based inverse virtual screening: methods, applications, and challenges. BIOPHYSICS REPORTS 2018; 4:1-16. [PMID: 29577065 PMCID: PMC5860130 DOI: 10.1007/s41048-017-0045-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/08/2017] [Indexed: 01/09/2023] Open
Abstract
Identifying potential protein targets for a small-compound ligand query is crucial to the process of drug development. However, there are tens of thousands of proteins in human alone, and it is almost impossible to scan all the existing proteins for a query ligand using current experimental methods. Recently, a computational technology called docking-based inverse virtual screening (IVS) has attracted much attention. In docking-based IVS, a panel of proteins is screened by a molecular docking program to identify potential targets for a query ligand. Ever since the first paper describing a docking-based IVS program was published about a decade ago, the approach has been gradually improved and utilized for a variety of purposes in the field of drug discovery. In this article, the methods employed in docking-based IVS are reviewed in detail, including target databases, docking engines, and scoring function methodologies. Several web servers developed for non-expert users are also reviewed. Then, a number of applications are presented according to different research purposes, such as target identification, side effects/toxicity, drug repositioning, drug-target network development, and receptor design. The review concludes by discussing the challenges that docking-based IVS needs to overcome to become a robust tool for pharmaceutical engineering.
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Affiliation(s)
- Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA
| | - Marshal Huang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA
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Template selection and refinement considerations for modelling aminergic GPCR-ligand complexes. J Mol Graph Model 2017; 76:488-503. [PMID: 28818718 DOI: 10.1016/j.jmgm.2017.07.030] [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] [Received: 04/23/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are important targets for development of drugs for the treatment of many diseases. However, crystal structures are available for only a small fraction of these membrane bound proteins. Accurate homology models will provide opportunities for effective drug design targeting GPCRs. Recently, several serotonin receptor crystal structures were solved and needed to be evaluated as potential templates. In the first part of this work different measures of similarity in template selection were explored and methods for homology modelling, docking and refinement of aminergic GPCR-ligand complexes were developed and evaluated by comparing models of the D3-R/eticlopride complex with the crystal structure. Homology models of the three α1 adrenergic receptor subtypes and of a serotonin receptor subtype were then constructed using these methods These models were evaluated by docking a range of antagonists into them.
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42
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Zemella A, Grossmann S, Sachse R, Sonnabend A, Schaefer M, Kubick S. Qualifying a eukaryotic cell-free system for fluorescence based GPCR analyses. Sci Rep 2017. [PMID: 28623260 PMCID: PMC5473880 DOI: 10.1038/s41598-017-03955-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Membrane proteins are key elements in cell-mediated processes. In particular, G protein-coupled receptors (GPCRs) have attracted increasing interest since they affect cellular signaling. Furthermore, mutations in GPCRs can cause acquired and inheritable diseases. Up to date, there still exist a number of GPCRs that has not been structurally and functionally analyzed due to difficulties in cell-based membrane protein production. A promising approach for membrane protein synthesis and analysis has emerged during the last years and is known as cell-free protein synthesis (CFPS). Here, we describe a simply portable method to synthesize GPCRs and analyze their ligand-binding properties without the requirement of additional supplements such as liposomes or nanodiscs. This method is based on eukaryotic cell lysates containing translocationally active endogenous endoplasmic reticulum-derived microsomes where the insertion of GPCRs into biologically active membranes is supported. In this study we present CFPS in combination with fast fluorescence-based screening methods to determine the localization, orientation and ligand-binding properties of the endothelin B (ET-B) receptor upon expression in an insect-based cell-free system. To determine the functionality of the cell-free synthesized ET-B receptor, we analyzed the binding of its ligand endothelin-1 (ET-1) in a qualitative fluorescence-based assay and in a quantitative radioligand binding assay.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Solveig Grossmann
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Rita Sachse
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Michael Schaefer
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany.
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43
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Andersson J, Knobloch JJ, Perkins MV, Holt SA, Köper I. Synthesis and Characterization of Novel Anchorlipids for Tethered Bilayer Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4444-4451. [PMID: 28387116 DOI: 10.1021/acs.langmuir.7b00778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Tethered bilayer lipid membranes are versatile solid-supported model membrane systems. Core to these systems is an anchorlipid that covalently links a lipid bilayer to a support. The molecular structure of these lipids can have a significant impact on the properties of the resulting bilayer. Here, the synthesis of anchorlipids containing ester groups in the tethering part is described. The lipids are used to form bilayer membranes, and the resulting structures are compared with membranes formed using conventional anchorlipids or sparsely tethered membranes. All membranes showed good electrical sealing properties; the disulphide-terminated anchorlipids could be used in a sparsely tethered system without significantly reducing the sealing properties of the lipid bilayers. The sparsely tethered systems also allowed for higher ion transport across the membrane, which is in good correlation with higher hydration of the spacer region as seen by neutron scattering.
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Affiliation(s)
- Jakob Andersson
- Flinders Centre for Nanoscalce Science and Technology and School of Chemical and Physical Sciences, Flinders University , Adelaide 5042, Australia
| | - Jacqueline J Knobloch
- Flinders Centre for Nanoscalce Science and Technology and School of Chemical and Physical Sciences, Flinders University , Adelaide 5042, Australia
| | - Michael V Perkins
- Flinders Centre for Nanoscalce Science and Technology and School of Chemical and Physical Sciences, Flinders University , Adelaide 5042, Australia
| | - Stephen A Holt
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation , Locked Bag 2001, Kirrawee DC, New South Wales 2234, Australia
| | - Ingo Köper
- Flinders Centre for Nanoscalce Science and Technology and School of Chemical and Physical Sciences, Flinders University , Adelaide 5042, Australia
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Kalxdorf M, Gade S, Eberl HC, Bantscheff M. Monitoring Cell-surface N-Glycoproteome Dynamics by Quantitative Proteomics Reveals Mechanistic Insights into Macrophage Differentiation. Mol Cell Proteomics 2017; 16:770-785. [PMID: 28336715 DOI: 10.1074/mcp.m116.063859] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/17/2017] [Indexed: 11/06/2022] Open
Abstract
The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival, and cell identity. As such, it is a prominent target for pharmacological intervention. The relatively low abundance of this subproteome in conjunction with challenging extractability and solubility still hampers its comprehensive analysis. Here, we combined a chemical glycoprotein-tagging strategy with mass spectrometry to enable comprehensive analysis of the cell-surface glycoproteome. To benchmark this workflow and to provide guidance for cell line selection for functional experiments, we generated an inventory of the N-linked cell-surface glycoproteomes of 15 standard laboratory human cell lines and three primary lymphocytic cell types. On average, about 900 plasma membrane and secreted proteins were identified per experiment, including more than 300 transporters and ion channels. Primary cells displayed distinct expression of surface markers and transporters underpinning the importance of carefully validating model cell lines selected for the study of cell surface-mediated processes. To monitor dynamic changes of the cell-surface proteome in a highly multiplexed experiment, we employed an isobaric mass tag-based chemical labeling strategy. This enabled the time-resolved analysis of plasma membrane protein presentation during differentiation of the monocytic suspension cell line THP-1 into macrophage-like adherent cells. Time-dependent changes observed in membrane protein presentation reflect functional remodeling during the phenotypic transition in three distinct phases: rapid surface presentation and secretion of proteins from intracellular pools concurrent with rapid internalization of no longer needed proteins and finally delayed presentation of newly synthesized macrophage markers. Perturbation of this process using marketed receptor tyrosine kinase inhibitors revealed dasatinib to severely compromise macrophage differentiation due to an off-target activity. This finding suggests that dynamic processes can be highly vulnerable to drug treatment and should be monitored more rigorously to identify adverse drug effects.
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Affiliation(s)
- Mathias Kalxdorf
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - H Christian Eberl
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- From ‡Cellzome, A GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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45
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Press O, Zvagelsky T, Vyazmensky M, Kleinau G, Engel S. Construction of Structural Mimetics of the Thyrotropin Receptor Intracellular Domain. Biophys J 2016; 111:2620-2628. [PMID: 28002738 PMCID: PMC5192603 DOI: 10.1016/j.bpj.2016.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 11/02/2016] [Indexed: 10/20/2022] Open
Abstract
The signaling of a G protein-coupled receptor (GPCR) is dictated by the complementary responsiveness of interacting intracellular effectors such as G proteins. Many GPCRs are known to couple to more than one G protein subtype and induce a multitude of signaling pathways, although the in vivo relevance of particular pathways is mostly unrecognized. Dissecting GPCR signaling in terms of the pathways that are activated will boost our understanding of the molecular fundamentals of hormone action. The structural determinants governing the selectivity of GPCR/G protein coupling, however, remain obscure. Here, we describe the design of soluble GPCR mimetics to study the details of the interplay between G-proteins and activators. We constructed functional mimetics of the intracellular domain of a model GPCR, the thyrotropin receptor. We based the construction on a unique scaffold, 6-Helix, an artificial protein that was derived from the elements of the trimer-of-hairpins structure of HIV gp41 and represents a bundle of six α-helices. The 6-Helix scaffold, which endowed the substituted thyrotropin receptor intracellular domain elements with spatial constraints analogous to those found in native receptors, enabled the reconstitution of a microdomain that consists of intracellular loops 2 and 3, and is capable of binding and activating Gα-(s). The 6-Helix-based mimetics could be used as a platform to study the molecular basis of GPCR/G protein recognition. Such knowledge could help investigators develop novel therapeutic strategies for GPCR-related disorders by targeting the GPCR/G protein interfaces and counteracting cellular dysfunctions via focused tuning of GPCR signaling.
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Affiliation(s)
- Olga Press
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tatiana Zvagelsky
- Department of Chemistry, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maria Vyazmensky
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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46
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Quo vadis G protein-coupled receptor ligands? A tool for analysis of the emergence of new groups of compounds over time. Bioorg Med Chem Lett 2016; 27:626-631. [PMID: 27993519 DOI: 10.1016/j.bmcl.2016.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/24/2022]
Abstract
Exponential growth in the number of compounds with experimentally verified activity towards particular target has led to the emergence of various databases gathering data on biological activity. In this study, the ligands of family A of the G Protein-Coupled Receptors that are collected in the ChEMBL database were examined, and special attention was given to serotonin receptors. Sets of compounds were examined in terms of their appearance over time, they were mapped to the chemical space of drugs deposited in DrugBank, and the emergence of structurally new clusters of compounds was indicated. In addition, a tool for detailed analysis of the obtained visualizations was prepared and made available online at http://chem.gmum.net/vischem, which enables the investigation of chemical structures while referring to particular data points depicted in the figures and changes in compounds datasets over time.
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47
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Food-Derived Natural Compounds for Pain Relief in Neuropathic Pain. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7917528. [PMID: 27891521 PMCID: PMC5116524 DOI: 10.1155/2016/7917528] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/29/2016] [Accepted: 10/16/2016] [Indexed: 12/17/2022]
Abstract
Neuropathic pain, defined as pain caused by a lesion or disease of the somatosensory nervous system, is characterized by dysesthesia, hyperalgesia, and allodynia. The number of patients with this type of pain has increased rapidly in recent years. Yet, available neuropathic pain medicines have undesired side effects, such as tolerance and physical dependence, and do not fully alleviate the pain. The mechanisms of neuropathic pain are still not fully understood. Injury causes inflammation and immune responses and changed expression and activity of receptors and ion channels in peripheral nerve terminals. Additionally, neuroinflammation is a known factor in the development and maintenance of neuropathic pain. During neuropathic pain development, the C-C motif chemokine receptor 2 (CCR2) acts as an important signaling mediator. Traditional plant treatments have been used throughout the world for treating diseases. We and others have identified food-derived compounds that alleviate neuropathic pain. Here, we review the natural compounds for neuropathic pain relief, their mechanisms of action, and the potential benefits of natural compounds with antagonistic effects on GPCRs, especially those containing CCR2, for neuropathic pain treatment.
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48
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Sridharan R, Connelly SM, Naider F, Dumont ME. Variable Dependence of Signaling Output on Agonist Occupancy of Ste2p, a G Protein-coupled Receptor in Yeast. J Biol Chem 2016; 291:24261-24279. [PMID: 27646004 DOI: 10.1074/jbc.m116.733006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/04/2016] [Indexed: 12/22/2022] Open
Abstract
We report here on the relationship between ligand binding and signaling responses in the yeast pheromone response pathway, a well characterized G protein-coupled receptor system. Responses to agonist (α-factor) by cells expressing widely varying numbers of receptors depend primarily on fractional occupancy, not the absolute number of agonist-bound receptors. Furthermore, the concentration of competitive antagonist required to inhibit α-factor-dependent signaling is more than 10-fold higher than predicted based on the known ligand affinities. Thus, responses to a particular number of agonist-bound receptors can vary greatly, depending on whether there are unoccupied or antagonist-bound receptors present on the same cell surface. This behavior does not appear to be due to pre-coupling of receptors to G protein or to the Sst2p regulator of G protein signaling. The results are consistent with a signaling response that is determined by the integration of positive signals from agonist-occupied receptors and inhibitory signals from unoccupied receptors, where the inhibitory signals can be diminished by antagonist binding.
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Affiliation(s)
- Rajashri Sridharan
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Sara M Connelly
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Fred Naider
- the Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, New York 10314, and.,the Ph.D. Programs in Biochemistry and Chemistry, Graduate Center of the City University of New York, New York, New York 10016
| | - Mark E Dumont
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642,
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49
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Wirngo FE, Lambert MN, Jeppesen PB. The Physiological Effects of Dandelion (Taraxacum Officinale) in Type 2 Diabetes. Rev Diabet Stud 2016; 13:113-131. [PMID: 28012278 DOI: 10.1900/rds.2016.13.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The tremendous rise in the economic burden of type 2 diabetes (T2D) has prompted a search for alternative and less expensive medicines. Dandelion offers a compelling profile of bioactive components with potential anti-diabetic properties. The Taraxacum genus from the Asteraceae family is found in the temperate zone of the Northern hemisphere. It is available in several areas around the world. In many countries, it is used as food and in some countries as therapeutics for the control and treatment of T2D. The anti-diabetic properties of dandelion are attributed to bioactive chemical components; these include chicoric acid, taraxasterol (TS), chlorogenic acid, and sesquiterpene lactones. Studies have outlined the useful pharmacological profile of dandelion for the treatment of an array of diseases, although little attention has been paid to the effects of its bioactive components on T2D to date. This review recapitulates previous work on dandelion and its potential for the treatment and prevention of T2D, highlighting its anti-diabetic properties, the structures of its chemical components, and their potential mechanisms of action in T2D. Although initial research appears promising, data on the cellular impact of dandelion are limited, necessitating further work on clonal β-cell lines (INS-1E), α-cell lines, and human skeletal cell lines for better identification of the active components that could be of use in the control and treatment of T2D. In fact, extensive in-vitro, in-vivo, and clinical research is required to investigate further the pharmacological, physiological, and biochemical mechanisms underlying the effects of dandelion-derived compounds on T2D.
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Affiliation(s)
- Fonyuy E Wirngo
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000 C, Denmark
| | - Max N Lambert
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000 C, Denmark
| | - Per B Jeppesen
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000 C, Denmark
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Andersson J, Köper I. Tethered and Polymer Supported Bilayer Lipid Membranes: Structure and Function. MEMBRANES 2016; 6:E30. [PMID: 27249006 PMCID: PMC4931525 DOI: 10.3390/membranes6020030] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 11/30/2022]
Abstract
Solid supported bilayer lipid membranes are model systems to mimic natural cell membranes in order to understand structural and functional properties of such systems. The use of a model system allows for the use of a wide variety of analytical tools including atomic force microscopy, impedance spectroscopy, neutron reflectometry, and surface plasmon resonance spectroscopy. Among the large number of different types of model membranes polymer-supported and tethered lipid bilayers have been shown to be versatile and useful systems. Both systems consist of a lipid bilayer, which is de-coupled from an underlying support by a spacer cushion. Both systems will be reviewed, with an emphasis on the effect that the spacer moiety has on the bilayer properties.
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Affiliation(s)
- Jakob Andersson
- Flinders Centre for Nanoscale Science and Technology, School of Chemical and Physical Sciences, Flinders University, Adelaide SA 5001, Australia.
| | - Ingo Köper
- Flinders Centre for Nanoscale Science and Technology, School of Chemical and Physical Sciences, Flinders University, Adelaide SA 5001, Australia.
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