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Sadybekov AA, Sadybekov AV, Liu Y, Iliopoulos-Tsoutsouvas C, Huang XP, Pickett J, Houser B, Patel N, Tran NK, Tong F, Zvonok N, Jain MK, Savych O, Radchenko DS, Nikas SP, Petasis NA, Moroz YS, Roth BL, Makriyannis A, Katritch V. Synthon-based ligand discovery in virtual libraries of over 11 billion compounds. Nature 2022; 601:452-459. [PMID: 34912117 PMCID: PMC9763054 DOI: 10.1038/s41586-021-04220-9] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022]
Abstract
Structure-based virtual ligand screening is emerging as a key paradigm for early drug discovery owing to the availability of high-resolution target structures1-4 and ultra-large libraries of virtual compounds5,6. However, to keep pace with the rapid growth of virtual libraries, such as readily available for synthesis (REAL) combinatorial libraries7, new approaches to compound screening are needed8,9. Here we introduce a modular synthon-based approach-V-SYNTHES-to perform hierarchical structure-based screening of a REAL Space library of more than 11 billion compounds. V-SYNTHES first identifies the best scaffold-synthon combinations as seeds suitable for further growth, and then iteratively elaborates these seeds to select complete molecules with the best docking scores. This hierarchical combinatorial approach enables the rapid detection of the best-scoring compounds in the gigascale chemical space while performing docking of only a small fraction (<0.1%) of the library compounds. Chemical synthesis and experimental testing of novel cannabinoid antagonists predicted by V-SYNTHES demonstrated a 33% hit rate, including 14 submicromolar ligands, substantially improving over a standard virtual screening of the Enamine REAL diversity subset, which required approximately 100 times more computational resources. Synthesis of selected analogues of the best hits further improved potencies and affinities (best inhibitory constant (Ki) = 0.9 nM) and CB2/CB1 selectivity (50-200-fold). V-SYNTHES was also tested on a kinase target, ROCK1, further supporting its use for lead discovery. The approach is easily scalable for the rapid growth of combinatorial libraries and potentially adaptable to any docking algorithm.
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Affiliation(s)
- Arman A. Sadybekov
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90089, USA,Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anastasiia V. Sadybekov
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90089, USA,Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yongfeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Julie Pickett
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Blake Houser
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Nilkanth Patel
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ngan K. Tran
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Fei Tong
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Nikolai Zvonok
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Manish K Jain
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Olena Savych
- Enamine Ltd, 78 Chervonotkatska Street, 02094, Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd, 78 Chervonotkatska Street, 02094, Ukraine,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Spyros P. Nikas
- Center for Drug Discovery and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Nicos A. Petasis
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yurii S. Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine,Chemspace LLC, 85 Chervonotkatska Street, 02094, Ukraine
| | - Bryan L. Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,National Institute of Mental Health Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA,Corresponding authors: Bryan L. Roth (), Alexandros Makriyannis (), Vsevolod Katritch ()
| | - Alexandros Makriyannis
- Center for Drug Discovery, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA. .,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. .,Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
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102
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Farooq Z, Howell LA, McCormick PJ. Probing GPCR Dimerization Using Peptides. Front Endocrinol (Lausanne) 2022; 13:843770. [PMID: 35909575 PMCID: PMC9329873 DOI: 10.3389/fendo.2022.843770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of membrane proteins and the most common and extensively studied pharmacological target. Numerous studies over the last decade have confirmed that GPCRs do not only exist and function in their monomeric form but in fact, have the ability to form dimers or higher order oligomers with other GPCRs, as well as other classes of receptors. GPCR oligomers have become increasingly attractive to investigate as they have the ability to modulate the pharmacological responses of the receptors which in turn, could have important functional roles in diseases, such as cancer and several neurological & neuropsychiatric disorders. Despite the growing evidence in the field of GPCR oligomerisation, the lack of structural information, as well as targeting the 'undruggable' protein-protein interactions (PPIs) involved in these complexes, has presented difficulties. Outside the field of GPCRs, targeting PPIs has been widely studied, with a variety of techniques being investigated; from small-molecule inhibitors to disrupting peptides. In this review, we will demonstrate several physiologically relevant GPCR dimers and discuss an array of strategies and techniques that can be employed when targeting these complexes, as well as provide ideas for future development.
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Affiliation(s)
- Zara Farooq
- Centre for Endocrinology, William Harvey Research Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Lesley A. Howell
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Peter J. McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- *Correspondence: Peter J. McCormick,
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103
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Boutin JA, Logez C, Damian M, Wagner R, Banères JL, Ferry G. MT1 Melatonin Receptor Reconstitution in Nanodiscs. Methods Mol Biol 2022; 2550:171-178. [PMID: 36180690 DOI: 10.1007/978-1-0716-2593-4_21] [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] [Indexed: 06/16/2023]
Abstract
A way to study G protein-coupled receptors in a minimal system is to reconstruct artificial membrane mimics, made of detergent and/or of lipids in which the purified receptor is maintained. In particular, it is now possible to generate lipid nanoparticles, such as nanodiscs, in which a single receptor molecule is included. Such objects offer the invaluable potential of studying an isolated receptor stabilized in a finely controlled membrane-like environment to evaluate its pharmacology, its function, and its structure at the molecular level. In this chapter, we detail the different steps from the extraction and isolation of a recombinant MT1 melatonin receptor in detergent, down to its reconstitution into nanodiscs. A G protein activation test is further described in order to exemplify how the functionality of such particles may be investigated.
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Affiliation(s)
- Jean A Boutin
- Pole d'expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, Croissy-sur-Seine, France.
- PHARMADEV (Pharmacochimie et biologie pour le développement), Faculté de Pharmacie, Toulouse, France.
| | - Christel Logez
- Pole d'expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, Croissy-sur-Seine, France
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
- Bioprocess Research & Development, SANOFI PASTEUR, Marcy l'Etoile, France
| | - Marjorie Damian
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Renaud Wagner
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | | | - Gilles Ferry
- Pole d'expertise Biotechnologie, Chimie & Biologie, Institut de Recherches Servier, Croissy-sur-Seine, France
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104
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Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. J Chem Inf Model 2021; 61:6024-6037. [PMID: 34780174 PMCID: PMC8715506 DOI: 10.1021/acs.jcim.1c00826] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nanobody binding
stabilizes G-protein-coupled receptors (GPCR)
in a fully active state and modulates their affinity for bound ligands.
However, the atomic-level basis for this allosteric regulation remains
elusive. Here, we investigate the conformational changes induced by
the binding of a nanobody (Nb80) on the active-like β2 adrenergic
receptor (β2AR) via enhanced sampling molecular dynamics simulations.
Dimensionality reduction analysis shows that Nb80 stabilizes structural
features of the β2AR with an ∼14 Å outward movement
of transmembrane helix 6 and a close proximity of transmembrane (TM)
helices 5 and 7, and favors the fully active-like conformation of
the receptor, independent of ligand binding, in contrast to the conditions
under which no intracellular binding partner is bound, in which case
the receptor is only stabilized in an intermediate-active state. This
activation is supported by the residues located at hotspots located
on TMs 5, 6, and 7, as shown by supervised machine learning methods.
Besides, ligand-specific subtle differences in the conformations assumed
by intracellular loop 2 and extracellular loop 2 are captured from
the trajectories of various ligand-bound receptors in the presence
of Nb80. Dynamic network analysis further reveals that Nb80 binding
triggers tighter and stronger local communication networks between
the Nb80 and the ligand-binding sites, primarily involving residues
around ICL2 and the intracellular end of TM3, TM5, TM6, as well as
ECL2, ECL3, and the extracellular ends of TM6 and TM7. In particular,
we identify unique allosteric signal transmission mechanisms between
the Nb80-binding site and the extracellular domains in conformations
modulated by a full agonist, BI167107, and a G-protein-biased partial
agonist, salmeterol, involving mainly TM1 and TM2, and TM5, respectively.
Altogether, our results provide insights into the effect of intracellular
binding partners on the GPCR activation mechanism, which should be
taken into account in structure-based drug discovery.
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Affiliation(s)
- Yue Chen
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Sergio Pérez-Conesa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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105
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Mahinthichaichan P, Vo QN, Ellis CR, Shen J. Kinetics and Mechanism of Fentanyl Dissociation from the μ-Opioid Receptor. JACS AU 2021; 1:2208-2215. [PMID: 34977892 PMCID: PMC8715493 DOI: 10.1021/jacsau.1c00341] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 06/14/2023]
Abstract
Driven by illicit fentanyl, opioid related deaths have reached the highest level in 2020. Currently, an opioid overdose is resuscitated by the use of naloxone, which competitively binds and antagonizes the μ-opioid receptor (mOR). Thus, knowledge of the residence times of opioids at mOR and the unbinding mechanisms is valuable for assessing the effectiveness of naloxone. In the present study, we calculate the fentanyl-mOR dissociation time and elucidate the mechanism by applying an enhanced sampling molecular dynamics (MD) technique. Two sets of metadynamics simulations with different initial structures were performed while accounting for the protonation state of the conserved H2976.52, which has been suggested to modulate the ligand-mOR affinity and binding mode. Surprisingly, with the Nδ-protonated H2976.52, fentanyl can descend as much as 10 Å below the level of the conserved D1473.32 before escaping the receptor and has a calculated residence time τ of 38 s. In contrast, with the Nϵ- and doubly protonated H2976.52, the calculated τ are 2.6 and 0.9 s, respectively. Analysis suggests that formation of the piperidine-Hid297 hydrogen bond strengthens the hydrophobic contacts with the transmembrane helix (TM) 6, allowing fentanyl to explore a deep pocket. Considering the experimental τ of ∼4 min for fentanyl and the role of TM6 in mOR activation, the deep insertion mechanism may be biologically relevant. The work paves the way for large-scale computational predictions of opioid dissociation rates to inform evaluation of strategies for opioid overdose reversal. The profound role of the histidine protonation state found here may shift the paradigm in computational studies of ligand-receptor kinetics.
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Affiliation(s)
- Paween Mahinthichaichan
- Division
of Applied Regulatory Science, Office of Clinical Pharmacology, Office
of Translational Sciences, Center for Drug
Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Quynh N. Vo
- Division
of Applied Regulatory Science, Office of Clinical Pharmacology, Office
of Translational Sciences, Center for Drug
Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Christopher R. Ellis
- Division
of Applied Regulatory Science, Office of Clinical Pharmacology, Office
of Translational Sciences, Center for Drug
Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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106
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Mori Y, Tsuchihira A, Yoshida T, Yoshida S, Fujiuchi A, Ohmi M, Isogai Y, Sakaguchi T, Eguchi S, Tsuda T, Kato K, Ohashi K, Ouchi N, Park HM, Murohara T, Takefuji M. Corticotropin releasing hormone receptor 2 antagonist, RQ-00490721, for the prevention of pressure overload-induced cardiac dysfunction. Biomed Pharmacother 2021; 146:112566. [PMID: 34954642 DOI: 10.1016/j.biopha.2021.112566] [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: 09/06/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) regulate the pathological and physiological functions of the heart. GPCR antagonists are widely used in the treatment of chronic heart failure. Despite therapeutic advances in the treatments for cardiovascular diseases, heart failure is a major clinical health problem, with significant mortality and morbidity. Corticotropin releasing hormone receptor 2 (CRHR2) is highly expressed in cardiomyocytes, and cardiomyocyte-specific deletion of the genes encoding CRHR2 suppresses pressure overload-induced cardiac dysfunction. This suggests that the negative modulation of CRHR2 may prevent the progression of heart failure. However, there are no systemic drugs against CRHR2. FINDINGS We developed a novel, oral, small molecule antagonist of CRHR2, RQ-00490721, to investigate the inhibition of CRHR2 as a potential therapeutic approach for the treatment of heart failure. In vitro, RQ-00490721 decreased CRHR2 agonist-induced 3', 5'-cyclic adenosine monophosphate (cAMP) production. In vivo, RQ-00490721 showed sufficient oral absorption and better distribution to peripheral organs than to the central nervous system. Oral administration of RQ-00490721 inhibited the CRHR2 agonist-induced phosphorylation of cAMP-response element binding protein (CREB) in the heart, which regulates a transcription activator involved in heart failure. RQ-00490721 administration was not found to affect basal heart function in mice but protected them from pressure overload-induced cardiac dysfunction. INTERPRETATION Our results suggest that RQ-00490721 is a promising agent for use in the treatment of chronic heart failure.
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Affiliation(s)
- Yu Mori
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | | | - Tatsuya Yoshida
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Satoya Yoshida
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Akiyoshi Fujiuchi
- Discovery Research, RaQualia Pharma Inc., Nagoya, Japan; RaQualia Pharma Industry-Academia Collaborative Research Center, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Masashi Ohmi
- Discovery Research, RaQualia Pharma Inc., Nagoya, Japan
| | - Yumi Isogai
- Discovery Research, RaQualia Pharma Inc., Nagoya, Japan
| | - Teruhiro Sakaguchi
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Shunsuke Eguchi
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Takuma Tsuda
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Katsuhiro Kato
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Koji Ohashi
- Department of Molecular Medicine and Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Noriyuki Ouchi
- Department of Molecular Medicine and Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Hyi-Man Park
- Discovery Research, RaQualia Pharma Inc., Nagoya, Japan; RaQualia Pharma Industry-Academia Collaborative Research Center, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Toyoaki Murohara
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan
| | - Mikito Takefuji
- Department of Cardiology, Nagoya University School of Medicine, Nagoya, Japan.
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107
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Abstract
Rapid flip-flop of phospholipids across the two leaflets of biological membranes is crucial for many aspects of cellular life. The transport proteins that facilitate this process are classified as pump-like flippases and floppases and channel-like scramblases. Unexpectedly, Class A G protein-coupled receptors (GPCRs), a large class of signaling proteins exemplified by the visual receptor rhodopsin and its apoprotein opsin, are constitutively active as scramblases in vitro. In liposomes, opsin scrambles lipids at a unitary rate of >100,000 per second. Atomistic molecular dynamics simulations of opsin in a lipid membrane reveal conformational transitions that expose a polar groove between transmembrane helices 6 and 7. This groove enables transbilayer lipid movement, conceptualized as the swiping of a credit card (lipid) through a card reader (GPCR). Conformational changes that facilitate scrambling are distinct from those associated with GPCR signaling. In this review, we discuss the physiological significance of GPCR scramblase activity and the modes of its regulation in cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA; .,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA;
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108
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Biswas AD, Catte A, Mancini G, Barone V. Analysis of L-DOPA and droxidopa binding to human β 2-adrenergic receptor. Biophys J 2021; 120:5631-5643. [PMID: 34767786 PMCID: PMC8715240 DOI: 10.1016/j.bpj.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last two decades, an increasing number of studies has been devoted to a deeper understanding of the molecular process involved in the binding of various agonists and antagonists to active and inactive conformations of β2-adrenergic receptor (β2AR). The 3.2 Å x-ray crystal structure of human β2AR active state in combination with the endogenous low affinity agonist adrenaline offers an ideal starting structure for studying the binding of various catecholamines to adrenergic receptors. We show that molecular docking of levodopa (L-DOPA) and droxidopa into rigid and flexible β2AR models leads for both ligands to binding anchor sites comparable to those experimentally reported for adrenaline, namely D113/N312 and S203/S204/S207 side chains. Both ligands have a hydrogen bond network that is extremely similar to those of noradrenaline and dopamine. Interestingly, redocking neutral and protonated versions of adrenaline to rigid and flexible β2AR models results in binding poses that are more energetically stable and distinct from the x-ray crystal structure. Similarly, lowest energy conformations of noradrenaline and dopamine generated by docking into flexible β2AR models had binding free energies lower than those of best poses in rigid receptor models. Furthermore, our findings show that L-DOPA and droxidopa molecules have binding affinities comparable to those predicted for adrenaline, noradrenaline, and dopamine, which are consistent with previous experimental and computational findings and supported by the molecular dynamics simulations of β2AR-ligand complexes performed here.
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109
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Chen Y, Tian R, Shang Y, Jiang Q, Ding B. Regulation of Biological Functions at the Cell Interface by DNA Nanostructures. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yongjian Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Sino-Danish College Sino-Danish Center for Education and Research University of Chinese Academy of Sciences 100049 Beijing China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
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110
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Lagunas-Rangel FA. G protein-coupled receptors that influence lifespan of human and animal models. Biogerontology 2021; 23:1-19. [PMID: 34860303 PMCID: PMC8888397 DOI: 10.1007/s10522-021-09945-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022]
Abstract
Humanity has always sought to live longer and for this, multiple strategies have been tried with varying results. In this sense, G protein-coupled receptors (GPCRs) may be a good option to try to prolong our life while maintaining good health since they have a substantial participation in a wide variety of processes of human pathophysiology and are one of the main therapeutic targets. In this way, we present the analysis of a series of GPCRs whose activity has been shown to affect the lifespan of animal and human models, and in which we put a special interest in describing the molecular mechanisms involved. Our compilation of data revealed that the mechanisms most involved in the role of GPCRs in lifespan are those that mimic dietary restriction, those related to insulin signaling and the AMPK and TOR pathways, and those that alter oxidative homeostasis and severe and/or chronic inflammation. We also discuss the possibility of using agonist or antagonist drugs, depending on the beneficial or harmful effects of each GPCR, in order to prolong people's lifespan and healthspan.
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111
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Felline A, Schiroli D, Comitato A, Marigo V, Fanelli F. Structure network-based landscape of rhodopsin misfolding by mutations and algorithmic prediction of small chaperone action. Comput Struct Biotechnol J 2021; 19:6020-6038. [PMID: 34849206 PMCID: PMC8605067 DOI: 10.1016/j.csbj.2021.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/09/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022] Open
Abstract
Failure of a protein to achieve its functional structural state and normal cellular location contributes to the etiology and pathology of heritable human conformational diseases. The autosomal dominant form of retinitis pigmentosa (adRP) is an incurable blindness largely linked to mutations of the membrane protein rod opsin. While the mechanisms underlying the noxious effects of the mutated protein are not completely understood, a common feature is the functional protein conformational loss. Here, the wild type and 39 adRP rod opsin mutants were subjected to mechanical unfolding simulations coupled to the graph theory-based protein structure network analysis. A robust computational model was inferred and in vitro validated in its ability to predict endoplasmic reticulum retention of adRP mutants, a feature linked to the mutation-caused misfolding. The structure-based approach could also infer the structural determinants of small chaperone action on misfolded protein mutants with therapeutic implications. The approach is exportable to conformational diseases linked to missense mutations in any membrane protein.
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Affiliation(s)
- Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Davide Schiroli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Antonella Comitato
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy.,Center for Neuroscience and Neurotechnology, Italy
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy.,Center for Neuroscience and Neurotechnology, Italy
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112
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Smith SO. Deconstructing the transmembrane core of class A G protein-coupled receptors. Trends Biochem Sci 2021; 46:1017-1029. [PMID: 34538727 PMCID: PMC8595765 DOI: 10.1016/j.tibs.2021.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023]
Abstract
Class A G protein-coupled receptors have evolved to recognize ligands ranging from small-molecule odorants to proteins. Although they are among the most diverse membrane receptors in eukaryotic organisms, they possess a highly conserved core within their seven-transmembrane helix framework. The conservation of the transmembrane core has led to the idea of a common mechanism by which ligand binding is coupled to the outward rotation of helix H6, the hallmark of an active receptor. Nevertheless, there is still no consensus on the mechanism of coupling or on the roles of specific residues within the core. Recent insights from crystallography and NMR spectroscopy provide a way to decompose the core into its essential structural and functional elements that shed new light on this important region.
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Affiliation(s)
- Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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113
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Bai J, Ye T, Wei YB, Yang Y, Yang HM, Lan Y. Opioid receptors modulate parallel fiber-Purkinje cell synaptic transmission in mouse cerebellum. Neurosci Lett 2021; 770:136356. [PMID: 34808268 DOI: 10.1016/j.neulet.2021.136356] [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: 09/27/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/20/2022]
Abstract
Opioid receptors play important roles in, among others, learning and memory, emotional responses, addiction, and pain. In recent years, the cerebellum has received increasing attention for its role in non-motor functions. The Purkinje cell (PC) is the only efferent neuron in the cerebellar cortex, and receives glutamatergic synaptic inputs from the parallel fibers (PF) formed by the axons of granule cells. Studies have shown that opioid receptors are expressed during the development of cerebellar cells. However, the distribution of opioid receptors, their subtypes in cerebellar PF-PC synapses, and their effects on synaptic transmission remain unclear. To examine these questions, we used whole-cell patch clamp recordings and pharmacological methods to determine the effects of activating three different opioid receptor subtypes on synaptic transmission at PF-PC synapses. In the presence of picrotoxin, mouse cerebellar slices were perfused with agonists or blockers of different opioid receptor subtypes, and the changes in excitatory postsynaptic currents (EPSCs) were examined. Both agonists of µ-opioid receptors (MOR) and δ-opioid receptors (DOR) significantly reduced the amplitude and area under the curve of PF-PC EPSCs in a concentration-dependent manner, accompanied by an increase in the paired-pulsed ratio (PPR). These effects could be blocked by respective receptor antagonists. In contrast, no significant changes were found after the application of κ-opioid receptor (KOR) agonists. In conclusion, MOR and DOR are present at the axon terminals of PF in the mouse cerebellar cortex, whereas no or negligible amounts of KOR are found. Activation of MOR and DOR regulates PF-PC synaptic transmission via inhibition of glutamate (Glu) release in cerebellar cortex in mice. We also found that endogenous opioid peptides are present in PF-PC synapses of mouse cerebellum, which also can inhibit the release of Glu.
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Affiliation(s)
- Jin Bai
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji City, Jilin Province 133002, China
| | - Ting Ye
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji City, Jilin Province 133002, China; Interdisciplinary Program of Biological Functional Molecules, College of Integration Science, Yanbian University, Yanji City, Jilin Province 133002, China
| | - Yan-Bin Wei
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji City, Jilin Province 133002, China
| | - Yi Yang
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji City, Jilin Province 133002, China
| | - He-Min Yang
- Central Laboratory, The 3rd Affiliated Hospital, Qiqihar Medical University, Qiqihar City, Heilongjiang Province 161006, China.
| | - Yan Lan
- Department of Physiology and Pathophysiology, College of Medicine, Yanbian University, Yanji City, Jilin Province 133002, China.
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114
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The marriage of chemokines and galectins as functional heterodimers. Cell Mol Life Sci 2021; 78:8073-8095. [PMID: 34767039 PMCID: PMC8629806 DOI: 10.1007/s00018-021-04010-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/05/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022]
Abstract
Trafficking of leukocytes and their local activity profile are of pivotal importance for many (patho)physiological processes. Fittingly, microenvironments are complex by nature, with multiple mediators originating from diverse cell types and playing roles in an intimately regulated manner. To dissect aspects of this complexity, effectors are initially identified and structurally characterized, thus prompting familial classification and establishing foci of research activity. In this regard, chemokines present themselves as role models to illustrate the diversification and fine-tuning of inflammatory processes. This in turn discloses the interplay among chemokines, their cell receptors and cognate glycosaminoglycans, as well as their capacity to engage in new molecular interactions that form hetero-oligomers between themselves and other classes of effector molecules. The growing realization of versatility of adhesion/growth-regulatory galectins that bind to glycans and proteins and their presence at sites of inflammation led to testing the hypothesis that chemokines and galectins can interact with each other by protein-protein interactions. In this review, we present some background on chemokines and galectins, as well as experimental validation of this chemokine-galectin heterodimer concept exemplified with CXCL12 and galectin-3 as proof-of-principle, as well as sketch out some emerging perspectives in this arena.
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115
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Liu X, Xue Q, Zhang H, Fu J, Zhang A. Structural basis for molecular recognition of G protein-coupled estrogen receptor by selected bisphenols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148558. [PMID: 34328988 DOI: 10.1016/j.scitotenv.2021.148558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Complicated ligand-dependent signaling pathways of bisphenol A (BPA) and its analogues involve not only intranuclear estrogen receptor but also membrane receptor G protein-coupled estrogen receptor (GPER). However, the structural basis for molecular recognition of GPER by the environmental chemicals remains unknown. To reveal the structural dependence of GPER recognition by bisphenols, a systematic molecular dynamics simulation study was performed for selected bisphenols with different electron hybrid orbitals and substituents on their C atoms connecting two phenol rings. BPA was used as a control, bisphenol C(BPC) as an example for a connecting C with sp2 hybrid orbitals to provide more ligand rigidity, bisphenol E(BPE) and bisphenol F(BPF) for decreased steric hindrance and hydrophobicity around the connecting C, and bisphenol B(BPB) and bisphenol AF(BPAF) for increased hydrophobicity and steric hindrance. All the tested bisphenols can bind with GPER at its classic orthosteric site to obtain GPER-ligand complexes, while van der Waals interactions and direct inter-molecular electrostatic energies provide the driving forces for ligand binding. Bulky substituents and structural rigidity of the connecting C dramatically impair hydrogen bonding between GPER and the bisphenols, which results in decreased contribution of both favorable intermolecular hydrogen bonds and unfavorable polar solvation effect to complex stability of BPB and BPC since decreased number of key residues is expected. Increase in substituent lipophilicity enhances the van der Waals interactions and favorable non-polar solvation effect. The six bisphenols of high structural similarity shared two key recognition residues, Leu137TM3 and Trp272TM6, the latter of which was in the highly conserved CWxP motif of TM6 and has been reported as key residue for G protein-coupled receptor activation. Based on the obtained knowledge, GPER affinity and relevant toxicity of BPA alternatives can be easily predicted, and the calculated binding free energies are consistent with the available experimental observations.
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Affiliation(s)
- Xiuchang Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China
| | - Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Huazhou Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310012, PR China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310012, PR China.
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116
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Sun D, Yang X, Wu B, Zhang XJ, Li H, She ZG. Therapeutic Potential of G Protein-Coupled Receptors Against Nonalcoholic Steatohepatitis. Hepatology 2021; 74:2831-2838. [PMID: 33826778 DOI: 10.1002/hep.31852] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Dating Sun
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Model Animal, Wuhan University, Wuhan, China
| | - Xia Yang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Model Animal, Wuhan University, Wuhan, China
| | - Bin Wu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Model Animal, Wuhan University, Wuhan, China
| | - Xiao-Jing Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Model Animal, Wuhan University, Wuhan, China.,Basic Medical School, Wuhan University, Wuhan, China
| | - Hongliang Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Model Animal, Wuhan University, Wuhan, China.,Basic Medical School, Wuhan University, Wuhan, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhi-Gang She
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Institute of Model Animal, Wuhan University, Wuhan, China
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117
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Sabbir MG, Inoue A, Taylor CG, Zahradka P. Loss of β-Arrestins or six Gα proteins in HEK293 cells caused Warburg effect and prevented progesterone-induced rapid proteasomal degradation of progesterone receptor membrane component 1. J Steroid Biochem Mol Biol 2021; 214:105995. [PMID: 34506922 DOI: 10.1016/j.jsbmb.2021.105995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
Hormonal dysregulation plays a significant role in the metabolic switching during malignant transformation. Progesterone Receptor Membrane Component 1 (PGRMC1) is a single-pass transmembrane receptor activated by the binding of progesterone (P4), a sex hormone. In a previous study, P4 treatment caused rapid (within 30 min) induction of aerobic glycolysis in transformed HEK293 cells, a hallmark malignant phenotype known as the Warburg effect. This metabolic reprogramming was associated with the proteasomal degradation of a 70 kilodalton (kDa) PGRMC1. PGRMC1 interacts with a variety of proteins, including G protein-coupled receptors (GPCRs) and P4-PGRMC1 signaling modulates cyclic adenosine monophosphate (cAMP) production. Therefore, we hypothesized that the P4-induced Warburg effect and proteasomal degradation of PGRMC1 involve G proteins and β-Arrestins (ARRBs). In the present study, we investigated P4-induced aerobic glycolysis, proteasomal degradation of p70 PGRMC1, as well as abundance and subcellular translocation of PGRMC1 along with two key glycolytic enzymes Hexokinase 1 (HK1) and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) in six Gα subunit (Gsix) proteins or ARRB1/2-deficient HEK293 cells. Loss of ARRB1/2 or Gsix proteins inhibited P4-induced p70 PGRMC1 degradation but failed to prevent the P4-induced Warburg effect. Also, deficiency of ARRB1/2 or Gsix proteins differentially affected the basal as well as P4-induced abundance and subcellular translocation of PGRMC1, HK1, and GAPDH proteins. Overall, the findings indicate that P4-PGRMC1-mediated metabolic reprogramming in HEK293 cells depends on β-Arrestins and Gα proteins suggesting the involvement of an underlying GPCR signal transduction pathway.
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Affiliation(s)
- Mohammad Golam Sabbir
- Canadian Centre for Agri-Food Research in Health and Medicine, St. Boniface Albrechtsen Research Centre, Winnipeg, MB, R2H 2A6, Canada; Alzo Biosciences Inc., San Diego, USA.
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Carla G Taylor
- Canadian Centre for Agri-Food Research in Health and Medicine, St. Boniface Albrechtsen Research Centre, Winnipeg, MB, R2H 2A6, Canada; Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada; Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Peter Zahradka
- Canadian Centre for Agri-Food Research in Health and Medicine, St. Boniface Albrechtsen Research Centre, Winnipeg, MB, R2H 2A6, Canada; Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada; Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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118
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Le HTT, Murugesan A, Ramesh T, Yli-Harja O, Konda Mani S, Kandhavelu M. Molecular interaction of HIC, an agonist of P2Y1 receptor, and its role in prostate cancer apoptosis. Int J Biol Macromol 2021; 189:142-150. [PMID: 34425116 DOI: 10.1016/j.ijbiomac.2021.08.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Prostate cancer is a heterogeneous, slow growing asymptomatic cancer that predominantly affects man. A purinergic G-protein coupled receptor, P2Y1R, is targeted for its therapeutic value since it plays a crucial role in many key molecular events of cancer progression and invasion. Our previous study demonstrated that indoline derivative, 1 ((1-(2-Hydroxy-5-nitrophenyl) (4-hydroxyphenyl) methyl)indoline-4‑carbonitrile; HIC), stimulates prostate cancer cell (PCa) growth inhibition via P2Y1R. However, the mode of interaction of P2Y1R with HIC involved in this process remains unclear. Here, we have reported the molecular interactions of HIC with P2Y1R. Molecular dynamics simulation was performed that revealed the stable specific binding of the protein-ligand complex. In vitro analysis has shown increased apoptosis of PCa-cells, PC3, and DU145, upon specific interaction of P2Y1R-HIC. This was further validated using siRNA analysis that showed a higher percentage of apoptotic cells in PCa-cells transfected with P2Y-siRNA-MRS2365 than P2Y-siRNA-HIC treatment. Decreased mitochondrial membrane potential (MMP) activity and reduced glutathione (GSH) level show their role in P2Y1R-HIC mediated apoptosis. These in silico and in vitro results confirmed that HIC could induce mitochondrial apoptotic signaling through the P2Y1R activation. Thus, HIC being a potential ligand upon interaction with P2Y1R might have therapeutic value for the treatment of prostate cancer.
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Affiliation(s)
- Hien Thi Thu Le
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; Department of Biotechnology, Lady Doak College, Thallakulam, Madurai 625002, India
| | - Thiyagarajan Ramesh
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Olli Yli-Harja
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98103-8904, USA
| | - Saravanan Konda Mani
- Scigen Research and Innovation Pvt Ltd, Periyar Technology Business Incubator, Thanjavur 613403, Tamil Nadu, India
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland.
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119
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Zebhi B, Lazkani M, Bark D. Calcific Aortic Stenosis-A Review on Acquired Mechanisms of the Disease and Treatments. Front Cardiovasc Med 2021; 8:734175. [PMID: 34604358 PMCID: PMC8486019 DOI: 10.3389/fcvm.2021.734175] [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: 06/30/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Calcific aortic stenosis is a progressive disease that has become more prevalent in recent decades. Despite advances in research to uncover underlying biomechanisms, and development of new generations of prosthetic valves and replacement techniques, management of calcific aortic stenosis still comes with unresolved complications. In this review, we highlight underlying molecular mechanisms of acquired aortic stenosis calcification in relation to hemodynamics, complications related to the disease, diagnostic methods, and evolving treatment practices for calcific aortic stenosis.
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Affiliation(s)
- Banafsheh Zebhi
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Mohamad Lazkani
- Medical Center of the Rockies, University of Colorado Health, Loveland, CO, United States
| | - David Bark
- Department of Pediatrics, Washington University in Saint Louis, Saint Louis, MO, United States.,Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, MO, United States
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120
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He Y, He G, He T. Specifically Targeted Transport of Plasma Membrane Transporters: From Potential Mechanisms for Regulating Cell Health or Disease to Applications. MEMBRANES 2021; 11:membranes11100736. [PMID: 34677502 PMCID: PMC8538571 DOI: 10.3390/membranes11100736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/23/2022]
Abstract
Normal substrate transport and signal transmission are the premise to ensure the health of biological somatic cells. Therefore, a comprehensive understanding of the molecular mechanism of intercellular substrate transport is of great significance for clinical treatment. In order to better understand the membrane protein through its interaction with receptors, to help maintain a healthy cell and the molecular mechanisms of disease, in this paper, we seek to clarify, first of all, the recognition mechanism for different types of membrane protein receptors; pathogen invasion using the transport pathway involved in the membrane; and the latest specific target sites of various kinds of membrane transport carriers; to provide an explanation and summary of the system. Secondly, the downstream receptor proteins and specific substrates of different membrane transporters were classified systematically; the functional differences of different subclasses and their relationship with intracellular transport disorders were analyzed to further explore the potential relationship between cell transport disorders and diseases. Finally, the paper summarizes the use of membrane transporter-specific targets for drug design and development from the latest research results; it points out the transporter-related results in disease treatment; the application prospects and the direction for drug development and disease treatment providing a new train of thought; also for disease-specific targeted therapy, it provides a certain reference value.
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Affiliation(s)
- Yeqing He
- College of Agricultural, Guizhou University, Guiyang 550025, China; (Y.H.); (T.H.)
| | - Guandi He
- College of Agricultural, Guizhou University, Guiyang 550025, China; (Y.H.); (T.H.)
- Correspondence:
| | - Tengbing He
- College of Agricultural, Guizhou University, Guiyang 550025, China; (Y.H.); (T.H.)
- Institute of New Rural Development, Guizhou University, Guiyang 550025, China
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121
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Bouysset C, Fiorucci S. ProLIF: a library to encode molecular interactions as fingerprints. J Cheminform 2021; 13:72. [PMID: 34563256 PMCID: PMC8466659 DOI: 10.1186/s13321-021-00548-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022] Open
Abstract
Interaction fingerprints are vector representations that summarize the three-dimensional nature of interactions in molecular complexes, typically formed between a protein and a ligand. This kind of encoding has found many applications in drug-discovery projects, from structure-based virtual-screening to machine-learning. Here, we present ProLIF, a Python library designed to generate interaction fingerprints for molecular complexes extracted from molecular dynamics trajectories, experimental structures, and docking simulations. It can handle complexes formed of any combination of ligand, protein, DNA, or RNA molecules. The available interaction types can be fully reparametrized or extended by user-defined ones. Several tutorials that cover typical use-case scenarios are available, and the documentation is accompanied with code snippets showcasing the integration with other data-analysis libraries for a more seamless user-experience. The library can be freely installed from our GitHub repository (https://github.com/chemosim-lab/ProLIF).
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Affiliation(s)
- Cédric Bouysset
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Sébastien Fiorucci
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
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122
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Zhao F, Wu Y, Zhou F, Xue D, Zhao S, Lu W, Liu X, Hu T, Qiu Y, Li R, Gu T, Xu Y, Xu F, Zhong G, Jiang Z, Zhao S, Tao H. Elucidation of Distinct Modular Assemblies of Smoothened Receptor by Bitopic Ligand Measurement. J Med Chem 2021; 64:13830-13840. [PMID: 34492176 DOI: 10.1021/acs.jmedchem.1c01220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Class F G protein-coupled receptors are characterized by a large extracellular domain (ECD) in addition to the common transmembrane domain (TMD) with seven α-helixes. For smoothened receptor (SMO), structural studies revealed dissected ECD and TMD, and their integrated assemblies. However, distinct assemblies were reported under different circumstances. Using an unbiased approach based on four series of cross-conjugated bitopic ligands, we explore the relationship between the active status and receptor assembly. Different activity dependency on the linker length for these bitopic ligands corroborates the various occurrences of SMO assembly. These results reveal a rigid "near" assembly for active SMO, which is in contrast to previous results. Conversely, inactive SMO adopts a free ECD, which would be remotely captured at "far" assembly by cholesterol. Altogether, we propose a mechanism of cholesterol flow-caused SMO activation involving an erection of ECD from far to near assembly.
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Affiliation(s)
- Fei Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Fang Zhou
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Dongxiang Xue
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Simeng Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Wanglong Lu
- School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Xiaoyan Liu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Tao Hu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanli Qiu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Rongyan Li
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tangjie Gu
- School of Physics Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yueming Xu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guisheng Zhong
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhongxing Jiang
- School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Shanghai 201210, China
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123
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Qiu W, Lv Z, Xiao X, Shao S, Lin H. EMCBOW-GPCR: A method for identifying G-protein coupled receptors based on word embedding and wordbooks. Comput Struct Biotechnol J 2021; 19:4961-4969. [PMID: 34527200 PMCID: PMC8437786 DOI: 10.1016/j.csbj.2021.08.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/07/2021] [Accepted: 08/27/2021] [Indexed: 11/15/2022] Open
Abstract
An computational method was developed to identify G-protein coupled receptors. Three word-embedding models and a bag-of-words model are used to extract original features. A high accuracy was achieved by using fusion information. A powerful tool was established.
G Protein-Coupled Receptors (GPCRs) are one of the largest membrane protein receptor family in human, which are also important targets for many drugs. Thence, it’s of great significance to judge whether a protein is a GPCR or not. However, identifying GPCRs by experimental methods is very expensive and time-consuming. As more and more GPCR primary sequences are accumulated, it’s feasible to develop a computational model to predict GPCRs precisely and quickly. In this paper, a novel method called EMCBOW-GPCR has been proposed to improve the accuracy of identifying GPCRs based on natural language processing (NLP). For representing GPCRs, three word-embedding models and a bag-of-words model are used to extract original features. Then, the original features are thrown into a Deep-learning algorithm to extract features further and reduce the dimension. Finally, the obtained features are fed into Extreme Gradient Boosting. As shown with the results comparison, the overall prediction metrics of EMCBOW-GPCR are higher than the state of the arts. In order to be convenient for more researchers to use EMCBOW-GPCR, the method and source code have been opened in github, which are available at https://github.com/454170054/EMCBOW-GPCR, and a user-friendly web-server for EMCBOW-GPCR has been established at http://www.jci-bioinfo.cn/emcbowgpcr.
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Affiliation(s)
- Wangren Qiu
- School of Information Engineering, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Zhe Lv
- School of Information Engineering, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Xuan Xiao
- School of Information Engineering, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Shuai Shao
- School of Information Engineering, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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124
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Seibel-Ehlert U, Plank N, Inoue A, Bernhardt G, Strasser A. Label-Free Investigations on the G Protein Dependent Signaling Pathways of Histamine Receptors. Int J Mol Sci 2021; 22:9739. [PMID: 34575903 PMCID: PMC8467282 DOI: 10.3390/ijms22189739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 01/14/2023] Open
Abstract
G protein activation represents an early key event in the complex GPCR signal transduction process and is usually studied by label-dependent methods targeting specific molecular events. However, the constrained environment of such "invasive" techniques could interfere with biological processes. Although histamine receptors (HRs) represent (evolving) drug targets, their signal transduction is not fully understood. To address this issue, we established a non-invasive dynamic mass redistribution (DMR) assay for the human H1-4Rs expressed in HEK cells, showing excellent signal-to-background ratios above 100 for histamine (HIS) and higher than 24 for inverse agonists with pEC50 values consistent with literature. Taking advantage of the integrative nature of the DMR assay, the involvement of endogenous Gαq/11, Gαs, Gα12/13 and Gβγ proteins was explored, pursuing a two-pronged approach, namely that of classical pharmacology (G protein modulators) and that of molecular biology (Gα knock-out HEK cells). We showed that signal transduction of hH1-4Rs occurred mainly, but not exclusively, via their canonical Gα proteins. For example, in addition to Gαi/o, the Gαq/11 protein was proven to contribute to the DMR response of hH3,4Rs. Moreover, the Gα12/13 was identified to be involved in the hH2R mediated signaling pathway. These results are considered as a basis for future investigations on the (patho)physiological role and the pharmacological potential of H1-4Rs.
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Affiliation(s)
- Ulla Seibel-Ehlert
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (N.P.); (G.B.)
| | - Nicole Plank
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (N.P.); (G.B.)
| | - Asuka Inoue
- Department of Pharmacological Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Guenther Bernhardt
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (N.P.); (G.B.)
| | - Andrea Strasser
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (N.P.); (G.B.)
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125
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Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, Gonen T. MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP. Proc Natl Acad Sci U S A 2021; 118:e2106041118. [PMID: 34462357 PMCID: PMC8433539 DOI: 10.1073/pnas.2106041118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs), or seven-transmembrane receptors, are a superfamily of membrane proteins that are critically important to physiological processes in the human body. Determining high-resolution structures of GPCRs without bound cognate signaling partners, such as a G protein, requires crystallization in lipidic cubic phase (LCP). GPCR crystals grown in LCP are often too small for traditional X-ray crystallography. These microcrystals are ideal for investigation by microcrystal electron diffraction (MicroED), but the gel-like nature of LCP makes traditional approaches to MicroED sample preparation insurmountable. Here, we show that the structure of a human A2A adenosine receptor can be determined by MicroED after converting the LCP into the sponge phase followed by focused ion-beam milling. We determined the structure of the A2A adenosine receptor to 2.8-Å resolution and resolved an antagonist in its orthosteric ligand-binding site, as well as four cholesterol molecules bound around the receptor. This study lays the groundwork for future structural studies of lipid-embedded membrane proteins by MicroED using single microcrystals that would be impossible with other crystallographic methods.
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Affiliation(s)
- Michael W Martynowycz
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Anna Shiriaeva
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Xuanrui Ge
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90007
| | - Johan Hattne
- HHMI, University of California, Los Angeles, CA 90095
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007;
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- HHMI, University of California, Los Angeles, CA 90095;
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095
- Department of Physiology, University of California, Los Angeles, CA 90095
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126
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Kulikova IV. Molecular Mechanisms and Gene Regulation of Melanic Plumage Coloration in Birds. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542108007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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127
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Roy S, Chompunud Na Ayudhya C, Thapaliya M, Deepak V, Ali H. Multifaceted MRGPRX2: New insight into the role of mast cells in health and disease. J Allergy Clin Immunol 2021; 148:293-308. [PMID: 33957166 PMCID: PMC8355064 DOI: 10.1016/j.jaci.2021.03.049] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/03/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Cutaneous mast cells (MCs) express Mas-related G protein-coupled receptor-X2 (MRGPRX2; mouse ortholog MrgprB2), which is activated by an ever-increasing number of cationic ligands. Antimicrobial host defense peptides (HDPs) generated by keratinocytes contribute to host defense likely by 2 mechanisms, one involving direct killing of microbes and the other via MC activation through MRGPRX2. However, its inappropriate activation may cause pseudoallergy and likely contribute to the pathogenesis of rosacea, atopic dermatitis, allergic contact dermatitis, urticaria, and mastocytosis. Gain- and loss-of-function missense single nucleotide polymorphisms in MRGPRX2 have been identified. The ability of certain ligands to serve as balanced or G protein-biased agonists has been defined. Small-molecule HDP mimetics that display both direct antimicrobial activity and activate MCs via MRGPRX2 have been developed. In addition, antibodies and reagents that modulate MRGPRX2 expression and signaling have been generated. In this article, we provide a comprehensive update on MrgprB2 and MRGPRX2 biology. We propose that harnessing MRGPRX2's host defense function by small-molecule HDP mimetics may provide a novel approach for the treatment of antibiotic-resistant cutaneous infections. In contrast, MRGPRX2-specific antibodies and inhibitors could be used for the modulation of allergic and inflammatory diseases that are mediated via this receptor.
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Affiliation(s)
- Saptarshi Roy
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, Pa
| | - Chalatip Chompunud Na Ayudhya
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, Pa
| | - Monica Thapaliya
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, Pa
| | - Vishwa Deepak
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, Pa
| | - Hydar Ali
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, Pa.
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128
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Abstract
Nanobodies have emerged as useful tools to study G protein-coupled receptor (GPCR) structure, dynamic, and subcellular localization. Initially, several nanobodies have been developed as chaperones to facilitate GPCR crystallization. To explore their potential as biosensors to monitor receptor activation and dynamics, we here described protocols to characterize nanobody's interaction with GPCRs and their application as probes for protein identification and visualization on the cellular level. We also introduced a chimeric approach to enable a kappa-opioid receptor derived nanobody to bind to other GPCRs, including orphan GPCRs whose endogenous ligand or intracellular transducers are unknown. This approach provides a reporter assay to identify tool molecules to study the function of orphan GPCRs.
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Affiliation(s)
- Amal El Daibani
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Tao Che
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, United States; Center for Clinical Pharmacology, University of Health Sciences and Pharmacy in St. Louis and Washington University School of Medicine, St. Louis, MO, United States.
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129
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Kovtun O, Torres R, Bellocchio LG, Rosenthal SJ. Membrane Nanoscopic Organization of D2L Dopamine Receptor Probed by Quantum Dot Tracking. MEMBRANES 2021; 11:578. [PMID: 34436341 PMCID: PMC8401772 DOI: 10.3390/membranes11080578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/11/2023]
Abstract
The role of lateral mobility and nanodomain organization of G protein-coupled receptors in modulating subcellular signaling has been under increasing scrutiny. Investigation of D2 dopamine receptor diffusion dynamics is of particular interest, as these receptors have been linked to altered neurotransmission in affective disorders and represent the primary target for commonly prescribed antipsychotics. Here, we applied our single quantum dot tracking approach to decipher intrinsic diffusion patterns of the wild-type long isoform of the D2 dopamine receptor and its genetic variants previously identified in several cohorts of schizophrenia patients. We identified a subtle decrease in the diffusion rate of the Val96Ala mutant that parallels its previously reported reduced affinity for potent neuroleptics clozapine and chlorpromazine. Slower Val96Ala variant diffusion was not accompanied by a change in receptor-receptor transient interactions as defined by the diffraction-limited quantum dot colocalization events. In addition, we implemented a Voronoї tessellation-based algorithm to compare nanoclustering of the D2 dopamine receptor to the dominant anionic phospholipid phosphatidylinositol 4,5-bisphosphate in the plasma membrane of live cells.
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Affiliation(s)
- Oleg Kovtun
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
| | - Ruben Torres
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Laurel G. Bellocchio
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
| | - Sandra Jean Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN 37235, USA
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130
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Unravelling the structural complexity of protein-lipid interactions with neutron reflectometry. Biochem Soc Trans 2021; 49:1537-1546. [PMID: 34240735 DOI: 10.1042/bst20201071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/02/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022]
Abstract
Neutron reflectometry (NR) is a large-facility technique used to examine structure at interfaces. In this brief review an introduction to the utilisation of NR in the study of protein-lipid interactions is given. Cold neutron beams penetrate matter deeply, have low energies, wavelengths in the Ångstrom regime and are sensitive to light elements. High differential hydrogen sensitivity (between protium and deuterium) enables solution and sample isotopic labelling to be utilised to enhance or diminish the scattering signal of individual components within complex biological structures. The combination of these effects means NR can probe buried structures such as those at the solid-liquid interface and encode molecular level structural information on interfacial protein-lipid complexes revealing the relative distribution of components as well as the overall structure. Model biological membrane sample systems can be structurally probed to examine phenomena such as antimicrobial mode of activity, as well as structural and mechanistic properties peripheral/integral proteins within membrane complexes. Here, the example of the antimicrobial protein α1-purothionin binding to a model Gram negative bacterial outer membrane is used to highlight the utilisation of this technique, detailing how changes in the protein/lipid distributions across the membrane before and after the protein interaction can be easily encoded using hydrogen isotope labelling.
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131
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Wu Y, Zeng L, Zhao S. Ligands of Adrenergic Receptors: A Structural Point of View. Biomolecules 2021; 11:biom11070936. [PMID: 34202543 PMCID: PMC8301793 DOI: 10.3390/biom11070936] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 01/14/2023] Open
Abstract
Adrenergic receptors are G protein-coupled receptors for epinephrine and norepinephrine. They are targets of many drugs for various conditions, including treatment of hypertension, hypotension, and asthma. Adrenergic receptors are intensively studied in structural biology, displayed for binding poses of different types of ligands. Here, we summarized molecular mechanisms of ligand recognition and receptor activation exhibited by structure. We also reviewed recent advances in structure-based ligand discovery against adrenergic receptors.
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Affiliation(s)
- Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (Y.W.); (L.Z.)
| | - Liting Zeng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (Y.W.); (L.Z.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (Y.W.); (L.Z.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Correspondence:
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132
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Donthamsetti P, Konrad DB, Hetzler B, Fu Z, Trauner D, Isacoff EY. Selective Photoswitchable Allosteric Agonist of a G Protein-Coupled Receptor. J Am Chem Soc 2021; 143:8951-8956. [PMID: 34115935 PMCID: PMC8227462 DOI: 10.1021/jacs.1c02586] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/03/2023]
Abstract
G protein-coupled receptors (GPCRs) are the most common targets of drug discovery. However, the similarity between related GPCRs combined with the complex spatiotemporal dynamics of receptor activation in vivo has hindered drug development. Photopharmacology offers the possibility of using light to control the location and timing of drug action by incorporating a photoisomerizable azobenzene into a GPCR ligand, enabling rapid and reversible switching between an inactive and active configuration. Recent advances in this area include (i) photoagonists and photoantagonists that directly control receptor activity but are nonselective because they bind conserved sites, and (ii) photoallosteric modulators that bind selectively to nonconserved sites but indirectly control receptor activity by modulating the response to endogenous ligand. In this study, we designed a photoswitchable allosteric agonist that targets a nonconserved allosteric site for selectivity and activates the receptor on its own to provide direct control. This work culminated in the development of aBINA, a photoswitchable allosteric agonist that selectively activates the Gi/o-coupled metabotropic glutamate receptor 2 (mGluR2). aBINA is the first example of a new class of precision drugs for GPCRs and other clinically important signaling proteins.
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Affiliation(s)
- Prashant Donthamsetti
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - David B. Konrad
- Department
of Pharmacy, Ludwig-Maximilians-Universität
München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Belinda Hetzler
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Zhu Fu
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Dirk Trauner
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Ehud Y. Isacoff
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Helen
Wills Neuroscience Institute, University
of California, Berkeley, California 94720, United States
- Molecular
Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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133
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Discovery of Novel Allosteric Modulators Targeting an Extra-Helical Binding Site of GLP-1R Using Structure- and Ligand-Based Virtual Screening. Biomolecules 2021; 11:biom11070929. [PMID: 34201418 PMCID: PMC8301998 DOI: 10.3390/biom11070929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/12/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Allosteric modulators have emerged with many potential pharmacological advantages as they do not compete the binding of agonist or antagonist to the orthosteric sites but ultimately affect downstream signaling. To identify allosteric modulators targeting an extra-helical binding site of the glucagon-like peptide-1 receptor (GLP-1R) within the membrane environment, the following two computational approaches were applied: structure-based virtual screening with consideration of lipid contacts and ligand-based virtual screening with the maintenance of specific allosteric pocket residue interactions. Verified by radiolabeled ligand binding and cAMP accumulation experiments, two negative allosteric modulators and seven positive allosteric modulators were discovered using structure-based and ligand-based virtual screening methods, respectively. The computational approach presented here could possibly be used to discover allosteric modulators of other G protein-coupled receptors.
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134
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Defining the Homo- and Heterodimerization Propensities of Metabotropic Glutamate Receptors. Cell Rep 2021; 31:107605. [PMID: 32375054 PMCID: PMC7271767 DOI: 10.1016/j.celrep.2020.107605] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/10/2020] [Accepted: 04/10/2020] [Indexed: 01/02/2023] Open
Abstract
The eight metabotropic glutamate receptors (mGluRs) serve critical modulatory roles throughout the nervous system. The molecular diversity of mGluRs is thought to be further expanded by the formation of heterodimers, but the co-expression of mGluR subtypes at the cellular level and the relative propensities of heterodimer formation are not well known. Here, we analyze single-cell RNA sequencing data and find that cortical pyramidal cells express multiple mGluR subtypes with distinct profiles for different receptor combinations. We then develop quantitative, fluorescence-based assays to define the relative homo- and heterodimer propensities across group-I, -II, and -III mGluRs. We find a strong preference for heterodimerization in a number of cases, including mGluR2 with mGluR3, which we confirm in frontal cortex using in situ RNA hybridization and co-immunoprecipitation. Together, our findings support the biological relevance of mGluR heterodimerization and highlight the complex landscape of mGluR populations in the brain.
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135
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Gertzen CGW, Gohlke H, Häussinger D, Herebian D, Keitel V, Kubitz R, Mayatepek E, Schmitt L. The many facets of bile acids in the physiology and pathophysiology of the human liver. Biol Chem 2021; 402:1047-1062. [PMID: 34049433 DOI: 10.1515/hsz-2021-0156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
Bile acids perform vital functions in the human liver and are the essential component of bile. It is therefore not surprising that the biology of bile acids is extremely complex, regulated on different levels, and involves soluble and membrane receptors as well as transporters. Hereditary disorders of these proteins manifest in different pathophysiological processes that result in liver diseases of varying severity. In this review, we summarize our current knowledge of the physiology and pathophysiology of bile acids with an emphasis on recently established analytical approaches as well as the molecular mechanisms that underlie signaling and transport of bile acids. In this review, we will focus on ABC transporters of the canalicular membrane and their associated diseases. As the G protein-coupled receptor, TGR5, receives increasing attention, we have included aspects of this receptor and its interaction with bile acids.
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Affiliation(s)
- Christoph G W Gertzen
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Diran Herebian
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ralf Kubitz
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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136
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Michaelian N, Sadybekov A, Besserer-Offroy É, Han GW, Krishnamurthy H, Zamlynny BA, Fradera X, Siliphaivanh P, Presland J, Spencer KB, Soisson SM, Popov P, Sarret P, Katritch V, Cherezov V. Structural insights on ligand recognition at the human leukotriene B4 receptor 1. Nat Commun 2021; 12:2971. [PMID: 34016973 PMCID: PMC8137929 DOI: 10.1038/s41467-021-23149-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 04/16/2021] [Indexed: 01/09/2023] Open
Abstract
The leukotriene B4 receptor 1 (BLT1) regulates the recruitment and chemotaxis of different cell types and plays a role in the pathophysiology of infectious, allergic, metabolic, and tumorigenic human diseases. Here we present a crystal structure of human BLT1 (hBLT1) in complex with a selective antagonist MK-D-046, developed for the treatment of type 2 diabetes and other inflammatory conditions. Comprehensive analysis of the structure and structure-activity relationship data, reinforced by site-directed mutagenesis and docking studies, reveals molecular determinants of ligand binding and selectivity toward different BLT receptor subtypes and across species. The structure helps to identify a putative membrane-buried ligand access channel as well as potential receptor binding modes of endogenous agonists. These structural insights of hBLT1 enrich our understanding of its ligand recognition and open up future avenues in structure-based drug design.
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Affiliation(s)
- Nairie Michaelian
- grid.42505.360000 0001 2156 6853Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Chemistry, University of Southern California, Los Angeles, CA USA
| | - Anastasiia Sadybekov
- grid.42505.360000 0001 2156 6853Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Chemistry, University of Southern California, Los Angeles, CA USA
| | - Élie Besserer-Offroy
- grid.86715.3d0000 0000 9064 6198Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC Canada ,grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA USA
| | - Gye Won Han
- grid.42505.360000 0001 2156 6853Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Chemistry, University of Southern California, Los Angeles, CA USA
| | - Harini Krishnamurthy
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Beata A. Zamlynny
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Xavier Fradera
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Phieng Siliphaivanh
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Jeremy Presland
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Kerrie B. Spencer
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Stephen M. Soisson
- grid.417993.10000 0001 2260 0793Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ USA
| | - Petr Popov
- grid.454320.40000 0004 0555 3608Center for Computational and Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia ,grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Philippe Sarret
- grid.86715.3d0000 0000 9064 6198Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Vsevolod Katritch
- grid.42505.360000 0001 2156 6853Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Chemistry, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA USA
| | - Vadim Cherezov
- grid.42505.360000 0001 2156 6853Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA USA ,grid.42505.360000 0001 2156 6853Department of Chemistry, University of Southern California, Los Angeles, CA USA ,grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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137
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de Felice A, Aureli S, Limongelli V. Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach. Front Mol Biosci 2021; 8:673053. [PMID: 34026848 PMCID: PMC8138314 DOI: 10.3389/fmolb.2021.673053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest human membrane receptor family regulating a wide range of cell signaling. For this reason, GPCRs are highly desirable drug targets, with approximately 40% of prescribed medicines targeting a member of this receptor family. The structural homology of GPCRs and the broad spectrum of applications of GPCR-acting drugs suggest an investigation of the cross-activity of a drug toward different GPCR receptors with the aim of rationalizing drug side effects, designing more selective and less toxic compounds, and possibly proposing off-label therapeutic applications. Herein, we present an original in silico approach named “Computational Profiling for GPCRs” (CPG), which is able to represent, in a one-dimensional (1D) string, the physico-chemical properties of a ligand–GPCR binding interaction and, through a tailored alignment algorithm, repurpose the ligand for a different GPCR. We show three case studies where docking calculations and pharmacological data confirm the drug repurposing findings obtained through CPG on 5-hydroxytryptamine receptor 2B, beta-2 adrenergic receptor, and M2 muscarinic acetylcholine receptor. The CPG code is released as a user-friendly graphical user interface with numerous options that make CPG a powerful tool to assist the drug design of GPCR ligands.
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Affiliation(s)
- Alessandra de Felice
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Simone Aureli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano, Switzerland.,Department of Pharmacy, University of Naples "Federico II", Naples, Italy
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138
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Obeng S, Hiranita T, León F, McMahon LR, McCurdy CR. Novel Approaches, Drug Candidates, and Targets in Pain Drug Discovery. J Med Chem 2021; 64:6523-6548. [PMID: 33956427 DOI: 10.1021/acs.jmedchem.1c00028] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because of the problems associated with opioids, drug discovery efforts have been employed to develop opioids with reduced side effects using approaches such as biased opioid agonism, multifunctional opioids, and allosteric modulation of opioid receptors. Receptor targets such as adrenergic, cannabinoid, P2X3 and P2X7, NMDA, serotonin, and sigma, as well as ion channels like the voltage-gated sodium channels Nav1.7 and Nav1.8 have been targeted to develop novel analgesics. Several enzymes, such as soluble epoxide hydrolase, sepiapterin reductase, and MAGL/FAAH, have also been targeted to develop novel analgesics. In this review, old and recent targets involved in pain signaling and compounds acting at these targets are summarized. In addition, strategies employed to reduce side effects, increase potency, and efficacy of opioids are also elaborated. This review should aid in propelling drug discovery efforts to discover novel analgesics.
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Affiliation(s)
- Samuel Obeng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.,Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Takato Hiranita
- Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Francisco León
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia 29208, United States
| | - Lance R McMahon
- Department Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States.,Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida 32610, United States
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139
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Zaidi SA, Katritch V. Structural Characterization of KOR Inactive and Active States for 3D Pharmacology and Drug Discovery. Handb Exp Pharmacol 2021; 271:41-64. [PMID: 33945028 DOI: 10.1007/164_2021_461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The structure of the human kappa opioid receptor (KOR) in complex with the long-acting antagonist JDTic was solved crystallographically in 2012 and, along with structures of other opioid receptors, revolutionized our understanding of opioid system function and pharmacology. More recently, active state KOR structure was also determined, giving important insights into activation mechanisms of the receptor. In this review, we will discuss how the understanding of atomistic structures of KOR established a key platform for deciphering details of subtype and functional selectivity of KOR-targeting ligands and for discovery of new chemical probes with potentially beneficial pharmacological profiles.
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Affiliation(s)
- Saheem A Zaidi
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA. .,Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
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140
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Scolari F, Valerio F, Benelli G, Papadopoulos NT, Vaníčková L. Tephritid Fruit Fly Semiochemicals: Current Knowledge and Future Perspectives. INSECTS 2021; 12:insects12050408. [PMID: 33946603 PMCID: PMC8147262 DOI: 10.3390/insects12050408] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
The Dipteran family Tephritidae (true fruit flies) comprises more than 5000 species classified in 500 genera distributed worldwide. Tephritidae include devastating agricultural pests and highly invasive species whose spread is currently facilitated by globalization, international trade and human mobility. The ability to identify and exploit a wide range of host plants for oviposition, as well as effective and diversified reproductive strategies, are among the key features supporting tephritid biological success. Intraspecific communication involves the exchange of a complex set of sensory cues that are species- and sex-specific. Chemical signals, which are standing out in tephritid communication, comprise long-distance pheromones emitted by one or both sexes, cuticular hydrocarbons with limited volatility deposited on the surrounding substrate or on the insect body regulating medium- to short-distance communication, and host-marking compounds deposited on the fruit after oviposition. In this review, the current knowledge on tephritid chemical communication was analysed with a special emphasis on fruit fly pest species belonging to the Anastrepha, Bactrocera, Ceratitis, and Rhagoletis genera. The multidisciplinary approaches adopted for characterising tephritid semiochemicals, and the real-world applications and challenges for Integrated Pest Management (IPM) and biological control strategies are critically discussed. Future perspectives for targeted research on fruit fly chemical communication are highlighted.
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Affiliation(s)
- Francesca Scolari
- Institute of Molecular Genetics IGM-CNR “Luigi Luca Cavalli-Sforza”, I-27100 Pavia, Italy
- Correspondence: (F.S.); (L.V.); Tel.: +39-0382-986421 (F.S.); +420-732-852-528 (L.V.)
| | - Federica Valerio
- Department of Biology and Biotechnology, University of Pavia, I-27100 Pavia, Italy;
| | - Giovanni Benelli
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy;
| | - Nikos T. Papadopoulos
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, Fytokou st., N. Ionia, 38446 Volos, Greece;
| | - Lucie Vaníčková
- Department of Chemistry and Biochemistry, Faculty of AgriSciences Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Department of Forest Botany, Dendrology and Geobiocoenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Correspondence: (F.S.); (L.V.); Tel.: +39-0382-986421 (F.S.); +420-732-852-528 (L.V.)
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141
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Unlocking the Non-IgE-Mediated Pseudo-Allergic Reaction Puzzle with Mas-Related G-Protein Coupled Receptor Member X2 (MRGPRX2). Cells 2021; 10:cells10051033. [PMID: 33925682 PMCID: PMC8146469 DOI: 10.3390/cells10051033] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 12/17/2022] Open
Abstract
Mas-related G-protein coupled receptor member X2 (MRGPRX2) is a class A GPCR expressed on mast cells. Mast cells are granulated tissue-resident cells known for host cell response, allergic response, and vascular homeostasis. Immunoglobulin E receptor (FcεRI)-mediated mast cell activation is a well-studied and recognized mechanism of allergy and hypersensitivity reactions. However, non-IgE-mediated mast cell activation is less explored and is not well recognized. After decades of uncertainty, MRGPRX2 was discovered as the receptor responsible for non-IgE-mediated mast cells activation. The puzzle of non-IgE-mediated pseudo-allergic reaction is unlocked by MRGPRX2, evidenced by a plethora of reported endogenous and exogenous MRGPRX2 agonists. MRGPRX2 is exclusively expressed on mast cells and exhibits varying affinity for many molecules such as antimicrobial host defense peptides, neuropeptides, and even US Food and Drug Administration-approved drugs. The discovery of MRGPRX2 has changed our understanding of mast cell biology and filled the missing link of the underlying mechanism of drug-induced MC degranulation and pseudo-allergic reactions. These non-canonical characteristics render MRGPRX2 an intriguing player in allergic diseases. In the present article, we reviewed the emerging role of MRGPRX2 as a non-IgE-mediated mechanism of mast cell activation in pseudo-allergic reactions. We have presented an overview of mast cells, their receptors, structural insight into MRGPRX2, MRGPRX2 agonists and antagonists, the crucial role of MRGPRX2 in pseudo-allergic reactions, current challenges, and the future research direction.
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142
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Directed evolution for high functional production and stability of a challenging G protein-coupled receptor. Sci Rep 2021; 11:8630. [PMID: 33883583 PMCID: PMC8060309 DOI: 10.1038/s41598-021-87793-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) carry out many fundamental biological functions, are involved in a large number of physiological responses, and are thus important drug targets. To allow detailed biophysical and structural studies, most of these important receptors have to be engineered to overcome their poor intrinsic stability and low expression levels. However, those GPCRs with especially poor properties cannot be successfully optimised even with the current technologies. Here, we present an engineering strategy, based on the combination of three previously developed directed evolution methods, to improve the properties of particularly challenging GPCRs. Application of this novel combination approach enabled the successful selection for improved and crystallisable variants of the human oxytocin receptor, a GPCR with particularly low intrinsic production levels. To analyse the selection results and, in particular, compare the mutations enriched in different hosts, we developed a Next-Generation Sequencing (NGS) strategy that combines long reads, covering the whole receptor, with exceptionally low error rates. This study thus gave insight into the evolution pressure on the same membrane protein in prokaryotes and eukaryotes. Our long-read NGS strategy provides a general methodology for the highly accurate analysis of libraries of point mutants during directed evolution.
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143
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Hilger D. The role of structural dynamics in GPCR‐mediated signaling. FEBS J 2021; 288:2461-2489. [DOI: 10.1111/febs.15841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel Hilger
- Department of Pharmaceutical Chemistry Philipps‐University Marburg Germany
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144
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Lima I, Cino EA. Sequence similarity in 3D for comparison of protein families. J Mol Graph Model 2021; 106:107906. [PMID: 33848948 DOI: 10.1016/j.jmgm.2021.107906] [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] [Received: 10/16/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 11/26/2022]
Abstract
Homologous proteins are often compared by pairwise sequence alignment, and structure superposition if the atomic coordinates are available. Unification of sequence and structure data is an important task in structural biology. Here, we present the Sequence Similarity 3D (SS3D) method of integrating sequence and structure information. SS3D is a distance and substitution matrix-based method for straightforward visualization of regions of similarity and difference between homologous proteins. This work details the SS3D approach, and demonstrates its utility through case studies comparing members of several protein families. The examples show that SS3D can effectively highlight biologically important regions of similarity and dissimilarity. We anticipate that the method will be useful for numerous structural biology applications, including, but not limited to, studies of binding specificity, structure-function relationships, and evolutionary pathways. SS3D is available with a manual and tutorial at https://github.com/0x462e41/SS3D/.
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Affiliation(s)
- Igor Lima
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Elio A Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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145
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Coevolution underlies GPCR-G protein selectivity and functionality. Sci Rep 2021; 11:7858. [PMID: 33846507 PMCID: PMC8041822 DOI: 10.1038/s41598-021-87251-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate diverse physiological events, which makes them as the major targets for many approved drugs. G proteins are downstream molecules that receive signals from GPCRs and trigger cell responses. The GPCR-G protein selectivity mechanism on how they properly and timely interact is still unclear. Here, we analyzed model GPCRs (i.e. HTR, DAR) and Gα proteins with a coevolutionary tool, statistical coupling analysis. The results suggested that 5-hydroxytryptamine receptors and dopamine receptors have common conserved and coevolved residues. The Gα protein also have conserved and coevolved residues. These coevolved residues were implicated in the molecular functions of the analyzed proteins. We also found specific coevolving pairs related to the selectivity between GPCR and G protein were identified. We propose that these results would contribute to better understandings of not only the functional residues of GPCRs and Gα proteins but also GPCR-G protein selectivity mechanisms.
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146
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Chaudhary PK, Kim S. The GRKs Reactome: Role in Cell Biology and Pathology. Int J Mol Sci 2021; 22:ijms22073375. [PMID: 33806057 PMCID: PMC8036551 DOI: 10.3390/ijms22073375] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptor kinases (GRKs) are protein kinases that function in concert with arrestins in the regulation of a diverse class of G protein-coupled receptors (GPCRs) signaling. Although GRKs and arrestins are key participants in the regulation of GPCR cascades, the complex regulatory mechanisms of GRK expression, its alternation, and their function are not thoroughly understood. Several studies together with the work from our lab in recent years have revealed the critical role of these kinases in various physiological and pathophysiological processes, including cardiovascular biology, inflammation and immunity, neurodegeneration, thrombosis, and hemostasis. A comprehensive understanding of the mechanisms underlying functional interactions with multiple receptor proteins and how these interactions take part in the development of various pathobiological processes may give rise to novel diagnostic and therapeutic strategies. In this review, we summarize the current research linking the role of GRKs to various aspects of cell biology, pathology, and therapeutics, with a particular focus on thrombosis and hemostasis.
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147
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Gupta A, Behl T, Sehgal A, Bhardwaj S, Singh S, Sharma N, Hafeez A. Exploring the recent molecular targets for diabetes and associated complications. Mol Biol Rep 2021; 48:2863-2879. [PMID: 33763776 DOI: 10.1007/s11033-021-06294-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022]
Abstract
Diabetes is likely one of the centenarian diseases which is apprehended with certainty to humans. According to established protocols of the World Health Organisation (WHO) and numerous investigated studies diabetes is analyzed as a stellar and leading health issue worldwide. Although, the implicit costs of this pathology are increasing every year, thus, there is a need to find a novel method which can provide promising results in the management of diabetes and can overcome the side effects associated with the conventional medication. Comprehensive review of this topic was undertaken through various research and review papers which were conducted using MEDLINE, BIOSIS and EMBASE database. Using various keywords, we retrieve the most relevant content for the thorough review on recent targets and novel molecular pathways for targeting diabetes and associated complications. From the detailed analysis, we have highlighted some molecular pathways and novel targets which had shown promising results in both in-vitro and in-vivo studies and may be considered as pipeline target for clinical trials. Furthermore, these targets not only abetted amelioration of diabetes but also helped in mitigation of diabetes associated complications as well. Thus, based on the available information and literature on these potential molecules, conclusive evidence can be drawn which confirms targeting these novel pathways may unleash an array of benefits that have the potential to overpower the benefits obtained from conventional therapy in the management of diabetes thereby decreasing morbidity and mortality associated with diabetic complications.
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Affiliation(s)
- Amit Gupta
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Shaveta Bhardwaj
- GHG Khalsa College of Pharmacy, Gurusar Sadhar, Ludhiana, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Mirzapur Pole, Uttar Pradesh, India
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148
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Zarnecka J, Lukac I, Messham SJ, Hussin A, Coppola F, Enoch SJ, Dossetter AG, Griffen EJ, Leach AG. Mapping Ligand-Shape Space for Protein-Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins. J Chem Inf Model 2021; 61:1859-1874. [PMID: 33755448 DOI: 10.1021/acs.jcim.1c00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many of the recently developed methods to study the shape of molecules permit one conformation of one molecule to be compared to another conformation of the same or a different molecule: a relative shape. Other methods provide an absolute description of the shape of a conformation that does not rely on comparisons or overlays. Any absolute description of shape can be used to generate a self-organizing map (shape map) that places all molecular shapes relative to one another; in the studies reported here, the shape fingerprint and ultrafast shape recognition methods are employed to create such maps. In the shape maps, molecules that are near one another have similar shapes, and the maps for the 102 targets in the DUD-E set have been generated. By examining the distribution of actives in comparison with their physical-property-matched decoys, we show that the proteins of key-in-lock type (relatively rigid receptor and ligand) can be distinguished from those that are more of a hand-in-glove type (more flexible receptor and ligand). These are linked to known differences in protein flexibility and binding-site size.
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Affiliation(s)
- Joanna Zarnecka
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Iva Lukac
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Stephen J Messham
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Alhusein Hussin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Francesco Coppola
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Steven J Enoch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | | | - Edward J Griffen
- MedChemica Limited, Biohub, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K.,MedChemica Limited, Biohub, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K.,Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
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149
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Barella LF, Jain S, Kimura T, Pydi SP. Metabolic roles of G protein-coupled receptor signaling in obesity and type 2 diabetes. FEBS J 2021; 288:2622-2644. [PMID: 33682344 DOI: 10.1111/febs.15800] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/31/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022]
Abstract
The incidence of obesity and type 2 diabetes (T2D) has been increasing steadily worldwide. It is estimated that by 2045 more than 800 million people will be suffering from diabetes. Despite the advancements in modern medicine, more effective therapies for treating obesity and T2D are needed. G protein-coupled receptors (GPCRs) have emerged as important drug targets for various chronic diseases, including obesity, T2D, and liver diseases. During the past two decades, many laboratories worldwide focused on understanding the role of GPCR signaling in regulating glucose metabolism and energy homeostasis. The information gained from these studies can guide the development of novel therapeutic agents. In this review, we summarize recent studies providing insights into the role of GPCR signaling in peripheral, metabolically important tissues such as pancreas, liver, skeletal muscle, and adipose tissue, focusing primarily on the use of mutant animal models and human data.
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Affiliation(s)
- Luiz F Barella
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.,Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Shanu Jain
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Takefumi Kimura
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sai P Pydi
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.,Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
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150
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Wang M, Hou S, Wei Y, Li D, Lin J. Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking. PLoS Comput Biol 2021; 17:e1008821. [PMID: 33739970 PMCID: PMC7978378 DOI: 10.1371/journal.pcbi.1008821] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Adenosine receptors (ARs) have been demonstrated to be potential therapeutic targets against Parkinson's disease (PD). In the present study, we describe a multistage virtual screening approach that identifies dual adenosine A1 and A2A receptor antagonists using deep learning, pharmacophore models, and molecular docking methods. Nineteen hits from the ChemDiv library containing 1,178,506 compounds were selected and further tested by in vitro assays (cAMP functional assay and radioligand binding assay); of these hits, two compounds (C8 and C9) with 1,2,4-triazole scaffolds possessing the most potent binding affinity and antagonistic activity for A1/A2A ARs at the nanomolar level (pKi of 7.16-7.49 and pIC50 of 6.31-6.78) were identified. Further molecular dynamics (MD) simulations suggested similarly strong binding interactions of the complexes between the A1/A2A ARs and two compounds (C8 and C9). Notably, the 1,2,4-triazole derivatives (compounds C8 and C9) were identified as the most potent dual A1/A2A AR antagonists in our study and could serve as a basis for further development. The effective multistage screening approach developed in this study can be utilized to identify potent ligands for other drug targets.
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Affiliation(s)
- Mukuo Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Shujing Hou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- * E-mail: (YW); (DL); (JL)
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- * E-mail: (YW); (DL); (JL)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin, China
- * E-mail: (YW); (DL); (JL)
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