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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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52
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Zhang X, Johnson RM, Drulyte I, Yu L, Kotecha A, Danev R, Wootten D, Sexton PM, Belousoff MJ. Evolving cryo-EM structural approaches for GPCR drug discovery. Structure 2021; 29:963-974.e6. [PMID: 33957078 DOI: 10.1016/j.str.2021.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/10/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest class of cell surface drug targets. Advances in stabilization of GPCR:transducer complexes, together with improvements in cryoelectron microscopy (cryo-EM) have recently been applied to structure-assisted drug design for GPCR agonists. Nonetheless, limitations in the commercial application of these approaches, including the use of nanobody 35 (Nb35) to aid complex stabilization and the high cost of 300 kV imaging, have restricted broad application of cryo-EM in drug discovery. Here, using the PF 06882961-bound GLP-1R as exemplar, we validated the formation of stable complexes with a modified Gs protein in the absence of Nb35. In parallel, we compare 200 versus 300 kV image acquisition using a Falcon 4 or K3 direct electron detector. Moreover, the 200 kV Glacios-Falcon 4 yielded a 3.2 Å map with clear density for bound drug and multiple structurally ordered waters. Our work paves the way for broader commercial application of cryo-EM for GPCR drug discovery.
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Affiliation(s)
- Xin Zhang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Rachel M Johnson
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Ieva Drulyte
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, 5651 GG Eindhoven, the Netherlands
| | - Lingbo Yu
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, 5651 GG Eindhoven, the Netherlands
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, 5651 GG Eindhoven, the Netherlands
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
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Ma N, Nivedha AK, Vaidehi N. Allosteric communication regulates ligand-specific GPCR activity. FEBS J 2021; 288:2502-2512. [PMID: 33738925 PMCID: PMC9805801 DOI: 10.1111/febs.15826] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 01/11/2023]
Abstract
G protein-coupled receptors (GPCRs) are membrane-bound proteins that are ubiquitously expressed in many cell types and take part in mediating multiple signaling pathways. GPCRs are dynamic proteins and exist in an equilibrium between an ensemble of conformational states such as inactive and fully active states. This dynamic nature of GPCRs is one of the factors that confers their basal activity even in the absence of any ligand-mediated activation. Ligands selectively bind and stabilize a subset of the conformations from the ensemble leading to a shift in the equilibrium toward the inactive or the active state depending on the nature of the ligand. This ligand-selective effect is achieved through allosteric communication between the ligand binding site and G protein or β-arrestin coupling site. Similarly, the G protein coupling to the receptor exerts the allosteric effect on the ligand binding region leading to increased binding affinity for agonists and decreased affinity for antagonists or inverse agonists. In this review, we enumerate the current state of our understanding of the mechanism of allosteric communication in GPCRs with a specific focus on the critical role of computational methods in delineating the residues involved in allosteric communication. Analyzing allosteric communication mechanism using molecular dynamics simulations has revealed (a) a structurally conserved mechanism of allosteric communication that regulates the G protein coupling, (b) a rational structure-based approach to designing selective ligands, and (c) an approach to designing allosteric GPCR mutants that are either ligand and G protein or β-arrestin selective.
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Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Anita K. Nivedha
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010,to whom correspondence should be addressed:
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Fantasia RJ, Nourmahnad A, Halpin E, Forman SA. Substituted Cysteine Modification and Protection with n-Alkyl- Methanethiosulfonate Reagents Yields a Precise Estimate of the Distance between Etomidate and a Residue in Activated GABA Type A Receptors. Mol Pharmacol 2021; 99:426-434. [PMID: 33766924 DOI: 10.1124/molpharm.120.000224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/10/2021] [Indexed: 11/22/2022] Open
Abstract
The anesthetic etomidate modulates synaptic α1β2/3γ2 GABAA receptors via binding sites located in transmembrane β+/α- interfaces. Various approaches indicate that etomidate binds near β2/3M286 side chains, including recent cryogenic electron microscopy images in α1β2γ2L receptors under nonphysiologic conditions with ∼3.5-Å resolution. We hypothesized that substituted cysteine modification and protection experiments using variably sized n-alkyl-methanethiosulfonate (MTS) reagents could precisely estimate the distance between bound etomidate and β3M286 side chains in activated functional receptors. Using voltage-clamp electrophysiology in Xenopus oocytes expressing α1β3M286Cγ2L GABAA receptors, we measured functional changes after exposing GABA-activated receptors to n-alkyl-MTS reagents, from methyl-MTS to n-decyl-MTS. Based on previous studies using a large sulfhydryl reagent, we anticipated that cysteine modifications large enough to overlap etomidate sites would cause persistently increased GABA sensitivity and decreased etomidate modulation and that etomidate would hinder these modifications, reducing effects. Based on altered GABA or etomidate sensitivity, ethyl-MTS and larger n-alkyl-MTS reagents modified GABA-activated α1β3M286Cγ2L GABAA receptors. Receptor modification by n-propyl-MTS or larger reagents caused persistently increased GABA sensitivity and decreased etomidate modulation. Receptor-bound etomidate blocked β3M286C modification by n-propyl-MTS, n-butyl-MTS, and n-hexyl-MTS. In contrast, GABA sensitivity was unaltered by receptor exposure to methyl-MTS or ethyl-MTS, and ethyl-MTS modification uniquely increased etomidate modulation. These results reveal a "cut-on" between ethyl-MTS and n-propyl-MTS, from which we infer that -S-(n-propyl) is the smallest β3M286C appendage that overlaps with etomidate sites. Molecular models of the native methionine and -S-ethyl and -S-(n-propyl) modified cysteines suggest that etomidate is located between 1.7 and 3.0 Å from the β3M286 side chain. SIGNIFICANCE STATEMENT: Precise spatial relationships between drugs and their receptor sites are essential for mechanistic understanding and drug development. This study combined electrophysiology, a cysteine substitution, and n-alkyl-methanethiosulfonate modifiers, creating a precise molecular ruler to estimate the distance between a α1β3γ2L GABA type A receptor residue and etomidate bound in the transmembrane β+/α- interface.
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Affiliation(s)
- Ryan J Fantasia
- Beecher-Mallinckrodt Laboratories, Department of Anesthesia Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Anahita Nourmahnad
- Beecher-Mallinckrodt Laboratories, Department of Anesthesia Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Elizabeth Halpin
- Beecher-Mallinckrodt Laboratories, Department of Anesthesia Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Stuart A Forman
- Beecher-Mallinckrodt Laboratories, Department of Anesthesia Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts
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Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence. Sci Rep 2021; 11:5910. [PMID: 33723285 PMCID: PMC7960716 DOI: 10.1038/s41598-021-84069-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A2A receptor (A2AR) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A2AR to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 2296.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150-350 ns), intermediate (50-60 μs) and slow (200-300 μs) conformational dynamics in A2AR, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-Gs). Most notably, the agonist binding and the coupling to mini-Gs accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y2887.53, and Y2907.55) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 2296.31 on TM6. This study provides a quantitative description of conformational dynamics in A2AR and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.
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56
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Waltenspühl Y, Ehrenmann J, Klenk C, Plückthun A. Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules 2021; 26:molecules26051465. [PMID: 33800379 PMCID: PMC7962830 DOI: 10.3390/molecules26051465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/14/2023] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) exert fundamental biological functions and are involved in a multitude of physiological responses, making these receptors ideal drug targets. Drug discovery programs targeting GPCRs have been greatly facilitated by the emergence of high-resolution structures and the resulting opportunities to identify new chemical entities through structure-based drug design. To enable the determination of high-resolution structures of GPCRs, most receptors have to be engineered to overcome intrinsic hurdles such as their poor stability and low expression levels. In recent years, multiple engineering approaches have been developed to specifically address the technical difficulties of working with GPCRs, which are now beginning to make more challenging receptors accessible to detailed studies. Importantly, successfully engineered GPCRs are not only valuable in X-ray crystallography, but further enable biophysical studies with nuclear magnetic resonance spectroscopy, surface plasmon resonance, native mass spectrometry, and fluorescence anisotropy measurements, all of which are important for the detailed mechanistic understanding, which is the prerequisite for successful drug design. Here, we summarize engineering strategies based on directed evolution to reduce workload and enable biophysical experiments of particularly challenging GPCRs.
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57
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Hu XM, Li ZX, Lin RH, Shan JQ, Yu QW, Wang RX, Liao LS, Yan WT, Wang Z, Shang L, Huang Y, Zhang Q, Xiong K. Guidelines for Regulated Cell Death Assays: A Systematic Summary, A Categorical Comparison, A Prospective. Front Cell Dev Biol 2021; 9:634690. [PMID: 33748119 PMCID: PMC7970050 DOI: 10.3389/fcell.2021.634690] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Over the past few years, the field of regulated cell death continues to expand and novel mechanisms that orchestrate multiple regulated cell death pathways are being unveiled. Meanwhile, researchers are focused on targeting these regulated pathways which are closely associated with various diseases for diagnosis, treatment, and prognosis. However, the complexity of the mechanisms and the difficulties of distinguishing among various regulated types of cell death make it harder to carry out the work and delay its progression. Here, we provide a systematic guideline for the fundamental detection and distinction of the major regulated cell death pathways following morphological, biochemical, and functional perspectives. Moreover, a comprehensive evaluation of different assay methods is critically reviewed, helping researchers to make a reliable selection from among the cell death assays. Also, we highlight the recent events that have demonstrated some novel regulated cell death processes, including newly reported biomarkers (e.g., non-coding RNA, exosomes, and proteins) and detection techniques.
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Affiliation(s)
- Xi-Min Hu
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhi-Xin Li
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Rui-Han Lin
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Jia-Qi Shan
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Qing-Wei Yu
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Rui-Xuan Wang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lv-Shuang Liao
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Wei-Tao Yan
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhen Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Lei Shang
- Jiangxi Research Institute of Ophthalmology and Visual Sciences, Affiliated Eye Hospital of Nanchang University, Nanchang, China
| | - Yanxia Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Qi Zhang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Ophthalmology, Changsha, China
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58
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Chemello K, García-Nafría J, Gallo A, Martín C, Lambert G, Blom D. Lipoprotein metabolism in familial hypercholesterolemia. J Lipid Res 2021; 62:100062. [PMID: 33675717 PMCID: PMC8050012 DOI: 10.1016/j.jlr.2021.100062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 02/06/2023] Open
Abstract
Familial hypercholesterolemia (FH) is one of the most common genetic disorders in humans. It is an extremely atherogenic metabolic disorder characterized by lifelong elevations of circulating LDL-C levels often leading to premature cardiovascular events. In this review, we discuss the clinical phenotypes of heterozygous and homozygous FH, the genetic variants in four genes (LDLR/APOB/PCSK9/LDLRAP1) underpinning the FH phenotype as well as the most recent in vitro experimental approaches used to investigate molecular defects affecting the LDL receptor pathway. In addition, we review perturbations in the metabolism of lipoproteins other than LDL in FH, with a major focus on lipoprotein (a). Finally, we discuss the mode of action and efficacy of many of the currently approved hypocholesterolemic agents used to treat patients with FH, with a special emphasis on the treatment of phenotypically more severe forms of FH.
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Affiliation(s)
- Kévin Chemello
- Inserm UMR 1188 DéTROI, Université de La Réunion, Saint- Denis de La Réunion, France
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of complex systems (BIFI), University of Zaragoza, Zaragoza, Spain; Laboratorio de Microscopías Avanzadas, University of Zaragoza, Zaragoza, Spain
| | - Antonio Gallo
- Cardiovascular Prevention Unit, Department of Endocrinology and Metabolism, Pitié-Salpêtrière University Hospital, Paris, France; Laboratoire d'imagerie Biomédicale, INSERM 1146, CNRS 7371, Sorbonne University, Paris, France
| | - Cesar Martín
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco UPV/EHU, Bilbao, Spain
| | - Gilles Lambert
- Inserm UMR 1188 DéTROI, Université de La Réunion, Saint- Denis de La Réunion, France.
| | - Dirk Blom
- Hatter Institute for Cardiovascular Research in Africa and Division of Lipidology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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Suzuki K, Katayama K, Sumii Y, Nakagita T, Suno R, Tsujimoto H, Iwata S, Kobayashi T, Shibata N, Kandori H. Vibrational analysis of acetylcholine binding to the M 2 receptor. RSC Adv 2021; 11:12559-12567. [PMID: 35423811 PMCID: PMC8696876 DOI: 10.1039/d1ra01030a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/13/2021] [Indexed: 01/14/2023] Open
Abstract
The M2 muscarinic acetylcholine receptor (M2R) is a prototypical G protein-coupled receptor (GPCR) that responds to acetylcholine (ACh) and mediates various cellular responses in the nervous system. We recently established Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy for ligand binding to M2R reconstituted in lipid membranes, paving the way to understand the mechanism in atomic detail. However, the obtained difference FTIR spectra upon ligand binding contained ligand, protein, lipid, and water signals, so a vibrational assignment was needed for a thorough understanding. In the present study, we compared difference FTIR spectra between unlabeled and 2-13C labeled ACh, and assigned the bands at 1741 and 1246 cm−1 as the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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O and C–O stretches of ACh, respectively. The CO stretch of ACh in M2R is close to that in aqueous solution (1736 cm−1), and much lower in frequency than the free CO stretch (1778–1794 cm−1), indicating a strong hydrogen bond, which probably formed with N4046.52. We propose that a water molecule bridges ACh and N4046.52. The other ACh terminal is positively charged, and it interacts with negatively charged D1033.32. The present study revealed that D1033.32 is deprotonated (negatively charged) in both ACh-bound and free states, a suggested mechanism to stabilize the negative charge of D1033.32 in the free M2R. We recently reported difference FTIR spectra upon binding of Ach to M2R.![]()
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60
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Uchański T, Masiulis S, Fischer B, Kalichuk V, López-Sánchez U, Zarkadas E, Weckener M, Sente A, Ward P, Wohlkönig A, Zögg T, Remaut H, Naismith JH, Nury H, Vranken W, Aricescu AR, Pardon E, Steyaert J. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Nat Methods 2021; 18:60-68. [PMID: 33408403 PMCID: PMC7611088 DOI: 10.1038/s41592-020-01001-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/22/2020] [Indexed: 01/28/2023]
Abstract
Nanobodies are popular and versatile tools for structural biology. They have a compact single immunoglobulin domain organization, bind target proteins with high affinities while reducing their conformational heterogeneity and stabilize multi-protein complexes. Here we demonstrate that engineered nanobodies can also help overcome two major obstacles that limit the resolution of single-particle cryo-electron microscopy reconstructions: particle size and preferential orientation at the water-air interfaces. We have developed and characterized constructs, termed megabodies, by grafting nanobodies onto selected protein scaffolds to increase their molecular weight while retaining the full antigen-binding specificity and affinity. We show that the megabody design principles are applicable to different scaffold proteins and recognition domains of compatible geometries and are amenable for efficient selection from yeast display libraries. Moreover, we demonstrate that megabodies can be used to obtain three-dimensional reconstructions for membrane proteins that suffer from severe preferential orientation or are otherwise too small to allow accurate particle alignment.
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Affiliation(s)
- Tomasz Uchański
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Simonas Masiulis
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Baptiste Fischer
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Valentina Kalichuk
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Uriel López-Sánchez
- CNRS, Université Grenoble Alpes, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Eleftherios Zarkadas
- CNRS, Université Grenoble Alpes, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Miriam Weckener
- Rosalind Franklin Institute, Rutherford Appleton Laboratory, Didcot, UK
| | - Andrija Sente
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Philip Ward
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexandre Wohlkönig
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Thomas Zögg
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - James H Naismith
- Rosalind Franklin Institute, Rutherford Appleton Laboratory, Didcot, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hugues Nury
- CNRS, Université Grenoble Alpes, CEA, Institut de Biologie Structurale, Grenoble, France
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - A Radu Aricescu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.
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Tiss A, Ben Boubaker R, Henrion D, Guissouma H, Chabbert M. Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom. Methods Mol Biol 2021; 2315:73-97. [PMID: 34302671 DOI: 10.1007/978-1-0716-1468-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With 700 members, G protein-coupled receptors (GPCRs) of the rhodopsin family (class A) form the largest membrane receptor family in humans and are the target of about 30% of presently available pharmaceutical drugs. The recent boom in GPCR structures led to the structural resolution of 57 unique receptors in different states (39 receptors in inactive state only, 2 receptors in active state only and 16 receptors in different activation states). In spite of these tremendous advances, most computational studies on GPCRs, including molecular dynamics simulations, virtual screening and drug design, rely on GPCR models obtained by homology modeling. In this protocol, we detail the different steps of homology modeling with the MODELLER software, from template selection to model evaluation. The present structure boom provides closely related templates for most receptors. If, in these templates, some of the loops are not resolved, in most cases, the numerous available structures enable to find loop templates with similar length for equivalent loops. However, simultaneously, the large number of putative templates leads to model ambiguities that may require additional information based on multiple sequence alignments or molecular dynamics simulations to be resolved. Using the modeling of the human bradykinin receptor B1 as a case study, we show how several templates are managed by MODELLER, and how the choice of template(s) and of template fragments can improve the quality of the models. We also give examples of how additional information and tools help the user to resolve ambiguities in GPCR modeling.
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Affiliation(s)
- Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.,Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
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Yang Z, Zhao Y, Hao D, Wang H, Li S, Jia L, Yuan X, Zhang L, Meng L, Zhang S. Computational identification of potential chemoprophylactic agents according to dynamic behavior of peroxisome proliferator-activated receptor gamma. RSC Adv 2020; 11:147-159. [PMID: 35423024 PMCID: PMC8690233 DOI: 10.1039/d0ra09059j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is an attractive target for chemoprevention of lung carcinoma, however its highly dynamic nature has plagued drug development for decades, with difficulties in receptor modeling for structure-based design. In this work, an integrated receptor-based virtual screening (VS) strategy was applied to identify PPARγ agonists as chemoprophylactic agents by using extensive docking and conformational sampling methods. Our results showed that the conformational plasticity of PPARγ, especially the H2 & S245 loop, H2' & Ω loop and AF-2 surface, is markedly affected by binding of full/partial agonists. To fully take the dynamic behavior of PPARγ into account, the VS approach effectively sorts out five commercial agents with reported antineoplastic properties. Among them, ZINC03775146 (gusperimus) and ZINC14087743 (miltefosine) might be novel PPARγ agonists with the potential for chemoprophylaxis, that simultaneously take part in a flexible switch of the AF-2 surface and state change of the Ω loop. Furthermore, the dynamic structural coupling between the H2 & S245 and H2' & Ω loops offers enticing hope for PPARγ-targeted therapeutics, by blocking kinase accessibility to PPARγ. These results might aid the development of chemopreventive drugs, and the integrated VS strategy could be conducive to drug design for highly flexible biomacromolecules.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University Xi'an 710049 China +86-29-82660915 +86-29-82660915
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Chemistry, Xi'an Jiaotong University Xi'an 710049 China
- School of Life Science and Technology, Xi'an Jiaotong University Xi'an 710049 China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University Xi'an 710049 China +86-29-82660915 +86-29-82660915
| | - Dongxiao Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University Xi'an 710049 China +86-29-82660915 +86-29-82660915
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University Xi'an 710049 China +86-29-82660915 +86-29-82660915
| | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University Shanghai 200041 China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University Xi'an 710032 China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University Guangzhou 510632 China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University Xi'an 710049 China +86-29-82660915 +86-29-82660915
| | - Lingjie Meng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Chemistry, Xi'an Jiaotong University Xi'an 710049 China
- Instrumental Analysis Center, Xi'an Jiao Tong University Xi'an 710049 China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University Xi'an 710049 China +86-29-82660915 +86-29-82660915
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63
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Cai H, Yao H, Li T, Hutter CAJ, Li Y, Tang Y, Seeger MA, Li D. An improved fluorescent tag and its nanobodies for membrane protein expression, stability assay, and purification. Commun Biol 2020; 3:753. [PMID: 33303987 PMCID: PMC7729955 DOI: 10.1038/s42003-020-01478-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 01/08/2023] Open
Abstract
Green fluorescent proteins (GFPs) are widely used to monitor membrane protein expression, purification, and stability. An ideal reporter should be stable itself and provide high sensitivity and yield. Here, we demonstrate that a coral (Galaxea fascicularis) thermostable GFP (TGP) is by such reasons an improved tag compared to the conventional jellyfish GFPs. TGP faithfully reports membrane protein stability at temperatures near 90 °C (20-min heating). By contrast, the limit for the two popular GFPs is 64 °C and 74 °C. Replacing GFPs with TGP increases yield for all four test membrane proteins in four expression systems. To establish TGP as an affinity tag for membrane protein purification, several high-affinity synthetic nanobodies (sybodies), including a non-competing pair, are generated, and the crystal structure of one complex is solved. Given these advantages, we anticipate that TGP becomes a widely used tool for membrane protein structural studies.
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Affiliation(s)
- Hongmin Cai
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Hebang Yao
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Tingting Li
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Yanfang Li
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Yannan Tang
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Dianfan Li
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China.
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64
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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Cryo-EM as a powerful tool for drug discovery. Bioorg Med Chem Lett 2020; 30:127524. [PMID: 32890683 PMCID: PMC7467112 DOI: 10.1016/j.bmcl.2020.127524] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The recent revolution in cryo-EM has produced an explosion of structures at near-atomic or better resolution. This has allowed cryo-EM structures to provide visualization of bound small-molecule ligands in the macromolecules, and these new structures have provided unprecedented insights into the molecular mechanisms of complex biochemical processes. They have also had a profound impact on drug discovery, defining the binding modes and mechanisms of action of well-known drugs as well as driving the design and development of new compounds. This review will summarize and highlight some of these structures. Most excitingly, the latest cryo-EM technology has produced structures at 1.2 Å resolution, further solidifying cryo-EM as a powerful tool for drug discovery. Therefore, cryo-EM will play an ever-increasing role in drug discovery in the coming years.
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66
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Dolphin AC, Insel PA, Blaschke TF, Meyer UA. Introduction to the Theme "Ion Channels and Neuropharmacology: From the Past to the Future". Annu Rev Pharmacol Toxicol 2020; 60:1-6. [PMID: 31914892 DOI: 10.1146/annurev-pharmtox-082719-110050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
"Ion Channels and Neuropharmacology: From the Past to the Future" is the main theme of articles in Volume 60 of the Annual Review of Pharmacology and Toxicology. Reviews in this volume discuss a wide spectrum of therapeutically relevant ion channels and GPCRs with a particular emphasis on structural studies that elucidate drug binding sites and mechanisms of action. The regulation of ion channels by second messengers, including Ca2+ and cyclic AMP, and lipid mediators is also highly relevant to several of the ion channels discussed, including KCNQ channels, HCN channels, L-type Ca2+ channels, and AMPA receptors, as well as the aquaporin channels. Molecular identification of exactly where drugs bind in the structure not only elucidates their mechanism of action but also aids future structure-based drug discovery efforts to focus on relevant pharmacophores. The ion channels discussed here are targets for multiple nervous system diseases, including epilepsy and neuropathic pain. This theme complements several previous themes, including "New Therapeutic Targets," "New Approaches for Studying Drug and Toxicant Action: Applications to Drug Discovery and Development," and "New Methods and Novel Therapeutic Approaches in Pharmacology and Toxicology."
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Affiliation(s)
- Annette C Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom;
| | - Paul A Insel
- Departments of Pharmacology and Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Terrence F Blaschke
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Urs A Meyer
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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67
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Pressly B, Lee RD, Barnych B, Hammock BD, Wulff H. Identification of the Functional Binding Site for the Convulsant Tetramethylenedisulfotetramine in the Pore of the α 2 β 3 γ 2 GABA A Receptor. Mol Pharmacol 2020; 99:78-91. [PMID: 33109687 PMCID: PMC7746976 DOI: 10.1124/molpharm.120.000090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/06/2020] [Indexed: 11/22/2022] Open
Abstract
Tetramethylenedisulfotetramine (TETS) is a so-called "caged" convulsant that is responsible for thousands of accidental and malicious poisonings. Similar to the widely used GABA receptor type A (GABAA) antagonist picrotoxinin, TETS has been proposed to bind to the noncompetitive antagonist (NCA) site in the pore of the receptor channel. However, the TETS binding site has never been experimentally mapped, and we here set out to gain atomistic level insights into how TETS inhibits the human α 2 β 3 γ 2 GABAA receptor. Using the Rosetta molecular modeling suite, we generated three homology models of the α 2 β 3 γ 2 receptor in the open, desensitized, and closed/resting state. Three different ligand-docking algorithms (RosettaLigand, Glide, and Swissdock) identified two possible TETS binding sites in the channel pore. Using a combination of site-directed mutagenesis, electrophysiology, and modeling to probe both sites, we demonstrate that TETS binds at the T6' ring in the closed/resting-state model, in which it shows perfect space complementarity and forms hydrogen bonds or makes hydrophobic interactions with all five pore-lining threonine residues of the pentameric receptor. Mutating T6' in either the α 2 or β 3 subunit reduces the IC50 of TETS by ∼700-fold in whole-cell patch-clamp experiments. TETS is thus interacting at the NCA site in the pore of the GABAA receptor at a location that is overlapping but not identical to the picrotoxinin binding site. SIGNIFICANCE STATEMENT: Our study identifies the binding site of the highly toxic convulsant tetramethylenedisulfotetramine (TETS), which is classified as a threat agent by the World Health Organization. Using a combination of homology protein modeling, ligand docking, site-directed mutagenesis, and electrophysiology, we show that TETS is binding in the pore of the α2β3γ2 GABA receptor type A receptor at the so-called T6' ring, wherein five threonine residues line the permeation pathway of the pentameric receptor channel.
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Affiliation(s)
- Brandon Pressly
- Departments of Pharmacology (B.P., R.D.L, H.W.) and Entomology and Nematology, and Comprehensive Cancer Center (B.B., B.D.H.), University of California, Davis, California
| | - Ruth D Lee
- Departments of Pharmacology (B.P., R.D.L, H.W.) and Entomology and Nematology, and Comprehensive Cancer Center (B.B., B.D.H.), University of California, Davis, California
| | - Bogdan Barnych
- Departments of Pharmacology (B.P., R.D.L, H.W.) and Entomology and Nematology, and Comprehensive Cancer Center (B.B., B.D.H.), University of California, Davis, California
| | - Bruce D Hammock
- Departments of Pharmacology (B.P., R.D.L, H.W.) and Entomology and Nematology, and Comprehensive Cancer Center (B.B., B.D.H.), University of California, Davis, California
| | - Heike Wulff
- Departments of Pharmacology (B.P., R.D.L, H.W.) and Entomology and Nematology, and Comprehensive Cancer Center (B.B., B.D.H.), University of California, Davis, California
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Jednačak T, Mikulandra I, Novak P. Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics. Int J Mol Sci 2020; 21:E7799. [PMID: 33096889 PMCID: PMC7589898 DOI: 10.3390/ijms21207799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.
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Affiliation(s)
- Tomislav Jednačak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
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69
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Han B, Salituro FG, Blanco MJ. Impact of Allosteric Modulation in Drug Discovery: Innovation in Emerging Chemical Modalities. ACS Med Chem Lett 2020; 11:1810-1819. [PMID: 33062158 DOI: 10.1021/acsmedchemlett.9b00655] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/10/2020] [Indexed: 01/04/2023] Open
Abstract
Recent years have seen an unprecedented level of innovation in allosteric drug discovery and development, with multiple drug candidates advancing into clinical studies. From early examples of allosteric drugs like GABAA receptor modulators (benzodiazepines) in the 1960s to more recent GPCR negative allosteric modulators of CCR5 (maraviroc) approved in 2007, the opportunities for interrogating allosteric sites in drug discovery have expanded to other target classes such as protein-protein interactions, kinases, and nuclear hormone receptors. In this Innovation Letter, the authors highlight the latest advances of allosteric drug discovery from different target classes and novel emerging chemical modalities beyond small molecules.
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Affiliation(s)
- Bingsong Han
- Medicinal Chemistry. Sage Therapeutics, Inc., 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Francesco G. Salituro
- Medicinal Chemistry. Sage Therapeutics, Inc., 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Maria-Jesus Blanco
- Medicinal Chemistry. Sage Therapeutics, Inc., 215 First Street, Cambridge, Massachusetts 02142, United States
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70
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de Oliveira TM, van Beek L, Shilliday F, Debreczeni JÉ, Phillips C. Cryo-EM: The Resolution Revolution and Drug Discovery. SLAS DISCOVERY 2020; 26:17-31. [PMID: 33016175 DOI: 10.1177/2472555220960401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has been elevated to the mainstream of structural biology propelled by technological advancements in numerous fronts, including imaging analysis and the development of direct electron detectors. The drug discovery field has watched with (initial) skepticism and wonder at the progression of the technique and how it revolutionized the molecular understanding of previously intractable targets. This article critically assesses how cryo-EM has impacted drug discovery in diverse therapeutic areas. Targets that have been brought into the realm of structure-based drug design by cryo-EM and are thus reviewed here include membrane proteins like the GABAA receptor, several TRP channels, and G protein-coupled receptors, and multiprotein complexes like the ribosomes, the proteasome, and eIF2B. We will describe these studies highlighting the achievements, challenges, and caveats.
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Affiliation(s)
| | - Lotte van Beek
- Structure, Biophysics and FBLG, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Fiona Shilliday
- Structure, Biophysics and FBLG, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Judit É Debreczeni
- Structure, Biophysics and FBLG, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Chris Phillips
- Structure, Biophysics and FBLG, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
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71
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Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
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72
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Sommer ME, Selent J, Carlsson J, De Graaf C, Gloriam DE, Keseru GM, Kosloff M, Mordalski S, Rizk A, Rosenkilde MM, Sotelo E, Tiemann JKS, Tobin A, Vardjan N, Waldhoer M, Kolb P. The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling. ACS Pharmacol Transl Sci 2020; 3:361-370. [PMID: 32296774 DOI: 10.1021/acsptsci.0c00024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 12/14/2022]
Abstract
G protein-coupled receptors (GPCRs) are intensively studied due to their therapeutic potential as drug targets. Members of this large family of transmembrane receptor proteins mediate signal transduction in diverse cell types and play key roles in human physiology and health. In 2013 the research consortium GLISTEN (COST Action CM1207) was founded with the goal of harnessing the substantial growth in knowledge of GPCR structure and dynamics to push forward the development of molecular modulators of GPCR function. The success of GLISTEN, coupled with new findings and paradigm shifts in the field, led in 2019 to the creation of a related consortium called ERNEST (COST Action CA18133). ERNEST broadens focus to entire signaling cascades, based on emerging ideas of how complexity and specificity in signal transduction are not determined by receptor-ligand interactions alone. A holistic approach that unites the diverse data and perspectives of the research community into a single multidimensional map holds great promise for improved drug design and therapeutic targeting.
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Affiliation(s)
- Martha E Sommer
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, Berlin, 10117, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Pompeu Fabra University (UPF), Barcelona, 08003, Spain
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, 752 36, Sweden
| | | | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, 1017, Denmark
| | - Gyorgy M Keseru
- Medicinal Chemistry Research Group, Research Center for Natural Sciences (RCNS), Budapest, H-1117, Hungary
| | - Mickey Kosloff
- Department of Human Biology, University of Haifa, Haifa, 3498838, Israel
| | - Stefan Mordalski
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, 1017, Denmark.,Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, 31-343, Poland
| | - Aurelien Rizk
- InterAx Biotech AG, PARK innovAARE, Villigen, 5234, Switzerland
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK 2200, Denmark
| | - Eddy Sotelo
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) and Facultade de Farmacia. Universidade de Santiago de Compostela, Santiago de compostela, 15782, Spain
| | - Johanna K S Tiemann
- Institute for Medical Physics and Biophysics, Leipzig University, Leipzig, 04109, Germany.,Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Kobenhavn, 2200, Denmark
| | - Andrew Tobin
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, U.K
| | - Nina Vardjan
- Laboratory of Neuroendocrinology-Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia.,Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, 1000, Slovenia
| | - Maria Waldhoer
- InterAx Biotech AG, PARK innovAARE, Villigen, 5234, Switzerland
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, 35039, Germany
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73
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The quest for high-resolution G protein-coupled receptor-G protein structures. Proc Natl Acad Sci U S A 2020; 117:6971-6973. [PMID: 32179692 DOI: 10.1073/pnas.2002665117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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74
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Akbar S, Mozumder S, Sengupta J. Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example. J Chem Inf Model 2020; 60:2448-2457. [DOI: 10.1021/acs.jcim.9b01015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shirin Akbar
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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75
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Proton-sensing G protein-coupled receptors: detectors of tumor acidosis and candidate drug targets. Future Med Chem 2020; 12:523-532. [PMID: 32116003 DOI: 10.4155/fmc-2019-0357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cells in tumor microenvironments (TMEs) use several mechanisms to sense their low pH (<7.0), including via proton-sensing G protein-coupled receptors (psGPCRs): GPR4, GPR65/TDAG8, GPR68/OGR1 and GPR132/G2A. Numerous cancers have increased expression of psGPCRs. The psGPCRs may contribute to features of the malignant phenotype via actions on specific cell-types in the TME and thereby promote tumor survival and growth. Here, we review data regarding psGPCR expression in tumors and cancer cells, impact of psGPCRs on survival in solid tumors and a bioinformatics approach to infer psGPCR expression in cell types in the TME. New tools are needed to help define contributions of psGPCRs in tumor biology and to identify potentially novel therapeutic agents for a variety of cancers.
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Gad AA, Balenga N. The Emerging Role of Adhesion GPCRs in Cancer. ACS Pharmacol Transl Sci 2020; 3:29-42. [PMID: 32259086 DOI: 10.1021/acsptsci.9b00093] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 02/08/2023]
Abstract
Aberrant expression, function, and mutation of G protein-coupled receptors (GPCRs) and their signaling partners, G proteins, have been well documented in many forms of cancer. These cell surface receptors and their endogenous ligands are implicated in all aspects of cancer including proliferation, angiogenesis, invasion, and metastasis. Adhesion GPCRs (aGPCRs) form the second largest family of GPCRs, most of which are orphan receptors with unknown physiological functions. This is mainly due to our limited insight into their structure, natural ligands, signaling pathways, and tissue expression profiles. Nevertheless, recent studies show that aGPCRs play important roles in cell adhesion to the extracellular matrix and cell-cell communication, processes that are dysregulated in cancer. Emerging evidence suggests that aGPCRs are implicated in migration, proliferation, and survival of tumor cells. We here review the role of aGPCRs in the five most common types of cancer (lung, breast, colorectal, prostate, and gastric) and emphasize the importance of further translational studies in this field.
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Affiliation(s)
- Abanoub A Gad
- Graduate Program in Life Sciences, University of Maryland, Baltimore, Maryland 20201, United States.,Division of General & Oncologic Surgery, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 20201, United States
| | - Nariman Balenga
- Division of General & Oncologic Surgery, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 20201, United States.,Molecular and Structural Biology program at University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland 20201, United States
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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