1
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Sharp AK, Newman D, Libonate G, Borns-Stern M, Bevan DR, Brown AM, Anandakrishnan R. Biophysical insights into OR2T7: Investigation of a potential prognostic marker for glioblastoma. Biophys J 2022; 121:3706-3718. [PMID: 35538663 PMCID: PMC9617130 DOI: 10.1016/j.bpj.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive and prevalent form of brain cancer, with an expected survival of 12-15 months following diagnosis. GBM affects the glial cells of the central nervous system, which impairs regular brain function including memory, hearing, and vision. GBM has virtually no long-term survival even with treatment, requiring novel strategies to understand disease progression. Here, we identified a somatic mutation in OR2T7, a G-protein-coupled receptor (GPCR), that correlates with reduced progression-free survival for glioblastoma (log rank p-value = 0.05), suggesting a possible role in tumor progression. The mutation, D125V, occurred in 10% of 396 glioblastoma samples in The Cancer Genome Atlas, but not in any of the 2504 DNA sequences in the 1000 Genomes Project, suggesting that the mutation may have a deleterious functional effect. In addition, transcriptome analysis showed that the p38α mitogen-activated protein kinase (MAPK), c-Fos, c-Jun, and JunB proto-oncogenes, and putative tumor suppressors RhoB and caspase-14 were underexpressed in glioblastoma samples with the D125V mutation (false discovery rate < 0.05). Molecular modeling and molecular dynamics simulations have provided preliminary structural insight and indicate a dynamic helical movement network that is influenced by the membrane-embedded, cytofacial-facing residue 125, demonstrating a possible obstruction of G-protein binding on the cytofacial exposed region. We show that the mutation impacts the "open" GPCR conformation, potentially affecting Gα-subunit binding and associated downstream activity. Overall, our findings suggest that the Val125 mutation in OR2T7 could affect glioblastoma progression by downregulating GPCR-p38 MAPK tumor-suppression pathways and impacting the biophysical characteristics of the structure that facilitates Gα-subunit binding. This study provides the theoretical basis for further experimental investigation required to confirm that the D125V mutation in OR2T7 is not a passenger mutation. With validation, the aforementioned mutation could represent an important prognostic marker and a potential therapeutic target for glioblastoma.
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Affiliation(s)
- Amanda K Sharp
- Interdisciplinary Program of Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, Virginia
| | - David Newman
- Biomedical Sciences, Edward Via College of Osteopathic Medicine (VCOM), Blacksburg, Virginia
| | - Gianna Libonate
- Biomedical Sciences, Edward Via College of Osteopathic Medicine (VCOM), Blacksburg, Virginia
| | - Mary Borns-Stern
- Biomedical Sciences, Edward Via College of Osteopathic Medicine (VCOM), Blacksburg, Virginia
| | - David R Bevan
- Interdisciplinary Program of Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, Virginia; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
| | - Anne M Brown
- Interdisciplinary Program of Genetics, Bioinformatics, and Computational Biology (GBCB), Virginia Tech, Blacksburg, Virginia; Department of Biochemistry, Virginia Tech, Blacksburg, Virginia; Research and Informatics, University Libraries, Virginia Tech, Blacksburg, Virginia.
| | - Ramu Anandakrishnan
- Biomedical Sciences, Edward Via College of Osteopathic Medicine (VCOM), Blacksburg, Virginia; Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia; Gibbs Cancer Center and Research Institute, Spartanburg, South Carolina.
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2
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Nikte SV, Sonar K, Tandale A, Joshi M, Sengupta D. Loss of a water-mediated network results in reduced agonist affinity in a β 2-adrenergic receptor clinical variant. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140605. [PMID: 33453412 DOI: 10.1016/j.bbapap.2021.140605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/19/2020] [Accepted: 01/07/2021] [Indexed: 11/26/2022]
Abstract
The β2-adrenergic receptor (β2AR) is a member of the G protein-coupled receptor (GPCR) family that is an important drug target for asthma and COPD. Clinical studies coupled with biochemical data have identified a critical receptor variant, Thr164Ile, to have a reduced response to agonist-based therapy, although the molecular mechanism underlying this seemingly "non-deleterious" substitution is not clear. Here, we couple molecular dynamics simulations with network analysis and free-energy calculations to identify the molecular determinants underlying the differential drug response. We are able to identify hydration sites in the transmembrane domain that are essential to maintain the integrity of the binding site but are absent in the variant. The loss of these hydration sites in the variant correlates with perturbations in the intra-protein interaction network and rearrangements in the orthosteric ligand binding site. In conjunction, we observe an altered binding and reduced free energy of a series of agonists, in line with experimental trends. Our work identifies a functional allosteric pathway connected by specific hydration sites in β2AR that has not been reported before and provides insight into water-mediated networks in GPCRs in general. Overall, the work is one of the first step towards developing variant-specific potent and selective agonists.
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Affiliation(s)
- Siddhanta V Nikte
- Physical Chemistry Division, National Chemical Laboratory, Pune 411 008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Krushna Sonar
- Physical Chemistry Division, National Chemical Laboratory, Pune 411 008, India
| | - Aditi Tandale
- Physical Chemistry Division, National Chemical Laboratory, Pune 411 008, India
| | - Manali Joshi
- Bioinformatics Centre, S. P. University, Pune 411 007, India.
| | - Durba Sengupta
- Physical Chemistry Division, National Chemical Laboratory, Pune 411 008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
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3
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Michel MC, Michel-Reher MB, Hein P. A Systematic Review of Inverse Agonism at Adrenoceptor Subtypes. Cells 2020; 9:E1923. [PMID: 32825009 PMCID: PMC7564766 DOI: 10.3390/cells9091923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
As many, if not most, ligands at G protein-coupled receptor antagonists are inverse agonists, we systematically reviewed inverse agonism at the nine adrenoceptor subtypes. Except for β3-adrenoceptors, inverse agonism has been reported for each of the adrenoceptor subtypes, most often for β2-adrenoceptors, including endogenously expressed receptors in human tissues. As with other receptors, the detection and degree of inverse agonism depend on the cells and tissues under investigation, i.e., they are greatest when the model has a high intrinsic tone/constitutive activity for the response being studied. Accordingly, they may differ between parts of a tissue, for instance, atria vs. ventricles of the heart, and within a cell type, between cellular responses. The basal tone of endogenously expressed receptors is often low, leading to less consistent detection and a lesser extent of observed inverse agonism. Extent inverse agonism depends on specific molecular properties of a compound, but inverse agonism appears to be more common in certain chemical classes. While inverse agonism is a fascinating facet in attempts to mechanistically understand observed drug effects, we are skeptical whether an a priori definition of the extent of inverse agonism in the target product profile of a developmental candidate is a meaningful option in drug discovery and development.
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Affiliation(s)
- Martin C. Michel
- Department of Pharmacology, Johannes Gutenberg University, 55131 Mainz, Germany;
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4
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Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. J Chem Inf Model 2020; 60:5103-5116. [PMID: 32786708 DOI: 10.1021/acs.jcim.0c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human G protein-coupled receptors (hGPCRs) are the most frequent targets of Food and Drug Administration (FDA)-approved drugs. Structural bioinformatics, along with molecular simulation, can support structure-based drug design targeting hGPCRs. In this context, several years ago, we developed a hybrid molecular mechanics (MM)/coarse-grained (CG) approach to predict ligand poses in low-resolution hGPCR models. The approach was based on the GROMOS96 43A1 and PRODRG united-atom force fields for the MM part. Here, we present a new MM/CG implementation using, instead, the Amber 14SB and GAFF all-atom potentials for proteins and ligands, respectively. The new implementation outperforms the previous one, as shown by a variety of applications on models of hGPCR/ligand complexes at different resolutions, and it is also more user-friendly. Thus, it emerges as a useful tool to predict poses in low-resolution models and provides insights into ligand binding similarly to all-atom molecular dynamics, albeit at a lower computational cost.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Biotechnology, University of Verona, 37314 Verona, Italy.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Cecile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
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5
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Yuan S, Dahoun T, Brugarolas M, Pick H, Filipek S, Vogel H. Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds. Commun Biol 2019; 2:141. [PMID: 31044166 PMCID: PMC6478719 DOI: 10.1038/s42003-019-0384-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
The mammalian olfactory system uses hundreds of specialized G-protein-coupled olfactory receptors (ORs) to discriminate a nearly unlimited number of odorants. Cognate agonists of most ORs have not yet been identified and potential non-olfactory processes mediated by ORs are unknown. Here, we used molecular modeling, fingerprint interaction analysis and molecular dynamics simulations to show that the binding pocket of the prototypical olfactory receptor Olfr73 is smaller, but more flexible, than binding pockets of typical non-olfactory G-protein-coupled receptors. We extended our modeling to virtual screening of a library of 1.6 million compounds against Olfr73. Our screen predicted 25 Olfr73 agonists beyond traditional odorants, of which 17 compounds, some with therapeutic potential, were validated in cell-based assays. Our modeling suggests a molecular basis for reduced interaction contacts between an odorant and its OR and thus the typical low potency of OR-activating compounds. These results provide a proof-of-principle for identifying novel therapeutic OR agonists.
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Affiliation(s)
- Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory of Biomodelling, Faculty of Chemistry & Biological and Chemical Research Centre, Uni-versity of Warsaw, 02-093 Warsaw, Poland
| | - Thamani Dahoun
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marc Brugarolas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Horst Pick
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodelling, Faculty of Chemistry & Biological and Chemical Research Centre, Uni-versity of Warsaw, 02-093 Warsaw, Poland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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6
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Chan HCS, Wang J, Palczewski K, Filipek S, Vogel H, Liu ZJ, Yuan S. Exploring a new ligand binding site of G protein-coupled receptors. Chem Sci 2018; 9:6480-6489. [PMID: 30310578 PMCID: PMC6115637 DOI: 10.1039/c8sc01680a] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023] Open
Abstract
Identifying a target ligand binding site is an important step for structure-based rational drug design as shown here for G protein-coupled receptors (GPCRs), which are among the most popular drug targets. We applied long-time scale molecular dynamics simulations, coupled with mutagenesis studies, to two prototypical GPCRs, the M3 and M4 muscarinic acetylcholine receptors. Our results indicate that unlike synthetic antagonists, which bind to the classic orthosteric site, the endogenous agonist acetylcholine is able to diffuse into a much deeper binding pocket. We also discovered that the most recently resolved crystal structure of the LTB4 receptor comprised a bound inverse agonist, which extended its benzamidine moiety to the same binding pocket discovered in this work. Analysis on all resolved GPCR crystal structures indicated that this new pocket could exist in most receptors. Our findings provide new opportunities for GPCR drug discovery.
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Affiliation(s)
| | - Jingjing Wang
- iHuman Institute , ShanghaiTech University , China .
| | | | - Slawomir Filipek
- Faculty of Chemistry , Biological and Chemical Research Centre , University of Warsaw , Poland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Switzerland . ;
| | - Zhi-Jie Liu
- iHuman Institute , ShanghaiTech University , China .
| | - Shuguang Yuan
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , Switzerland . ;
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7
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Gupta A, Chaudhary N, Aparoy P. MM-PBSA and per-residue decomposition energy studies on 7-Phenyl-imidazoquinolin-4(5H)-one derivatives: Identification of crucial site points at microsomal prostaglandin E synthase-1 (mPGES-1) active site. Int J Biol Macromol 2018; 119:352-359. [PMID: 30031079 DOI: 10.1016/j.ijbiomac.2018.07.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/29/2022]
Abstract
The huge therapeutic potential and the market share of painkillers are well-known. Due to the side effects associated with traditional NSAIDs and selective cyclooxygenase (COX-2) inhibitors, a new generation of painkillers is the need of the hour. In this regard, microsomal prostaglandin E synthase-1 (mPGES-1) offers great potential as an alternative drug target against inflammatory disorders. The present study is aimed at identifying the amino acids crucial in effective inhibitor binding at the mPGES-1 active site by performing molecular dynamics based studies on a series of 7-Phenyl-imidazoquinolin-4(5H)-one derivatives. Molecular dynamics (MD) simulations, MM-PBSA, per-residue energy decomposition and Dimensionality Reduction through Covariance matrix Transformation for Identification of Differences in dynamics (DIRECT-ID) analysis were performed to get insights into the structural details that can aid in novel drug design against mPGES-1. The high correlations of electrostatic and polar energy terms with biological activity highlight their importance and applicability in in silico screening studies. Further, per-residue energy decomposition studies revealed that Lys42, Arg52, Arg122, Pro124, Ser127, Val128 and Thr131 were contributing more towards inhibitor binding energy. The results clearly show that MM-PBSA can act as a filter in virtual screening experiments and can play major role in facilitating various mPGES-1 drug discovery studies.
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Affiliation(s)
- Ashish Gupta
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh 176215, India
| | - Neha Chaudhary
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh 176215, India
| | - Polamarasetty Aparoy
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh 176215, India.
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8
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Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli. Antimicrob Agents Chemother 2017; 61:AAC.01572-17. [PMID: 28874374 DOI: 10.1128/aac.01572-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/20/2017] [Indexed: 01/05/2023] Open
Abstract
Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependent transferase that catalyzes the conjugation of glutathione to fosfomycin, rendering the antibiotic inactive. In this study, we solved the crystal structures of two of the most clinically relevant FosA enzymes: plasmid-encoded FosA3 from Escherichia coli and chromosomally encoded FosA from Klebsiella pneumoniae (FosAKP). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosAKP were also compared to those of FosA from Pseudomonas aeruginosa (FosAPA), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosAKP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosAPA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosAKP enzymes. Interestingly, these differences in enzyme activity could not be attributed to structural differences at their active sites. Instead, molecular dynamics simulations and hydrogen-deuterium exchange experiments with FosAKP revealed dynamic interconnectivity between its active sites and a loop structure that extends from the active site of each monomer and traverses the dimer interface. This dimer interface loop is longer and more extended in FosAKP and FosA3 than in FosAPA, and kinetic analyses of FosAKP and FosAPA loop-swapped chimeric enzymes highlighted its importance in FosA activity. Collectively, these data yield novel insights into fosfomycin resistance that could be leveraged to develop new strategies to inhibit FosA and potentiate fosfomycin activity.
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9
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Huang J, Lakkaraju SK, Coop A, MacKerell AD. Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor. J Phys Chem B 2016; 120:11897-11904. [PMID: 27801588 DOI: 10.1021/acs.jpcb.6b09351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
G-protein coupled receptors (GPCRs), including the μ-opioid receptor, interact with G-proteins and other proteins via their intracellular face as required for signal transduction. However, characterization of the structure of the intracellular face of GPCRs is complicated by the experimental methods used for structural characterization. In the present study we undertook a series of long-time molecular dynamics (MD) simulations, ranging from 1 to 5 μs, on the μ-opioid receptor in both the dimeric and monomeric states. Results show intracellular loop 2 (ICL2) to sample an equilibrium between coiled and helical states. Intracellular loop 3 (ICL3) samples a wider range of conformations. Previously unobserved β-sheet structures were primarily sampled in the simulations initiated from the inactive dimer conformation. In contrast, helical structures were sampled in simulations initiated from the active, monomer conformation. Notably, in the dimeric form of the receptor, both intramolecular and intermolecular β-sheet structures were sampled, with the latter occurring between the two monomers. These results indicate that the sampling of β-sheet structures can maintain the ICL3 in an inactive conformation that contributes to stabilization of the dimeric form of the receptor via interchain β-sheet structures.
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Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Sirish Kaushik Lakkaraju
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Andrew Coop
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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10
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Yuan S, Chan HCS, Vogel H, Filipek S, Stevens RC, Palczewski K. The Molecular Mechanism of P2Y1 Receptor Activation. Angew Chem Int Ed Engl 2016; 55:10331-5. [PMID: 27460867 PMCID: PMC4996126 DOI: 10.1002/anie.201605147] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/27/2016] [Indexed: 01/07/2023]
Abstract
Human purinergic G protein-coupled receptor P2Y1 (P2Y1 R) is activated by adenosine 5'-diphosphate (ADP) to induce platelet activation and thereby serves as an important antithrombotic drug target. Crystal structures of P2Y1 R revealed that one ligand (MRS2500) binds to the extracellular vestibule of this GPCR, whereas another (BPTU) occupies the surface between transmembrane (TM) helices TM2 and TM3. We introduced a total of 20 μs all-atom long-timescale molecular dynamic (MD) simulations to inquire why two molecules in completely different locations both serve as antagonists while ADP activates the receptor. Our results indicate that BPTU acts as an antagonist by stabilizing extracellular helix bundles leading to an increase of the lipid order, whereas MRS2500 blocks signaling by occupying the ligand binding site. Both antagonists stabilize an ionic lock within the receptor. However, binding of ADP breaks this ionic lock, forming a continuous water channel that leads to P2Y1 R activation.
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Affiliation(s)
- Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | | | - Horst Vogel
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodeling, Faculty of Chemistry & Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Raymond C Stevens
- iHuman Institute, Shanghai Technical University, China and, Departments of Biological Sciences and Chemistry, University of Southern California, USA.
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, USA.
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11
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Yuan S, Chan HCS, Vogel H, Filipek S, Stevens RC, Palczewski K. The Molecular Mechanism of P2Y 1Receptor Activation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | | | - Horst Vogel
- Laboratory of Physical Chemistry of Polymers and Membranes; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodeling; Faculty of Chemistry & Biological and Chemical Research Centre; University of Warsaw; Warsaw Poland
| | - Raymond C. Stevens
- iHuman Institute; Shanghai Technical University, China and; Departments of Biological Sciences and Chemistry; University of Southern California; USA
| | - Krzysztof Palczewski
- Department of Pharmacology; School of Medicine; Case Western Reserve University; Cleveland USA
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12
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Yuan S, Peng Q, Palczewski K, Vogel H, Filipek S. Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT1A Receptor. Angew Chem Int Ed Engl 2016; 55:8661-5. [PMID: 27244650 PMCID: PMC4957245 DOI: 10.1002/anie.201603766] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 01/03/2023]
Abstract
G‐protein‐coupled receptors (GPCRs) are involved in a wide range of physiological processes, and they have attracted considerable attention as important targets for developing new medicines. A central and largely unresolved question in drug discovery, which is especially relevant to GPCRs, concerns ligand selectivity: Why do certain molecules act as activators (agonists) whereas others, with nearly identical structures, act as blockers (antagonists) of GPCRs? To address this question, we employed all‐atom, long‐timescale molecular dynamics simulations to investigate how two diastereomers (epimers) of dihydrofuroaporphine bind to the serotonin 5‐HT1A receptor and exert opposite effects. By using molecular interaction fingerprints, we discovered that the agonist could mobilize nearby amino acid residues to act as molecular switches for the formation of a continuous water channel. In contrast, the antagonist epimer remained firmly stabilized in the binding pocket.
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Affiliation(s)
- Shuguang Yuan
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Qian Peng
- Department of Chemistry, University of Oxford, UK
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, USA
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodeling, Faculty of Chemistry & Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
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13
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Yuan S, Peng Q, Palczewski K, Vogel H, Filipek S. Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT 1AReceptor. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Shuguang Yuan
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Qian Peng
- Department of Chemistry; University of Oxford; UK
| | - Krzysztof Palczewski
- Department of Pharmacology; School of Medicine; Case Western Reserve University; Cleveland USA
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne Switzerland
| | - Slawomir Filipek
- Laboratory of Biomodeling; Faculty of Chemistry & Biological and Chemical Research Centre; University of Warsaw; Warsaw Poland
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