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Plotnikov D, Ahn SH. Optimization of the resampling method in the weighted ensemble simulation toolkit with parallelization and analysis (WESTPA). J Chem Phys 2024; 161:046101. [PMID: 39037142 DOI: 10.1063/5.0197141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Affiliation(s)
- Dennis Plotnikov
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, USA
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, USA
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2
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Gaiser BI, Danielsen M, Xu X, Røpke Jørgensen K, Fronik P, Märcher-Rørsted E, Wróbel TM, Liu X, Mosolff Mathiesen J, Sejer Pedersen D. Bitopic Ligands Support the Presence of a Metastable Binding Site at the β 2 Adrenergic Receptor. J Med Chem 2024; 67:11053-11068. [PMID: 38952152 DOI: 10.1021/acs.jmedchem.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Metastable binding sites (MBS) have been observed in a multitude of molecular dynamics simulations and can be considered low affinity allosteric binding sites (ABS) that function as stepping stones as the ligand moves toward the orthosteric binding site (OBS). Herein, we show that MBS can be utilized as ABS in ligand design, resulting in ligands with improved binding kinetics. Four homobivalent bitopic ligands (1-4) were designed by molecular docking of (S)-alprenolol ((S)-ALP) in the cocrystal structure of the β2 adrenergic receptor (β2AR) bound to the antagonist ALP. Ligand 4 displayed a potency and affinity similar to (S)-ALP, but with a >4-fold increase in residence time. The proposed binding mode was confirmed by X-ray crystallography of ligand 4 in complex with the β2AR. This ligand design principle can find applications beyond the β2AR and G protein-coupled receptors (GPCRs) as a general approach for improving the pharmacological profile of orthosteric ligands by targeting the OBS and an MBS simultaneously.
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Affiliation(s)
- Birgit Isabel Gaiser
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Mia Danielsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Xinyu Xu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084 ,China
| | - Kira Røpke Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Philipp Fronik
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Emil Märcher-Rørsted
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Tomasz M Wróbel
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Chodźki 4a, 20093 Lublin, Poland
| | - Xiangyu Liu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084 ,China
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
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3
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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4
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Jung YH, Salmaso V, Wen Z, Bennett JM, Phung NB, Lieberman DI, Gopinatth V, Randle JCR, Chen Z, Salvemini D, Karcz TP, Cook DN, Jacobson KA. Structure-Activity Relationship of Heterocyclic P2Y 14 Receptor Antagonists: Removal of the Zwitterionic Character with Piperidine Bioisosteres. J Med Chem 2021; 64:5099-5122. [PMID: 33787273 PMCID: PMC8317135 DOI: 10.1021/acs.jmedchem.1c00164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A known zwitterionic, heterocyclic P2Y14R antagonist 3a was substituted with diverse groups on the central phenyl and terminal piperidine moieties, following a computational selection process. The most potent analogues contained an uncharged piperidine bioisostere, prescreened in silico, while an aza-scan (central phenyl ring) reduced P2Y14R affinity. Piperidine amide 11, 3-aminopropynyl 19, and 5-(hydroxymethyl)isoxazol-3-yl) 29 congeners in the triazole series maintained moderate receptor affinity. Adaption of 5-(hydroxymethyl)isoxazol-3-yl gave the most potent naphthalene-containing (32; MRS4654; IC50, 15 nM) and less active phenylamide-containing (33) scaffolds. Thus, a zwitterion was nonessential for receptor binding, and molecular docking and dynamics probed the hydroxymethylisoxazole interaction with extracellular loops. Also, amidomethyl ester prodrugs were explored to reversibly block the conserved carboxylate group to provide neutral analogues, which were cleavable by liver esterase, and in vivo efficacy demonstrated. We have, in stages, converted zwitterionic antagonists into neutral molecules designed to produce potent P2Y14R antagonists for in vivo application.
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Affiliation(s)
- Young-Hwan Jung
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhiwei Wen
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John M Bennett
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ngan B Phung
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David I Lieberman
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Varun Gopinatth
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John C R Randle
- Random Walk Ventures, LLC, 108 Lincoln Street Unit 6B, Boston, Massachusetts 02111, United States
| | - Zhoumou Chen
- Department of Pharmacology and Physiology and the Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Daniela Salvemini
- Department of Pharmacology and Physiology and the Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Tadeusz P Karcz
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Donald N Cook
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina 27709, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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5
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Shechter S, Thomas DR, Jans DA. Application of In Silico and HTS Approaches to Identify Nuclear Import Inhibitors for Venezuelan Equine Encephalitis Virus Capsid Protein: A Case Study. Front Chem 2020; 8:573121. [PMID: 33505952 PMCID: PMC7832173 DOI: 10.3389/fchem.2020.573121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/12/2020] [Indexed: 01/16/2023] Open
Abstract
The development of new drugs is costly and time-consuming, with estimates of over $US1 billion and 15 years for a product to reach the market. As understanding of the molecular basis of disease improves, various approaches have been used to target specific molecular interactions in the search for effective drugs. These include high-throughput screening (HTS) for novel drug identification and computer-aided drug design (CADD) to assess the properties of putative drugs before experimental work begins. We have applied conventional HTS and CADD approaches to the problem of identifying antiviral compounds to limit infection by Venezuelan equine encephalitis virus (VEEV). Nuclear targeting of the VEEV capsid (CP) protein through interaction with the host nuclear import machinery has been shown to be essential for viral pathogenicity, with viruses incapable of this interaction being greatly attenuated. Our previous conventional HTS and in silico structure-based drug design (SBDD) screens were successful in identifying novel inhibitors of CP interaction with the host nuclear import machinery, thus providing a unique opportunity to assess the relative value of the two screening approaches directly. This focused review compares and contrasts the two screening approaches, together with the properties of the inhibitors identified, as a case study for parallel use of the two approaches to identify antivirals. The utility of SBDD screens, especially when used in parallel with traditional HTS, in identifying agents of interest to target the host-pathogen interface is highlighted.
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Affiliation(s)
- Sharon Shechter
- Shechter Computational Solutions, Andover, MA, United States.,Department of Chemistry, College of Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - David R Thomas
- Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Monash, VIC, Australia
| | - David A Jans
- Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Monash, VIC, Australia
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6
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Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein. J Comput Aided Mol Des 2020; 35:195-207. [PMID: 33103220 PMCID: PMC7585834 DOI: 10.1007/s10822-020-00356-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules in silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting that it is important to consider the dynamic formation of the heterodimer between RBD and ACE2 when judging any potential candidate.
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7
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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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8
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Gabr MT, Deganutti G, Reynolds CA. Peptidomimetic-based approach toward inhibitors of microbial trimethylamine lyases. Chem Biol Drug Des 2020; 97:231-236. [PMID: 32772476 DOI: 10.1111/cbdd.13775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/27/2020] [Accepted: 08/01/2020] [Indexed: 12/30/2022]
Abstract
The development of gut microbiota-targeted small molecules represents a promising platform for the identification of new therapeutics based on the implication of human gut bacteria with different diseases. Bacterial trimethylamine (TMA)-lyase (CutC) is expressed in gut bacteria and catalyzes the conversion of choline to TMA. The association of elevated TMA production with various disorders has directed research efforts toward identification of CutC inhibitors. Herein, we introduce peptidomimetics as a promising toolbox for the discovery of CutC inhibitors. Our approach starts with screening a library of peptidomimetics for intestinal metabolic stability followed by in vitro CutC inhibition. Compound 5 was identified from this screening platform with IC50 value of 5.9 ± 0.6 μM for CutC inhibition. Unlike previously reported CutC inhibitors, compound 5 possessed universal CutC inhibitory activity in different bacterial strains. Molecular dynamics simulations suggested a plausible binding site and inhibition mechanism for compound 5. Therefore, compound 5 is a promising lead for further structural optimization in the search for CutC-targeted small molecules.
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Affiliation(s)
- Moustafa T Gabr
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
| | - Christopher A Reynolds
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, United Kingdom
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9
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Salmaso V, Jacobson KA. In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors. Biomolecules 2020; 10:E812. [PMID: 32466404 PMCID: PMC7356333 DOI: 10.3390/biom10060812] [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: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Molecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery.
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Affiliation(s)
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
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10
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Ding F, Peng W, Peng YK, Liu BQ. Estimating the potential toxicity of chiral diclofop-methyl: Mechanistic insight into the enantioselective behavior. Toxicology 2020; 438:152446. [DOI: 10.1016/j.tox.2020.152446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/26/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
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11
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Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions. PLoS Comput Biol 2020; 16:e1007818. [PMID: 32298258 PMCID: PMC7188303 DOI: 10.1371/journal.pcbi.1007818] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/28/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.
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12
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Federico S, Margiotta E, Moro S, Kozma E, Gao ZG, Jacobson KA, Spalluto G. Conjugable A 3 adenosine receptor antagonists for the development of functionalized ligands and their use in fluorescent probes. Eur J Med Chem 2019; 186:111886. [PMID: 31787357 DOI: 10.1016/j.ejmech.2019.111886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
Abstract
Compounds able to simultaneously bind a biological target and be conjugated to a second specific moiety are attractive tools for the development of multi-purpose ligands useful as multi-target ligands, receptor probes or drug delivery systems, with both therapeutic and diagnostic applications. The human A3 adenosine receptor is a G protein-coupled receptor involved in many physio-pathological conditions, e.g. cancer and inflammation, thus representing a promising research target. In this work, two series of conjugable hA3AR antagonists, based on the pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine nucleus, were developed. The introduction of an aromatic ring at the 5 position of the scaffold, before (phenylacetamido moiety) or after (1,2,3-triazole obtained by click chemistry) the conjugation is aimed to increase affinity and selectivity towards the hA3AR receptor. As expected, conjugable compounds showed good affinity towards the hA3AR. In order to prove their potential in the development of hA3AR ligands for different purposes, compounds were also functionalized with fluorescent probes. Unfortunately, conjugation decreased affinity and selectivity for the target as compared to the hA2AAR. Computational studies identified specific non-conserved residues of the extracellular loops which constitute a structural barrier able to discriminate between ligands, giving insights into the rational development of new highly selective ligands.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via Licio Giorgeri 1, 34127, Trieste, Italy.
| | - Enrico Margiotta
- Molecular Modeling Section (MMS), Dipartimento di Scienze Del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze Del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Eszter Kozma
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via Licio Giorgeri 1, 34127, Trieste, Italy
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13
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Al-Attraqchi OH, Attimarad M, Venugopala KN, Nair A, Al-Attraqchi NH. Adenosine A2A Receptor as a Potential Drug Target - Current Status and Future Perspectives. Curr Pharm Des 2019; 25:2716-2740. [DOI: 10.2174/1381612825666190716113444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
Abstract
Adenosine receptors (ARs) are a class of G-protein coupled receptors (GPCRs) that are activated by
the endogenous substance adenosine. ARs are classified into 4 subtype receptors, namely, the A1, A2A, A2B and A3
receptors. The wide distribution and expression of the ARs in various body tissues as well as the roles they have
in controlling different functions in the body make them potential drug targets for the treatment of various pathological
conditions, such as cardiac diseases, cancer, Parkinson’s disease, inflammation and glaucoma. Therefore,
in the past decades, there have been extensive investigations of ARs with a high number of agonists and antagonists
identified that can interact with these receptors. This review shall discuss the A2A receptor (A2AAR) subtype
of the ARs. The structure, properties and the recent advances in the therapeutic potential of the receptor are discussed
with an overview of the recent advances in the methods of studying the receptor. Also, molecular modeling
approaches utilized in the design of A2AAR ligands are highlighted with various recent examples.
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Affiliation(s)
- Omar H.A. Al-Attraqchi
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O BOX (1), Philadelphia University-19392, Amman, Jordan
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Anroop Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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14
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Gaiser BI, Danielsen M, Marcher-Rørsted E, Røpke Jørgensen K, Wróbel TM, Frykman M, Johansson H, Bräuner-Osborne H, Gloriam DE, Mathiesen JM, Sejer Pedersen D. Probing the Existence of a Metastable Binding Site at the β 2-Adrenergic Receptor with Homobivalent Bitopic Ligands. J Med Chem 2019; 62:7806-7839. [PMID: 31298548 DOI: 10.1021/acs.jmedchem.9b00595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Herein, we report the development of bitopic ligands aimed at targeting the orthosteric binding site (OBS) and a metastable binding site (MBS) within the same receptor unit. Previous molecular dynamics studies on ligand binding to the β2-adrenergic receptor (β2AR) suggested that ligands pause at transient, less-conserved MBSs. We envisioned that MBSs can be regarded as allosteric binding sites and targeted by homobivalent bitopic ligands linking two identical pharmacophores. Such ligands were designed based on docking of the antagonist (S)-alprenolol into the OBS and an MBS and synthesized. Pharmacological characterization revealed ligands with similar potency and affinity, slightly increased β2/β1AR-selectivity, and/or substantially slower β2AR off-rates compared to (S)-alprenolol. Truncated bitopic ligands suggested the major contribution of the metastable pharmacophore to be a hydrophobic interaction with the β2AR, while the linkers alone decreased the potency of the orthosteric fragment. Altogether, the study underlines the potential of targeting MBSs for improving the pharmacological profiles of ligands.
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Affiliation(s)
- Birgit I Gaiser
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Mia Danielsen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Emil Marcher-Rørsted
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Kira Røpke Jørgensen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Tomasz M Wróbel
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark.,Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Faculty of Pharmacy , Medical University of Lublin , 4A Chodźki 20093 Lublin , Poland
| | - Mikael Frykman
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Henrik Johansson
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology , University of Copenhagen , Jagtvej 162 , 2100 Copenhagen , Denmark
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15
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Deb PK. Recent Updates in the Computer Aided Drug Design Strategies for the Discovery of Agonists and Antagonists of Adenosine Receptors. Curr Pharm Des 2019; 25:747-749. [DOI: 10.2174/1381612825999190515120510] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University, PO Box 1, 19392, Amman, Jordan
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16
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Al-Shar'i NA, Al-Balas QA. Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends. Curr Pharm Des 2019; 25:783-816. [DOI: 10.2174/1381612825666190304123414] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/09/2023]
Abstract
:
Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors
(GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known,
namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of
activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological
conditions had made them pivotal therapeutic targets for developing clinically effective agents.
:
The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched
our understanding of their structural and functional properties such as ligand binding and signal transduction.
This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular
dynamics (MD) simulations, toward further investigation of their molecular properties and designing
bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating
ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs
in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms
of activation, collectively aiding in the design of subtype selective ligands.
:
In this review, we focused on the advances and different applications of MD simulations utilized to study the
structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition,
relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug
discovery to this pivotal group of drug targets.
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Affiliation(s)
- Nizar A. Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Qosay A. Al-Balas
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
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17
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Samanta PN, Kar S, Leszczynski J. Recent Advances of In-Silico Modeling of Potent Antagonists for the Adenosine Receptors. Curr Pharm Des 2019; 25:750-773. [DOI: 10.2174/1381612825666190304123545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]
Abstract
The rapid advancement of computer architectures and development of mathematical algorithms offer a
unique opportunity to leverage the simulation of macromolecular systems at physiologically relevant timescales.
Herein, we discuss the impact of diverse structure-based and ligand-based molecular modeling techniques in
designing potent and selective antagonists against each adenosine receptor (AR) subtype that constitutes multitude
of drug targets. The efficiency and robustness of high-throughput empirical scoring function-based approaches
for hit discovery and lead optimization in the AR family are assessed with the help of illustrative examples
that have led to nanomolar to sub-micromolar inhibition activities. Recent progress in computer-aided drug
discovery through homology modeling, quantitative structure-activity relation, pharmacophore models, and molecular
docking coupled with more accurate free energy calculation methods are reported and critically analyzed
within the framework of structure-based virtual screening of AR antagonists. Later, the potency and applicability
of integrated molecular dynamics (MD) methods are addressed in the context of diligent inspection of intricated
AR-antagonist binding processes. MD simulations are exposed to be competent for studying the role of the membrane
as well as the receptor flexibility toward the precise evaluation of the biological activities of antagonistbound
AR complexes such as ligand binding modes, inhibition affinity, and associated thermodynamic and kinetic
parameters.
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Affiliation(s)
- Pabitra Narayan Samanta
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
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18
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Molecular dynamics of fentanyl bound to μ-opioid receptor. J Mol Model 2019; 25:144. [DOI: 10.1007/s00894-019-3999-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/21/2019] [Indexed: 12/17/2022]
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19
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Acúrcio RC, Scomparin A, Satchi‐Fainaro R, Florindo HF, Guedes RC. Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rita C. Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Anna Scomparin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Helena F. Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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20
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Ladefoged LK, Zeppelin T, Schiøtt B. Molecular modeling of neurological membrane proteins − from binding sites to synapses. Neurosci Lett 2019; 700:38-49. [DOI: 10.1016/j.neulet.2018.05.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 01/07/2023]
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21
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Lipiński PFJ, Kosson P, Matalińska J, Roszkowski P, Czarnocki Z, Jarończyk M, Misicka A, Dobrowolski JC, Sadlej J. Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis. Molecules 2019; 24:E740. [PMID: 30791394 PMCID: PMC6412969 DOI: 10.3390/molecules24040740] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022] Open
Abstract
Interactions of 21 fentanyl derivatives with μ-opioid receptor (μOR) were studied using experimental and theoretical methods. Their binding to μOR was assessed with radioligand competitive binding assay. A uniform set of binding affinity data contains values for two novel and one previously uncharacterized derivative. The data confirms trends known so far and thanks to their uniformity, they facilitate further comparisons. In order to provide structural hypotheses explaining the experimental affinities, the complexes of the studied derivatives with μOR were modeled and subject to molecular dynamics simulations. Five common General Features (GFs) of fentanyls' binding modes stemmed from these simulations. They include: GF1) the ionic interaction between D147 and the ligands' piperidine NH⁺ moiety; GF2) the N-chain orientation towards the μOR interior; GF3) the other pole of ligands is directed towards the receptor outlet; GF4) the aromatic anilide ring penetrates the subpocket formed by TM3, TM4, ECL1 and ECL2; GF5) the 4-axial substituent (if present) is directed towards W318. Except for the ionic interaction with D147, the majority of fentanyl-μOR contacts is hydrophobic. Interestingly, it was possible to find nonlinear relationships between the binding affinity and the volume of the N-chain and/or anilide's aromatic ring. This kind of relationships is consistent with the apolar character of interactions involved in ligand⁻receptor binding. The affinity reaches the optimum for medium size while it decreases for both large and small substituents. Additionally, a linear correlation between the volumes and the average dihedral angles of W293 and W133 was revealed by the molecular dynamics study. This seems particularly important, as the W293 residue is involved in the activation processes. Further, the Y326 (OH) and D147 (Cγ) distance found in the simulations also depends on the ligands' size. In contrast, neither RMSF measures nor D114/Y336 hydrations show significant structure-based correlations. They also do not differentiate studied fentanyl derivatives. Eventually, none of 14 popular scoring functions yielded a significant correlation between the predicted and observed affinity data (R < 0.30, n = 28).
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Affiliation(s)
- Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Piotr Kosson
- Toxicology Research Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Piotr Roszkowski
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | | | | | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | | | - Joanna Sadlej
- National Medicines Institute, 00-725 Warsaw, Poland.
- Faculty of Mathematics and Natural Sciences, University of Cardinal Stefan Wyszyński, 1/3 Wóycickiego-Str., 01-938 Warsaw, Poland.
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22
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Designing Hybrids Targeting the Cholinergic System by Modulating the Muscarinic and Nicotinic Receptors: A Concept to Treat Alzheimer's Disease. Molecules 2018; 23:molecules23123230. [PMID: 30544533 PMCID: PMC6320942 DOI: 10.3390/molecules23123230] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 01/02/2023] Open
Abstract
The cholinergic hypothesis has been reported first being the cause of memory dysfunction in the Alzheimer's disease. Researchers around the globe have focused their attention on understanding the mechanisms of how this complicated system contributes to processes such as learning, memory, disorientation, linguistic problems, and behavioral issues in the indicated chronic neurodegenerative disease. The present review reports recent updates in hybrid molecule design as a strategy for selectively addressing multiple target proteins involved in Alzheimer's disease (AD) and the study of their therapeutic relevance. The rationale and the design of the bifunctional compounds will be discussed in order to understand their potential as tools to investigate the role of the cholinergic system in AD.
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23
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Congreve M, Brown GA, Borodovsky A, Lamb ML. Targeting adenosine A2A receptor antagonism for treatment of cancer. Expert Opin Drug Discov 2018; 13:997-1003. [DOI: 10.1080/17460441.2018.1534825] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | - Giles A. Brown
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | | | - Michelle L. Lamb
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
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24
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Salmaso V, Moro S. Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview. Front Pharmacol 2018; 9:923. [PMID: 30186166 PMCID: PMC6113859 DOI: 10.3389/fphar.2018.00923] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Computational techniques have been applied in the drug discovery pipeline since the 1980s. Given the low computational resources of the time, the first molecular modeling strategies relied on a rigid view of the ligand-target binding process. During the years, the evolution of hardware technologies has gradually allowed simulating the dynamic nature of the binding event. In this work, we present an overview of the evolution of structure-based drug discovery techniques in the study of ligand-target recognition phenomenon, going from the static molecular docking toward enhanced molecular dynamics strategies.
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Affiliation(s)
- Veronica Salmaso
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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25
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Pantsar T, Poso A. Binding Affinity via Docking: Fact and Fiction. Molecules 2018; 23:molecules23081899. [PMID: 30061498 PMCID: PMC6222344 DOI: 10.3390/molecules23081899] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/03/2023] Open
Abstract
In 1982, Kuntz et al. published an article with the title “A Geometric Approach to Macromolecule-Ligand Interactions”, where they described a method “to explore geometrically feasible alignment of ligands and receptors of known structure”. Since then, small molecule docking has been employed as a fast way to estimate the binding pose of a given compound within a specific target protein and also to predict binding affinity. Remarkably, the first docking method suggested by Kuntz and colleagues aimed to predict binding poses but very little was specified about binding affinity. This raises the question as to whether docking is the right tool to estimate binding affinity. The short answer is no, and this has been concluded in several comprehensive analyses. However, in this opinion paper we discuss several critical aspects that need to be reconsidered before a reliable binding affinity prediction through docking is realistic. These are not the only issues that need to be considered, but they are perhaps the most critical ones. We also consider that in spite of the huge efforts to enhance scoring functions, the accuracy of binding affinity predictions is perhaps only as good as it was 10–20 years ago. There are several underlying reasons for this poor performance and these are analyzed. In particular, we focus on the role of the solvent (water), the poor description of H-bonding and the lack of the systems’ true dynamics. We hope to provide readers with potential insights and tools to overcome the challenging issues related to binding affinity prediction via docking.
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Affiliation(s)
- Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany.
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26
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Igonet S, Raingeval C, Cecon E, Pučić-Baković M, Lauc G, Cala O, Baranowski M, Perez J, Jockers R, Krimm I, Jawhari A. Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor. Sci Rep 2018; 8:8142. [PMID: 29802269 PMCID: PMC5970182 DOI: 10.1038/s41598-018-26113-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Structural studies of integral membrane proteins have been limited by the intrinsic conformational flexibility and the need to stabilize the proteins in solution. Stabilization by mutagenesis was very successful for structural biology of G protein-coupled receptors (GPCRs). However, it requires heavy protein engineering and may introduce structural deviations. Here we describe the use of specific calixarenes-based detergents for native GPCR stabilization. Wild type, full length human adenosine A2A receptor was used to exemplify the approach. We could stabilize native, glycosylated, non-aggregated and homogenous A2AR that maintained its ligand binding capacity. The benefit of the preparation for fragment screening, using the Saturation-Transfer Difference nuclear magnetic resonance (STD-NMR) experiment is reported. The binding of the agonist adenosine and the antagonist caffeine were observed and competition experiments with CGS-21680 and ZM241385 were performed, demonstrating the feasibility of the STD-based fragment screening on the native A2A receptor. Interestingly, adenosine was shown to bind a second binding site in the presence of the agonist CGS-21680 which corroborates published results obtained with molecular dynamics simulation. Fragment-like compounds identified using STD-NMR showed antagonistic effects on A2AR in the cAMP cellular assay. Taken together, our study shows that stabilization of native GPCRs represents an attractive approach for STD-based fragment screening and drug design.
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Affiliation(s)
| | - Claire Raingeval
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | - Gordan Lauc
- GENOS, Borongajska cesta 83h, 10000, Zagreb, Croatia
| | - Olivier Cala
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Maciej Baranowski
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Javier Perez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Krimm
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Anass Jawhari
- CALIXAR, 60 avenue Rockefeller, 69008, Lyon, France.
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27
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Lagarias P, Vrontaki E, Lambrinidis G, Stamatis D, Convertino M, Ortore G, Mavromoustakos T, Klotz KN, Kolocouris A. Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode. J Chem Inf Model 2018; 58:794-815. [PMID: 29485875 DOI: 10.1021/acs.jcim.7b00455] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An intense effort is made by pharmaceutical and academic research laboratories to identify and develop selective antagonists for each adenosine receptor (AR) subtype as potential clinical candidates for "soft" treatment of various diseases. Crystal structures of subtypes A2A and A1ARs offer exciting opportunities for structure-based drug design. In the first part of the present work, Maybridge HitFinder library of 14400 compounds was utilized to apply a combination of structure-based against the crystal structure of A2AAR and ligand-based methodologies. The docking poses were rescored by CHARMM energy minimization and calculation of the desolvation energy using Poisson-Boltzmann equation electrostatics. Out of the eight selected and tested compounds, five were found positive hits (63% success). Although the project was initially focused on targeting A2AAR, the identified antagonists exhibited low micromolar or micromolar affinity against A2A/A3, ARs, or A3AR, respectively. Based on these results, 19 compounds characterized by novel chemotypes were purchased and tested. Sixteen of them were identified as AR antagonists with affinity toward combinations of the AR family isoforms (A2A/A3, A1/A3, A1/A2A/A3, and A3). The second part of this work involves the performance of hundreds of molecular dynamics (MD) simulations of complexes between the ARs and a total of 27 ligands to resolve the binding interactions of the active compounds, which were not achieved by docking calculations alone. This computational work allowed the prediction of stable and unstable complexes which agree with the experimental results of potent and inactive compounds, respectively. Of particular interest is that the 2-amino-thiophene-3-carboxamides, 3-acylamino-5-aryl-thiophene-2-carboxamides, and carbonyloxycarboximidamide derivatives were found to be selective and possess a micromolar to low micromolar affinity for the A3 receptor.
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Affiliation(s)
- Panagiotis Lagarias
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Eleni Vrontaki
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - George Lambrinidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Dimitrios Stamatis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Marino Convertino
- Department of Biochemistry & Biophysics , University of North Carolina at Chapel Hill , 120 Mason Farm Road , Chapel Hill , North Carolina 27599 , United States
| | - Gabriella Ortore
- Department of Pharmacy , University of Pisa , 56126 Pisa , Italy
| | - Thomas Mavromoustakos
- Division of Organic Chemistry, Department of Chemistry, School of Science , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Karl-Norbert Klotz
- Institute of Pharmacology and Toxicology , University of Würzburg Versbacher Str. 9 , 97078 Würzburg , Germany
| | - Antonios Kolocouris
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
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28
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Abstract
In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available.
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Affiliation(s)
- Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy.
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy
| | - Matteo Floris
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, v.le San Pietro 43/C, 07100, Sassari, Italy
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29
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Wang YT, Chan YH. Understanding the molecular basis of agonist/antagonist mechanism of human mu opioid receptor through gaussian accelerated molecular dynamics method. Sci Rep 2017; 7:7828. [PMID: 28798303 PMCID: PMC5552784 DOI: 10.1038/s41598-017-08224-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/10/2017] [Indexed: 01/01/2023] Open
Abstract
The most powerful analgesic and addictive properties of opiate alkaloids are mediated by the μ opioid receptor (MOR). The MOR has been extensively investigated as a drug target in the twentieth century, with numerous compounds of varying efficacy being identified. We employed molecular dynamics and Gaussian accelerated molecular dynamics techniques to identify the binding mechanisms of MORs to BU72 (agonist) and β-funaltrexamine (antagonist). Our approach theoretically suggests that the 34 residues (Lys209–Phe221 and Ile301–Cys321) of the MORs were the key regions enabling the two compounds to bind to the active site of the MORs. When the MORs were in the holo form, the key region was in the open conformation. When the MORs were in the apo form, the key region was in the closed conformation. The key region might be responsible for the selectivity of new MOR agonists and antagonists.
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Affiliation(s)
- Yeng-Tseng Wang
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Yang-Hsiang Chan
- Department of Chemistry, National Sun Yat-sen University, 70 Lien Hai Road, Kaohsiung, Taiwan
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30
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Sayama M, Inoue A, Nakamura S, Jung S, Ikubo M, Otani Y, Uwamizu A, Kishi T, Makide K, Aoki J, Hirokawa T, Ohwada T. Probing the Hydrophobic Binding Pocket of G-Protein-Coupled Lysophosphatidylserine Receptor GPR34/LPS 1 by Docking-Aided Structure-Activity Analysis. J Med Chem 2017; 60:6384-6399. [PMID: 28715213 DOI: 10.1021/acs.jmedchem.7b00693] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ligands of certain G-protein-coupled receptors (GPCRs) have been identified as endogenous lipids, such as lysophosphatidylserine (LysoPS). Here, we analyzed the molecular basis of the structure-activity relationship of ligands of GPR34, one of the LysoPS receptor subtypes, focusing on recognition of the long-chain fatty acid moiety by the hydrophobic pocket. By introducing benzene ring(s) into the fatty acid moiety of 2-deoxy-LysoPS, we explored the binding site's preference for the hydrophobic shape. A tribenzene-containing fatty acid surrogate with modifications of the terminal aromatic moiety showed potent agonistic activity toward GPR34. Computational docking of these derivatives with a homology modeling/molecular dynamics-based virtual binding site of GPR34 indicated that a kink in the benzene-based lipid surrogates matches the L-shaped hydrophobic pocket of GPR34. A tetrabenzene-based lipid analogue bearing a bulky tert-butyl group at the 4-position of the terminal benzene ring exhibited potent GPR34 agonistic activity, validating the present hydrophobic binding pocket model.
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Affiliation(s)
- Misa Sayama
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asuka Inoue
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Sho Nakamura
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sejin Jung
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaya Ikubo
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuko Otani
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiharu Uwamizu
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takayuki Kishi
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kumiko Makide
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Junken Aoki
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,AMED-CREST, Japan Agency for Medical Research and Development , 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , 1-1-1 Tennodai, Tsukuba-shi, Ibaraki 305-8575, Japan
| | - Tomohiko Ohwada
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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31
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Fredriksson K, Lottmann P, Hinz S, Onila I, Shymanets A, Harteneck C, Müller CE, Griesinger C, Exner TE. Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kai Fredriksson
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
- Present address: Fakultät für Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
| | - Philip Lottmann
- Max Planck Institute for Biophysical Chemistry; Am Faßberg 11 37077 Göttingen Germany
| | - Sonja Hinz
- Universität Bonn; Pharma-Zentrum Bonn; Pharmazeutisches Institut; Pharmazeutische Chemie; An der Immenburg 4 53121 Bonn Germany
| | - Iounut Onila
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
| | - Aliaksei Shymanets
- Department of Pharmacology and Experimental Therapy; Institute of Experimental and Clinical Pharmacology and Toxicology; Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA); University of Tübingen; Tübingen Germany
| | - Christian Harteneck
- Department of Pharmacology and Experimental Therapy; Institute of Experimental and Clinical Pharmacology and Toxicology; Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA); University of Tübingen; Tübingen Germany
| | - Christa E. Müller
- Universität Bonn; Pharma-Zentrum Bonn; Pharmazeutisches Institut; Pharmazeutische Chemie; An der Immenburg 4 53121 Bonn Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry; Am Faßberg 11 37077 Göttingen Germany
| | - Thomas E. Exner
- Institute of Pharmacy; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and Zukunftskolleg; Universität Konstanz; 78457 Konstanz Germany
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32
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Fredriksson K, Lottmann P, Hinz S, Onila I, Shymanets A, Harteneck C, Müller CE, Griesinger C, Exner TE. Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor. Angew Chem Int Ed Engl 2017; 56:5750-5754. [PMID: 28429411 DOI: 10.1002/anie.201612547] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/09/2017] [Indexed: 11/11/2022]
Abstract
G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A2A R with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A2A R.
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Affiliation(s)
- Kai Fredriksson
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany.,Present address: Fakultät für Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Philip Lottmann
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Sonja Hinz
- Universität Bonn, Pharma-Zentrum Bonn, Pharmazeutisches Institut, Pharmazeutische Chemie, An der Immenburg 4, 53121, Bonn, Germany
| | - Iounut Onila
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany
| | - Aliaksei Shymanets
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Christian Harteneck
- Department of Pharmacology and Experimental Therapy, Institute of Experimental and Clinical Pharmacology and Toxicology, Interfaculty Center of Pharmacogenomics and Pharmaceutical Research (ICePhA), University of Tübingen, Tübingen, Germany
| | - Christa E Müller
- Universität Bonn, Pharma-Zentrum Bonn, Pharmazeutisches Institut, Pharmazeutische Chemie, An der Immenburg 4, 53121, Bonn, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Thomas E Exner
- Institute of Pharmacy, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Chemistry and Zukunftskolleg, Universität Konstanz, 78457, Konstanz, Germany
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33
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Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies. Future Med Chem 2017; 9:507-523. [DOI: 10.4155/fmc-2016-0224] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Kinetic and thermodynamic ligand–protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand–protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand–protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand–protein binding.
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34
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Fronik P, Gaiser BI, Sejer Pedersen D. Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry. J Med Chem 2017; 60:4126-4134. [DOI: 10.1021/acs.jmedchem.6b01601] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Philipp Fronik
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Birgit I. Gaiser
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
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35
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Tosh DK, Ciancetta A, Warnick E, Crane S, Gao ZG, Jacobson KA. Structure-Based Scaffold Repurposing for G Protein-Coupled Receptors: Transformation of Adenosine Derivatives into 5HT 2B/5HT 2C Serotonin Receptor Antagonists. J Med Chem 2016; 59:11006-11026. [PMID: 27933810 DOI: 10.1021/acs.jmedchem.6b01183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenosine derivatives developed to activate adenosine receptors (ARs) revealed micromolar activity at serotonin 5HT2B and 5HT2C receptors (5HTRs). We explored the structure-activity relationship at 5HT2Rs and modeled receptor interactions in order to optimize affinity and simultaneously reduce AR affinity. Depending on N6 substitution, small 5'-alkylamide modification maintained 5HT2BR affinity, which was enhanced upon ribose substitution with rigid bicyclo[3.1.0]hexane (North (N)-methanocarba), e.g., N6-dicyclopropylmethyl 4'-CH2OH derivative 14 (Ki 11 nM). 5'-Methylamide 23 was 170-fold selective as antagonist for 5HT2BR vs 5HT2CR. 5'-Methyl 25 and ethyl 26 esters potently antagonized 5HT2Rs with moderate selectivity in comparison to ARs; related 6-N,N-dimethylamino analogue 30 was 5HT2R-selective. 5' position flexibility of substitution was indicated in 5HT2BR docking. Both 5'-ester and 5'-amide derivatives displayed in vivo t1/2 of 3-4 h. Thus, we used G protein-coupled receptor modeling to repurpose nucleoside scaffolds in favor of binding at nonpurine receptors as novel 5HT2R antagonists, with potential for cardioprotection, liver protection, or central nervous system activity.
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Affiliation(s)
- Dilip K Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Eugene Warnick
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Steven Crane
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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36
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Gahbauer S, Böckmann RA. Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function. Front Physiol 2016; 7:494. [PMID: 27826255 PMCID: PMC5078798 DOI: 10.3389/fphys.2016.00494] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/11/2016] [Indexed: 12/18/2022] Open
Abstract
The dimerization or even oligomerization of G protein coupled receptors (GPCRs) causes ongoing, controversial debates about its functional role and the coupled biophysical, biochemical or biomedical implications. A continously growing number of studies hints to a relation between oligomerization and function of GPCRs and strengthens the assumption that receptor assembly plays a key role in the regulation of protein function. Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signaling complexes. Recent findings further suggest that the surrounding membrane, i.e., its lipid composition may modulate the preferred dimerization interface and as a result the abundance of distinct dimeric conformations. In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed. An overview of the different reported oligomeric interfaces is provided and their capability for signaling discussed. The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.
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Affiliation(s)
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-NürnbergErlangen, Germany
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37
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Salmaso V, Sturlese M, Cuzzolin A, Moro S. DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015. J Comput Aided Mol Des 2016; 30:773-789. [PMID: 27638810 DOI: 10.1007/s10822-016-9966-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/07/2016] [Indexed: 11/24/2022]
Abstract
Structure-based drug design (SBDD) has matured within the last two decades as a valuable tool for the optimization of low molecular weight lead compounds to highly potent drugs. The key step in SBDD requires knowledge of the three-dimensional structure of the target-ligand complex, which is usually determined by X-ray crystallography. In the absence of structural information for the complex, SBDD relies on the generation of plausible molecular docking models. However, molecular docking protocols suffer from inaccuracies in the description of the interaction energies between the ligand and the target molecule, and often fail in the prediction of the correct binding mode. In this context, the appropriate selection of the most accurate docking protocol is absolutely relevant for the final molecular docking result, even if addressing this point is absolutely not a trivial task. D3R Grand Challenge 2015 has represented a precious opportunity to test the performance of DockBench, an integrate informatics platform to automatically compare RMDS-based molecular docking performances of different docking/scoring methods. The overall performance resulted in the blind prediction are encouraging in particular for the pose prediction task, in which several complex were predicted with a sufficient accuracy for medicinal chemistry purposes.
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Affiliation(s)
- Veronica Salmaso
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Alberto Cuzzolin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, Padua, Italy.
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38
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Toti KS, Osborne D, Ciancetta A, Boison D, Jacobson KA. South (S)- and North (N)-Methanocarba-7-Deazaadenosine Analogues as Inhibitors of Human Adenosine Kinase. J Med Chem 2016; 59:6860-77. [PMID: 27410258 PMCID: PMC5032833 DOI: 10.1021/acs.jmedchem.6b00689] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Adenosine kinase (AdK) inhibitors raise endogenous adenosine levels, particularly in disease states, and have potential for treatment of seizures, neurodegeneration, and inflammation. On the basis of the South (S) ribose conformation and molecular dynamics (MD) analysis of nucleoside inhibitors bound in AdK X-ray crystallographic structures, (S)- and North (N)-methanocarba (bicyclo[3.1.0]hexane) derivatives of known inhibitors were prepared and compared as human (h) AdK inhibitors. 5'-Hydroxy (34, MRS4202 (S); 55, MRS4380 (N)) and 5'-deoxy 38a (MRS4203 (S)) analogues, containing 7- and N(6)-NH phenyl groups in 7-deazaadenine, robustly inhibited AdK activity (IC50 ∼ 100 nM), while the 5'-hydroxy derivative 30 lacking the phenyl substituents was weak. Docking in the hAdK X-ray structure and MD simulation suggested a mode of binding similar to 5'-deoxy-5-iodotubercidin and other known inhibitors. Thus, a structure-based design approach for further potency enhancement is possible. The potent AdK inhibitors in this study are ready to be further tested in animal models of epilepsy.
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Affiliation(s)
- Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Danielle Osborne
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute , 1225 NE Second Avenue, Portland, Oregon 97232, United States
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute , 1225 NE Second Avenue, Portland, Oregon 97232, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
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39
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Ciancetta A, Cuzzolin A, Deganutti G, Sturlese M, Salmaso V, Cristiani A, Sabbadin D, Moro S. New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova. Mol Inform 2016; 35:440-8. [PMID: 27546048 DOI: 10.1002/minf.201501011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/10/2016] [Indexed: 11/07/2022]
Abstract
In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand-GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand-protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.
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Affiliation(s)
- Antonella Ciancetta
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Alberto Cuzzolin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Giuseppe Deganutti
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Veronica Salmaso
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Andrea Cristiani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Davide Sabbadin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
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Jazayeri A, Andrews SP, Marshall FH. Structurally Enabled Discovery of Adenosine A 2A Receptor Antagonists. Chem Rev 2016; 117:21-37. [PMID: 27333206 DOI: 10.1021/acs.chemrev.6b00119] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade there has been a revolution in the field of G protein-coupled receptor (GPCR) structural biology. Many years of innovative research from different areas have come together to fuel this significant change in the fortunes of this field, which for many years was characterized by the paucity of high-resolution structures. The determination to succeed has been in part due to the recognized importance of these proteins as drug targets, and although the pharmaceutical industry has been focusing on these receptors, it can be justifiably argued and demonstrated that many of the approved and commercially successful GPCR drugs can be significantly improved to increase efficacy and/or reduce undesired side effects. In addition, many validated targets in this class remain to be drugged. It is widely recognized that application of structure-based drug design approaches can help medicinal chemists a long way toward discovering better drugs. The achievement of structural biologists in providing high-resolution insight is beginning to transform drug discovery efforts, and there are a number of GPCR drugs that have been discovered by use of structural information that are in clinical development. This review aims to highlight the key developments that have brought success to GPCR structure resolution efforts and exemplify the practical application of structural information for the discovery of adenosine A2A receptor antagonists that have potential to treat multiple conditions.
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Affiliation(s)
- Ali Jazayeri
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Stephen P Andrews
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
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41
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Méndez-Luna D, Bello M, Correa-Basurto J. Understanding the molecular basis of agonist/antagonist mechanism of GPER1/GPR30 through structural and energetic analyses. J Steroid Biochem Mol Biol 2016; 158:104-116. [PMID: 26772481 DOI: 10.1016/j.jsbmb.2016.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/13/2015] [Accepted: 01/04/2016] [Indexed: 12/25/2022]
Abstract
The G-protein coupled receptors (GPCRs) represent the largest superfamily of membrane proteins in charge to pass the cell signaling after binding with their cognate ligands to the cell interior. In breast cancer, a GPCR named GPER1 plays a key role in the process of growth and the proliferation of cancer cells. In a previous study, theoretical methods were applied to construct a model of GPER1, which later was submitted to molecular dynamics (MD) simulations to perform a docking calculation. Based on this preceding work, it is known that GPER1 is sensitive to structural differences in its binding site. However, due to the nature of that past study, conformational changes linked to the ligand binding were not observed. Therefore, in this study, in order to explore the conformational changes coupled to the agonist/antagonist binding, MD simulations of about 0.25μs were performed for the free and bound states, summarizing 0.75μs of MD simulation in total. For the bound states, one agonist (G-1) and antagonist (G-15) were chosen since is widely known that these two molecules cause an impact on GPER1 mobility. Based on the conformational ensemble generated through MD simulations, we found that despite G-1 and G-15 being stabilized by similar map of residues, the structural differences between both ligands impact the hydrogen bond pattern not only at the GPER1 binding site but also along the seven-helix bundle, causing significant differences in the conformational mobility along the extracellular and cytoplasmic domain, and to a lesser degree in the curvatures of helix 2, helix 3 and helix 7 between the free and bound states, which is in agreement with reported literature, and might be linked to microscopic characteristics of the activated-inactivated transition. Furthermore, binding free energy calculations using the MM/GBSA method for the bound states, followed by an alanine scanning analysis allowed us to identify some important residues for the complex stabilization.
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Affiliation(s)
- David Méndez-Luna
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City CP 11340, Mexico
| | - Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City CP 11340, Mexico.
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City CP 11340, Mexico
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42
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De Vivo M, Masetti M, Bottegoni G, Cavalli A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J Med Chem 2016; 59:4035-61. [DOI: 10.1021/acs.jmedchem.5b01684] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marco De Vivo
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- IAS-5/INM-9 Computational
Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Matteo Masetti
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Giovanni Bottegoni
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
- BiKi Technologies
srl, Via XX Settembre 33/10, 16121 Genova, Italy
| | - Andrea Cavalli
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
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43
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Advances in Computational Techniques to Study GPCR–Ligand Recognition. Trends Pharmacol Sci 2015; 36:878-890. [DOI: 10.1016/j.tips.2015.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 12/16/2022]
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44
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Towards predictive docking at aminergic G-protein coupled receptors. J Mol Model 2015; 21:284. [PMID: 26453085 DOI: 10.1007/s00894-015-2824-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/15/2015] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) are hard to crystallize. However, attempts to predict their structure have boomed as a result of advancements in crystallographic techniques. This trend has allowed computer-aided molecular modeling of GPCRs. We analyzed the performance of four molecular modeling programs in pose evaluation of re-docked antagonists / inverse agonists to 11 original crystal structures of aminergic GPCRs using an induced fit-docking procedure. AutoDock and Glide were used for docking. AutoDock binding energy function, GlideXP, Prime MM-GB/SA, and YASARA binding function were used for pose scoring. Root mean square deviation (RMSD) of the best pose ranged from 0.09 to 1.58 Å, and median RMSD of the top 60 poses ranged from 1.47 to 3.83 Å. However, RMSD of the top pose ranged from 0.13 to 7.33 Å and ranking of the best pose ranged from the 1st to 60th out of 60 poses. Moreover, analysis of ligand-receptor interactions of top poses revealed substantial differences from interactions found in crystallographic structures. Bad ranking of top poses and discrepancies between top docked poses and crystal structures render current simple docking methods unsuitable for predictive modeling of receptor-ligand interactions. Prime MM-GB/SA optimized for 3NY9 by multiple linear regression did not work well at 3NY8 and 3NYA, structures of the same receptor with different ligands. However, 9 of 11 trajectories of molecular dynamics simulations by Desmond of top poses converged with trajectories of crystal structures. Key interactions were properly detected for all structures. This procedure also worked well for cross-docking of tested β2-adrenergic antagonists. Thus, this procedure represents a possible way to predict interactions of antagonists with aminergic GPCRs.
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Structure versus function—The impact of computational methods on the discovery of specific GPCR–ligands. Bioorg Med Chem 2015; 23:3907-12. [DOI: 10.1016/j.bmc.2015.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/26/2022]
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Cao R, Rossetti G, Bauer A, CarIoni P. Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions. PLoS One 2015; 10:e0126833. [PMID: 25992797 PMCID: PMC4439127 DOI: 10.1371/journal.pone.0126833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/08/2015] [Indexed: 12/27/2022] Open
Abstract
Lipid composition may significantly affect membrane proteins function, yet its impact on the protein structural determinants is not well understood. Here we present a comparative molecular dynamics (MD) study of the human adenosine receptor type 2A (hA(2A)R) in complex with caffeine--a system of high neuro-pharmacological relevance--within different membrane types. These are POPC, mixed POPC/POPE and cholesterol-rich membranes. 0.8-μs MD simulations unambiguously show that the helical folding of the amphipathic helix 8 depends on membrane contents. Most importantly, the distinct cholesterol binding into the cleft between helix 1 and 2 stabilizes a specific caffeine-binding pose against others visited during the simulation. Hence, cholesterol presence (~33%-50% in synaptic membrane in central nervous system), often neglected in X-ray determination of membrane proteins, affects the population of the ligand binding poses. We conclude that including a correct description of neuronal membranes may be very important for computer-aided design of ligands targeting hA(2A)R and possibly other GPCRs.
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Affiliation(s)
- Ruyin Cao
- German Research School for Simulation Sciences (joint venture of RWTH Aachen University and Forschungszentrum Jülich GmbH), D-52425, Jülich, Germany
- Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Giulia Rossetti
- German Research School for Simulation Sciences (joint venture of RWTH Aachen University and Forschungszentrum Jülich GmbH), D-52425, Jülich, Germany
- Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Andreas Bauer
- Institute of Neuroscience and Medicine (INM-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Paolo CarIoni
- German Research School for Simulation Sciences (joint venture of RWTH Aachen University and Forschungszentrum Jülich GmbH), D-52425, Jülich, Germany
- Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
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Trujillo K, Paoletta S, Kiselev E, Jacobson KA. Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands. Bioorg Med Chem 2015; 23:4056-64. [PMID: 25868749 DOI: 10.1016/j.bmc.2015.03.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 10/23/2022]
Abstract
The P2Y14 receptor (P2Y14R) is a Gi protein-coupled receptor that is activated by uracil nucleotides UDP and UDP-glucose. The P2Y14R structure has yet to be solved through X-ray crystallography, but the recent agonist-bound crystal structure of the P2Y12R provides a potentially suitable template for its homology modeling for rational structure-based design of selective and high-affinity ligands. In this study, we applied ligand docking and molecular dynamics refinement to a P2Y14R homology model to qualitatively explain structure-activity relationships of previously published synthetic nucleotide analogues and to probe the quality of P2Y14R homology modeling as a template for structure-based design. The P2Y14R model supports the hypothesis of a conserved binding mode of nucleotides in the three P2Y12-like receptors involving functionally conserved residues. We predict phosphate group interactions with R253(6.55), K277(7.35), Y256(6.58) and Q260(6.62), nucleobase (anti-conformation) π-π stacking with Y102(3.33) and the role of F191(5.42) as a means for selectivity among P2Y12-like receptors. The glucose moiety of UDP-glucose docked in a secondary subpocket at the P2Y14R homology model. Thus, P2Y14R homology modeling may allow detailed prediction of interactions to facilitate the design of high affinity, selective agonists as pharmacological tools to study the P2Y14R.
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Affiliation(s)
- Kevin Trujillo
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, MD 20892-0810, USA
| | - Silvia Paoletta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, MD 20892-0810, USA
| | - Evgeny Kiselev
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, MD 20892-0810, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, MD 20892-0810, USA.
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48
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Rodríguez D, Gao ZG, Moss SM, Jacobson KA, Carlsson J. Molecular docking screening using agonist-bound GPCR structures: probing the A2A adenosine receptor. J Chem Inf Model 2015; 55:550-63. [PMID: 25625646 DOI: 10.1021/ci500639g] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Crystal structures of G protein-coupled receptors (GPCRs) have recently revealed the molecular basis of ligand binding and activation, which has provided exciting opportunities for structure-based drug design. The A2A adenosine receptor (A2AAR) is a promising therapeutic target for cardiovascular diseases, but progress in this area is limited by the lack of novel agonist scaffolds. We carried out docking screens of 6.7 million commercially available molecules against active-like conformations of the A2AAR to investigate whether these structures could guide the discovery of agonists. Nine out of the 20 predicted agonists were confirmed to be A2AAR ligands, but none of these activated the ARs. The difficulties in discovering AR agonists using structure-based methods originated from limited atomic-level understanding of the activation mechanism and a chemical bias toward antagonists in the screened library. In particular, the composition of the screened library was found to strongly reduce the likelihood of identifying AR agonists, which reflected the high ligand complexity required for receptor activation. Extension of this analysis to other pharmaceutically relevant GPCRs suggested that library screening may not be suitable for targets requiring a complex receptor-ligand interaction network. Our results provide specific directions for the future development of novel A2AAR agonists and general strategies for structure-based drug discovery.
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Affiliation(s)
- David Rodríguez
- †Science for Life Laboratory, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.,‡Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.,§Department of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Zhang-Guo Gao
- ∥Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Steven M Moss
- ∥Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kenneth A Jacobson
- ∥Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jens Carlsson
- †Science for Life Laboratory, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.,‡Swedish e-Science Research Center (SeRC), SE-100 44 Stockholm, Sweden.,§Department of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
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49
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Xiao X, Zeng X, Yuan Y, Gao N, Guo Y, Pu X, Li M. Understanding the conformation transition in the activation pathway of β2 adrenergic receptor via a targeted molecular dynamics simulation. Phys Chem Chem Phys 2015; 17:2512-22. [DOI: 10.1039/c4cp04528a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformation transition in the activation pathway of β2 adrenergic receptor was explored mainly using a target molecular dynamics simulation.
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Affiliation(s)
- Xiuchan Xiao
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xiaojun Zeng
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu
- People's Republic of China
| | - Nan Gao
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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50
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Sindhu T, Srinivasan P. Exploring the binding properties of agonists interacting with human TGR5 using structural modeling, molecular docking and dynamics simulations. RSC Adv 2015. [DOI: 10.1039/c4ra16617e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
TGR5, act as a potential pharmacological target in the treatment of type II diabetes. In the computational study, structural modeling and binding site prediction of TGR5 receptor was performed. Two well-known agonists of TGR5 used to investigate the mode and mechanism of binding.
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Affiliation(s)
- Thangaraj Sindhu
- Molecular Biology Lab
- Department of Bioinformatics
- Alagappa University
- Karaikudi-630004
- India
| | - Pappu Srinivasan
- Molecular Biology Lab
- Department of Bioinformatics
- Alagappa University
- Karaikudi-630004
- India
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