1
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Nicholson JM, Yang D, Koelblen T, Hu EL, Coss CC, Burris TP, Hu X, Micalizio GC. Merging Natural Product Structures with Pharmaceutical Leads: Unnatural Enantiomers of Estranes as Glucocorticoid Receptor Modulators That Suppress TNF-α and IL-6 Release. J Med Chem 2024; 67:16185-16194. [PMID: 39240657 DOI: 10.1021/acs.jmedchem.4c01007] [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: 09/07/2024]
Abstract
Natural products are widely recognized as valuable starting points for the development of therapeutics, with synthetic tetracyclic triterpenoids (e.g., steroids) being the most well represented among the drugs approved by the Food and Drug Administration. Here, recently developed synthetic tools for concise, asymmetric, and convergent construction of steroidal systems are leveraged to drive a program aimed at identifying novel glucocorticoid receptor (GR) modulators. While glucocorticoids have been extensively used as anti-inflammatory agents, they are plagued by severe side effects that include bone loss, muscle wasting, and metabolic disease. Ultimately, a program targeting the unnatural enantiomers of estranes (ent-estranes) that are practically inaccessible from natural product derivatization (semisynthesis) has resulted in the identification of a new class of potent dissociated GR modulators. We identify several leads with >99% efficacy as antagonists of GR trans-activation (potency within 10-fold of that of mifepristone) and further characterize examples that also inhibit release of pro-inflammatory cytokines IL-6 and TNF-α.
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Affiliation(s)
- Joshua M Nicholson
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Dexi Yang
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
| | - Thomas Koelblen
- University of Florida Genetics Institute, Gainesville, Florida 32610, United States
| | - Eric L Hu
- Computational Biology Undergraduate Concentration, Brown University, 69 Brown Street, Mail no. 4277, Providence, Rhode Island 02912, United States
| | - Christopher C Coss
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Thomas P Burris
- University of Florida Genetics Institute, Gainesville, Florida 32610, United States
| | - Xiao Hu
- Accunet LLC BioPharma Consulting, 1805 Olive Green Street, Chula Vista, California 91913, United States
| | - Glenn C Micalizio
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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2
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Đurić L, Milanović M, Drljača Lero J, Milošević N, Milić N. In silico analysis of endocrine-disrupting potential of triclosan, bisphenol A, and their analogs and derivatives. J Appl Toxicol 2024. [PMID: 39129338 DOI: 10.1002/jat.4685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/16/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
Owning to the increasing body of evidence about the ubiquitous exposure to endocrine disruptors (EDCs), particularly bisphenol A (BPA), and associated health effects, BPA has been gradually substituted with insufficiently tested structural analogs. The unmanaged excessive use of antimicrobial agents such as triclosan (TCS) during the COVID-19 outbreak has also raised concerns about its possible interferences with hormonal functions. The similarity of BPA and estradiol, as well as TCS and non-steroidal estrogens, imply that endocrine-disrupting properties of their analogs could be predicted based on the chemical structure. Hence, this study aimed to evaluate the endocrine-disrupting potential of BPA substitutes as well as TCS derivatives and degradation/biotransformation metabolites, in comparison to BPA and TCS based on their molecular properties, computational predictions of pharmacokinetics and binding affinities to nuclear receptors. Based on the obtained results several under-researched BPA analogs exhibited higher binding affinities for nuclear receptors than BPA. Notable analogs included compounds detected in receipts (DD-70, BTUM-70, TGSA, and BisOPP-A), along with a flame retardant, BDP. The possible health hazards linked to exposure to TCS and its mono-hydroxylated metabolites were also found. Further research is needed in order to elucidate the health impacts of these compounds and promote better regulation practices.
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Affiliation(s)
- Larisa Đurić
- Faculty of Medicine, Department of Pharmacy, University of Novi Sad, Novi Sad, Serbia
| | - Maja Milanović
- Faculty of Medicine, Department of Pharmacy, University of Novi Sad, Novi Sad, Serbia
| | - Jovana Drljača Lero
- Faculty of Medicine, Department of Pharmacy, University of Novi Sad, Novi Sad, Serbia
| | - Nataša Milošević
- Faculty of Medicine, Department of Pharmacy, University of Novi Sad, Novi Sad, Serbia
| | - Nataša Milić
- Faculty of Medicine, Department of Pharmacy, University of Novi Sad, Novi Sad, Serbia
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3
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Chen Y, Anderson MT, Payne N, Santori FR, Ivanova NB. Nuclear Receptors and the Hidden Language of the Metabolome. Cells 2024; 13:1284. [PMID: 39120315 PMCID: PMC11311682 DOI: 10.3390/cells13151284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Nuclear hormone receptors (NHRs) are a family of ligand-regulated transcription factors that control key aspects of development and physiology. The regulation of NHRs by ligands derived from metabolism or diet makes them excellent pharmacological targets, and the mechanistic understanding of how NHRs interact with their ligands to regulate downstream gene networks, along with the identification of ligands for orphan NHRs, could enable innovative approaches for cellular engineering, disease modeling and regenerative medicine. We review recent discoveries in the identification of physiologic ligands for NHRs. We propose new models of ligand-receptor co-evolution, the emergence of hormonal function and models of regulation of NHR specificity and activity via one-ligand and two-ligand models as well as feedback loops. Lastly, we discuss limitations on the processes for the identification of physiologic NHR ligands and emerging new methodologies that could be used to identify the natural ligands for the remaining 17 orphan NHRs in the human genome.
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Affiliation(s)
- Yujie Chen
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Matthew Tom Anderson
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Nathaniel Payne
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Fabio R. Santori
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Natalia B. Ivanova
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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4
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Seaton WB, Burke SJ, Fisch AR, Schilletter WA, Beck MGA, Cassagne GA, Harvey I, Fontenot MS, Collier JJ, Campagna SR. Channel Expansion in the Ligand-Binding Domain of the Glucocorticoid Receptor Contributes to the Activity of Highly Potent Glucocorticoid Analogues. Molecules 2024; 29:1546. [PMID: 38611825 PMCID: PMC11013598 DOI: 10.3390/molecules29071546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Glucocorticoids (GCs) act through the glucocorticoid receptor (GR) and are commonly used as anti-inflammatory and immunosuppressant medications. Chronic GC use has been linked with unwanted complications such as steroid-induced diabetes mellitus (SIDM), although the mechanisms for these effects are not completely understood. Modification of six GC parent molecules with 2-mercaptobenzothiazole resulted in consistently less promoter activity in transcriptional activation assays using a 3xGRE reporter construct while constantly reducing inflammatory pathway activity. The most selective candidate, DX1, demonstrated a significant reduction (87%) in transactivation compared to commercially available dexamethasone. DX1 also maintained 90% of the anti-inflammatory potential of dexamethasone while simultaneously displaying a reduced toxicity profile. Additionally, two novel and highly potent compounds, DX4 and PN4, were developed and shown to elicit similar mRNA expression at attomolar concentrations that dexamethasone exhibits at nanomolar dosages. To further explain these results, Molecular Dynamic (MD) simulations were performed to examine structural changes in the ligand-binding domain of the glucocorticoid receptor in response to docking with the top ligands. Differing interactions with the transcriptional activation function 2 (AF-2) region of the GR may be responsible for lower transactivation capacity in DX1. DX4 and PN4 lose contact with Arg611 due to a key interaction changing from a stronger hydrophilic to a weaker hydrophobic one, which leads to the formation of an unoccupied channel at the location of the deacylcortivazol (DAC)-expanded binding pocket. These findings provide insights into the structure-function relationships important for regulating anti-inflammatory activity, which has implications for clinical utility.
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Affiliation(s)
- Wesley B. Seaton
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; (W.B.S.)
| | - Susan J. Burke
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA (J.J.C.)
| | - Alexander R. Fisch
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; (W.B.S.)
| | | | - Mary Grace A. Beck
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA (J.J.C.)
| | | | - Innocence Harvey
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA (J.J.C.)
| | - Molly S. Fontenot
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA (J.J.C.)
| | - J. Jason Collier
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA (J.J.C.)
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA; (W.B.S.)
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5
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Deploey N, Van Moortel L, Rogatsky I, Peelman F, De Bosscher K. The Biologist's Guide to the Glucocorticoid Receptor's Structure. Cells 2023; 12:1636. [PMID: 37371105 PMCID: PMC10297449 DOI: 10.3390/cells12121636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The glucocorticoid receptor α (GRα) is a member of the nuclear receptor superfamily and functions as a glucocorticoid (GC)-responsive transcription factor. GR can halt inflammation and kill off cancer cells, thus explaining the widespread use of glucocorticoids in the clinic. However, side effects and therapy resistance limit GR's therapeutic potential, emphasizing the importance of resolving all of GR's context-specific action mechanisms. Fortunately, the understanding of GR structure, conformation, and stoichiometry in the different GR-controlled biological pathways is now gradually increasing. This information will be crucial to close knowledge gaps on GR function. In this review, we focus on the various domains and mechanisms of action of GR, all from a structural perspective.
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Affiliation(s)
- Nick Deploey
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (N.D.); (L.V.M.); (F.P.)
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Translational Nuclear Receptor Research (TNRR) Laboratory, VIB, 9052 Ghent, Belgium
| | - Laura Van Moortel
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (N.D.); (L.V.M.); (F.P.)
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Translational Nuclear Receptor Research (TNRR) Laboratory, VIB, 9052 Ghent, Belgium
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Z. Rosensweig Genomics Center, New York, NY 10021, USA;
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Frank Peelman
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (N.D.); (L.V.M.); (F.P.)
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Karolien De Bosscher
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (N.D.); (L.V.M.); (F.P.)
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Translational Nuclear Receptor Research (TNRR) Laboratory, VIB, 9052 Ghent, Belgium
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6
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Sørensen DM, Büll C, Madsen TD, Lira-Navarrete E, Clausen TM, Clark AE, Garretson AF, Karlsson R, Pijnenborg JFA, Yin X, Miller RL, Chanda SK, Boltje TJ, Schjoldager KT, Vakhrushev SY, Halim A, Esko JD, Carlin AF, Hurtado-Guerrero R, Weigert R, Clausen H, Narimatsu Y. Identification of global inhibitors of cellular glycosylation. Nat Commun 2023; 14:948. [PMID: 36804936 PMCID: PMC9941569 DOI: 10.1038/s41467-023-36598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Small molecule inhibitors of glycosylation enzymes are valuable tools for dissecting glycan functions and potential drug candidates. Screening for inhibitors of glycosyltransferases are mainly performed by in vitro enzyme assays with difficulties moving candidates to cells and animals. Here, we circumvent this by employing a cell-based screening assay using glycoengineered cells expressing tailored reporter glycoproteins. We focused on GalNAc-type O-glycosylation and selected the GalNAc-T11 isoenzyme that selectively glycosylates endocytic low-density lipoprotein receptor (LDLR)-related proteins as targets. Our screen of a limited small molecule compound library did not identify selective inhibitors of GalNAc-T11, however, we identify two compounds that broadly inhibited Golgi-localized glycosylation processes. These compounds mediate the reversible fragmentation of the Golgi system without affecting secretion. We demonstrate how these inhibitors can be used to manipulate glycosylation in cells to induce expression of truncated O-glycans and augment binding of cancer-specific Tn-glycoprotein antibodies and to inhibit expression of heparan sulfate and binding and infection of SARS-CoV-2.
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Affiliation(s)
- Daniel Madriz Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Thomas Mandel Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Johan F A Pijnenborg
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Thomas J Boltje
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ramon Hurtado-Guerrero
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Roberto Weigert
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
- GlycoDisplay ApS, Copenhagen, Denmark.
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7
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Metin R, Akten ED. Drug repositioning to propose alternative modulators for glucocorticoid receptor through structure-based virtual screening. J Biomol Struct Dyn 2022; 40:11418-11433. [PMID: 34355665 DOI: 10.1080/07391102.2021.1960608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Drug repositioning has recently become one of the widely used drug design approaches in proposing alternative compounds with potentially fewer side effects. In this study, structure-based pharmacophore modelling and docking was used to screen existing drug molecules to bring forward potential modulators for ligand-binding domain of human glucocorticoid receptor (hGR). There exist several drug molecules targeting hGR, yet their apparent side effects still persist. Our goal was to disclose new compounds via screening existing drug compounds to bring forward fast and explicit solutions. The so-called shared pharmacophore model was created using the most persistent pharmacophore features shared by several crystal structures of the receptor. The shared model was first used to screen a small database of 75 agonists and 300 antagonists/decoys, and exhibited a successful outcome in its ability to distinguish agonists from antagonists/decoys. Then, it was used to screen a database of over 5000 molecules composed of FDA-approved, worldwide used and investigational drug compounds. A total of 110 compounds satisfying the pharmacophore requirements were subjected to different docking experiments for further assessment of their binding ability. In the final hit list of 54 compounds which fulfilled all scoring criteria, 19 of them were nonsteroidal and when further investigated, each presented a unique scaffold with little structural resemblance to any known nonsteroidal GR modulators. Independent 100 ns long MD simulations conducted on three selected drug candidates in complex with hGR displayed stable conformations incorporating several hydrogen bonds common to all three compounds and the reference molecule dexamethasone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reyhan Metin
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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8
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Lato A, Burke SJ, Ducote MP, Kennedy BJ, Collier JJ, Campagna SR. Stereoisomers of an Aryl Pyrazole Glucocorticoid Receptor Agonist Scaffold Elicit Differing Anti-inflammatory Responses. ACS Med Chem Lett 2022; 13:1493-1499. [PMID: 36105346 PMCID: PMC9465825 DOI: 10.1021/acsmedchemlett.2c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/17/2022] [Indexed: 11/30/2022] Open
Abstract
Glucocorticoids (GCs) are heavily prescribed to control inflammation in various human diseases; however, side effects associated with GCs are well documented and lead to serious metabolic and immunological complications with long-term use. The paradigm for GC function includes two well described modes of activity: dimer formation of the glucocorticoid receptor (GR) promotes transactivation, while monomeric interaction with co-regulators promotes transrepression. Previously, a set of aryl pyrazole-derived glucocorticoid receptor agonists (APGRAs) with potency rivaling current commercially available glucocorticoids were described. In this study, a further series of existing and novel stereopure APGRAs were thoroughly examined for biological activity and evaluated for structure-activity relationships (SARs). The si isomers with an upward OH moiety were ∼70% more active on average than the re isomers. Additionally, AP13 was found to elicit 79% transrepression of dexamethasone while eliciting less than half the transactivation response in 832/13 cells, a rat insulinoma cell line.
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Affiliation(s)
- Ashley
M. Lato
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Susan J. Burke
- Pennington
Biomedical Research Center, Baton Rouge, Louisiana 70808, United States
| | - Maggie P. Ducote
- Pennington
Biomedical Research Center, Baton Rouge, Louisiana 70808, United States
| | - Brandon J. Kennedy
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - J. Jason Collier
- Pennington
Biomedical Research Center, Baton Rouge, Louisiana 70808, United States
| | - Shawn R. Campagna
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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9
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Shi Y, Cao S, Ni D, Fan J, Lu S, Xue M. The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor. Front Mol Biosci 2022; 9:933676. [PMID: 35874618 PMCID: PMC9300934 DOI: 10.3389/fmolb.2022.933676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Glucocorticoid receptor (GR) regulates various cellular functions. Given its broad influence on metabolic activities, it has been the target of drug discovery for decades. However, how drugs induce conformational changes in GR has remained elusive. Herein, we used five GR agonists (dex, AZ938, pred, cor, and dibC) with different efficacies to investigate which aspect of the ligand induced the differences in efficacy. We performed molecular dynamics simulations on the five systems (dex-, AZ938-, pred-, cor-, and dibC-bound systems) and observed a distinct discrepancy in the conformation of the cofactor TIF2. Moreover, we discovered ligand-induced differences regarding the level of conformational changes posed by the binding of cofactor TIF2 and identified a pair of essential residues D590 and T39. We further found a positive correlation between the efficacies of ligands and the interaction of the two binding pockets' domains, where D590 and T739 were involved, implying their significance in the participation of allosteric communication. Using community network analysis, two essential communities containing D590 and T739 were identified with their connectivity correlating to the efficacy of ligands. The potential communication pathways between these two residues were revealed. These results revealed the underlying mechanism of allosteric communication between the ligand-binding and cofactor-binding pockets and identified a pair of important residues in the allosteric communication pathway, which can serve as a guide for future drug discovery.
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Affiliation(s)
- Yuxin Shi
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shu Cao
- Department of Urology, Ezhou Central Hospital, Hubei, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mintao Xue
- Department of Orthopedics, Second Affiliated Hospital of Naval Medical University, Shanghai, China
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10
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Structural insights into glucocorticoid receptor function. Biochem Soc Trans 2021; 49:2333-2343. [PMID: 34709368 DOI: 10.1042/bst20210419] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/02/2023]
Abstract
The glucocorticoid receptor (GR) is a steroid hormone-activated transcription factor that binds to various glucocorticoid response elements to up- or down- regulate the transcription of thousands of genes involved in metabolism, development, stress and inflammatory responses. GR consists of two domains enabling interaction with glucocorticoids, DNA response elements and coregulators, as well as a large intrinsically disordered region that mediates condensate formation. A growing body of structural studies during the past decade have shed new light on GR interactions, providing a new understanding of the mechanisms driving context-specific GR activity. Here, we summarize the established and emerging mechanisms of action of GR, primarily from a structural perspective. This minireview also discusses how the current state of knowledge of GR function may guide future glucocorticoid design with an improved therapeutic index for different inflammatory disorders.
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11
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Kennedy BJ, Lato AM, Fisch AR, Burke SJ, Kirkland JK, Prevatte CW, Dunlap LE, Smith RT, Vogiatzis KD, Collier JJ, Campagna SR. Potent Anti-Inflammatory, Arylpyrazole-Based Glucocorticoid Receptor Agonists That Do Not Impair Insulin Secretion. ACS Med Chem Lett 2021; 12:1568-1577. [PMID: 34676039 DOI: 10.1021/acsmedchemlett.1c00379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 11/28/2022] Open
Abstract
Glucocorticoids (GCs) are widely used in medicine for their role in the treatment of autoimmune-mediated conditions, certain cancers, and organ transplantation. The transcriptional activities GCs elicit include transrepression, postulated to be responsible for the anti-inflammatory activity, and transactivation, proposed to underlie the undesirable side effects associated with long-term use. A GC analogue that could elicit only transrepression and beneficial transactivation properties would be of great medicinal value and is highly sought after. In this study, a series of 1-(4-substituted phenyl)pyrazole-based GC analogues were synthesized, biologically screened, and evaluated for SARs leading to the desired activity. Activity observed in compounds bearing an electron deficient arylpyrazole moiety showed promise toward a dissociated steroid, displaying transrepression while having limited transactivation activity. In addition, compounds 11aa and 11ab were found to have anti-inflammatory efficacy comparable to that of dexamethasone at 10 nM, with minimal transactivation activity and no reduction of insulin secretion in cultured rat 832/13 beta cells.
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Affiliation(s)
- Brandon J. Kennedy
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ashley M. Lato
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Alexander R. Fisch
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Susan J. Burke
- Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, United States
| | - Justin K. Kirkland
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Carson W. Prevatte
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Lee E. Dunlap
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Russell T. Smith
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | | | - J. Jason Collier
- Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, United States
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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12
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Chen H, Zhou R, Pang J, Guo Y, Chen J, Kang Y, Duan M, Hou T. Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. J Chem Inf Model 2021; 62:5233-5245. [PMID: 34506144 DOI: 10.1021/acs.jcim.1c00150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
As a major drug target for anti-inflammatory therapy, the glucocorticoid receptor (GR) regulates a wide range of physiological processes through transactivation (TA) or transrepression. GR TA is involved in many adverse effects of GR-targeting drugs, and therefore, the discovery of novel GR ligands with lower TA activity and longer residence time is quite urgent. Undoubtedly, understanding the ligand dissociation mechanisms and the structural basis of the TA regulation is crucial for the development of novel GR-targeting drugs. Here, we used random accelerated molecular dynamics (RAMD) and funnel metadynamics (FM) simulations to explore the dissociation mechanisms of 5 classic glucocorticoids and 6 nonsteroidal GR ligands. Multiple ligand dissociation pathways were discovered. The classic glucocorticoids exhibit a strong preference for Path I, and most nonsteroidal ligands tend to dissociate along mixed pathways. We also find that the distinct unbinding preferences for AZD2906 and AZD9567, two representative nonsteroidal ligands with similar scaffolds but different TA activities, are primarily determined by their different polar interactions with the surrounding residues. Notably, the binding of AZD9567 poses a substantial impact on the conformation of the GR homodimer interface, which provides a valuable clue to understand the mechanisms of the TA-related side effects induced by the adjustments of the homodimerization process. These findings are critical for the structure-based rational design of novel GR ligands with more potent anti-inflammatory potency and reduced side effects.
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Affiliation(s)
- Haiyi Chen
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China.,National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Jinping Pang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Yue Guo
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Jiawen Chen
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071 Hubei, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
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13
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Kroon J, Viho EMG, Gentenaar M, Koorneef LL, van Kooten C, Rensen PCN, Kooijman S, Hunt H, Meijer OC. The development of novel glucocorticoid receptor antagonists: From rational chemical design to therapeutic efficacy in metabolic disease models. Pharmacol Res 2021; 168:105588. [PMID: 33798733 DOI: 10.1016/j.phrs.2021.105588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/02/2023]
Abstract
Glucocorticoids regulate numerous processes in human physiology, but deregulated or excessive glucocorticoid receptor (GR) signaling contributes to the development of various pathologies including metabolic syndrome. For this reason, GR antagonists have considerable therapeutic value. Yet, the only GR antagonist that is clinically approved to date - mifepristone - exhibits cross-reactivity with other nuclear steroid receptors like the progesterone receptor. In this study, we set out to identify novel selective GR antagonists by combining rational chemical design with an unbiased in vitro and in vivo screening approach. Using this pipeline, we were able to identify CORT125329 as the compound with the best overall profile from our octahydro series of novel GR antagonists, and demonstrated that CORT125329 does not exhibit cross-reactivity with the progesterone receptor. Further in vivo testing showed beneficial activities of CORT125329 in models for excessive corticosterone exposure and short- and long-term high-fat diet-induced metabolic complications. Upon CORT125329 treatment, most metabolic parameters that deteriorated upon high-fat diet feeding were similarly improved in male and female mice, confirming activity in both sexes. However, some sexually dimorphic effects were observed including male-specific antagonism of GR activity in brown adipose tissue and female-specific lipid lowering activities after short-term CORT125329 treatment. Remarkably, CORT125329 exhibits beneficial metabolic effects despite its lack of GR antagonism in white adipose tissue. Rather, we propose that CORT125329 treatment restores metabolic activity in brown adipose tissue by stimulating lipolysis, mitochondrial activity and thermogenic capacity. In summary, we have identified CORT125329 as a selective GR antagonist with strong beneficial activities in metabolic disease models, paving the way for further clinical investigation.
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Affiliation(s)
- Jan Kroon
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.
| | - Eva M G Viho
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Max Gentenaar
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Lisa L Koorneef
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Cees van Kooten
- Department of Medicine, Division of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Sander Kooijman
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Hazel Hunt
- Corcept Therapeutics, Menlo Park, CA, USA
| | - Onno C Meijer
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
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14
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Browning C, McEwen AG, Mori K, Yokoi T, Moras D, Nakagawa Y, Billas IML. Nonsteroidal ecdysone receptor agonists use a water channel for binding to the ecdysone receptor complex EcR/USP. JOURNAL OF PESTICIDE SCIENCE 2021; 46:88-100. [PMID: 33746550 PMCID: PMC7953031 DOI: 10.1584/jpestics.d20-095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/16/2021] [Indexed: 05/27/2023]
Abstract
The ecdysone receptor (EcR) possesses the remarkable capacity to adapt structurally to different types of ligands. EcR binds ecdysteroids, including 20-hydroxyecdysone (20E), as well as nonsteroidal synthetic agonists such as insecticidal dibenzoylhydrazines (DBHs). Here, we report the crystal structures of the ligand-binding domains of Heliothis virescens EcR/USP bound to the DBH agonist BYI09181 and to the imidazole-type compound BYI08346. The region delineated by helices H7 and H10 opens up to tightly fit a phenyl ring of the ligands to an extent that depends on the bulkiness of ring substituent. In the structure of 20E-bound EcR, this part of the ligand-binding pocket (LBP) contains a channel filled by water molecules that form an intricate hydrogen bond network between 20E and LBP. The water channel present in the nuclear receptor bound to its natural hormone acts as a critical molecular adaptation spring used to accommodate synthetic agonists inside its binding cavity.
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Affiliation(s)
- Christopher Browning
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Alastair G. McEwen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Kotaro Mori
- Graduate School of Agriculture, Kyoto University, Kyoto 606–8502, Japan
| | - Taiyo Yokoi
- Graduate School of Agriculture, Kyoto University, Kyoto 606–8502, Japan
| | - Dino Moras
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Yoshiaki Nakagawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606–8502, Japan
| | - Isabelle M. L. Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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15
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Xu X, Chen Y, Zhu D, Zhao T, Xu R, Wang J, Hu L, Shen X. FX5 as a non-steroidal GR antagonist improved glucose homeostasis in type 2 diabetic mice via GR/HNF4α/miR-122-5p pathway. Aging (Albany NY) 2020; 13:2436-2458. [PMID: 33316780 PMCID: PMC7880398 DOI: 10.18632/aging.202275] [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: 03/28/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease characterized by glucose metabolic disorders, and gluconeogenesis inhibiting is a promisingly therapeutic strategy for T2DM. Glucocorticoid receptor (GR) is tightly implicated in the regulation of gluconeogenesis, although the underlying mechanism remains obscure. Here, we discovered that small molecule, 5-chloro-N-[4-chloro-3-(trifluoromethyl)phenyl]thiophene-2-sulfonamide (FX5) as a new non-steroidal GR antagonist efficiently ameliorated glucose homeostasis in db/db and HFD/STZ-induced T2DM mice. The mechanism underlying the suppression of FX5 against gluconeogenesis was highly investigated. FX5 suppressed gluconeogenetic genes G6Pase and PEPCK in mouse primary hepatocytes and liver tissues of T2DM mice. Results of mammalian one-hybrid and transactivation as well as nuclear translocation assays totally evaluated the antagonistic features of FX5 against GR. Moreover, siRNA and overexpression related assays verified that FX5 alleviated gluconeogenesis either directly by antagonizing GR or indirectly through GR/HNF4α/miR122-5p signaling pathway. Our work has presented a new mode for GR antagonist in the regulation of gluconeogenesis, which is expected to highlight the potential of FX5 in the treatment of T2DM.
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Affiliation(s)
- Xin Xu
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yidi Chen
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Danyang Zhu
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Tong Zhao
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Rui Xu
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jiaying Wang
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lihong Hu
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xu Shen
- Key Laboratory of Drug Target and Drug for Degenerative Disease of Jiangsu Province, Nanjing University of Chinese Medicine, Nanjing 210023, China
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16
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Zimmerman JAO, Fang M, Doumbia B, Neyman A, Cha JH, Thomas M, Hall B, Wu M, Wilson AM, Pufall MA. Deacylcortivazol-like pyrazole regioisomers reveal a more accommodating expanded binding pocket for the glucocorticoid receptor. RSC Med Chem 2020; 12:203-212. [PMID: 34046609 DOI: 10.1039/d0md00278j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/26/2020] [Indexed: 01/26/2023] Open
Abstract
Glucocorticoids (GCs) are widely used, potent anti-inflammatory and chemotherapeutic drugs. They work by binding to the glucocorticoid receptor (GR), a ligand-activated transcription factor, inducing translocation to the nucleus and regulation of genes that influence a variety of cellular activities. Despite being effective for a broad number of conditions, GC use is limited by severe side effects. To identify ligands that are more selective, we synthesized pairs of regioisomers in the pyrazole ring that probe the expanded binding pocket of GR opened by deacylcortivazol (DAC). Using an Ullmann-type reaction, a deacylcortivazol-like (DAC-like) backbone was modified with five pendant groups at the 1'- and 2'-positions of the pyrazole ring, yielding 9 ligands. Most of the compounds were cytotoxic to leukemia cells, and all required GR expression. Both aliphatic and other aromatic groups substituted at the 2'-position produced ligands with GC activity, with phenyl and 4-fluorophenyl substitutions exhibiting high cellular affinity for the receptor and >5× greater potency than dexamethasone, a commonly used strong GC. Surprisingly, phenyl substitution at the 1'-position produced a high-affinity ligand with ∼10× greater potency than dexamethasone, despite little apparent room in the expanded binding pocket to accommodate 1'-modifications. Other 1'-modifications, however, were markedly less potent. The potency of the 2'-substituted and 1'-substituted DAC-like compounds tracked linearly with cellular affinity but had different slopes, suggesting a different mode of interaction with GR. These data provide evidence that the expanded binding pocket opened by deacylcortivazol is more accommodating that expected, allowing development of new, and possibly selective, GCs by substitution within the pyrazole ring.
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Affiliation(s)
- Jessica A O Zimmerman
- Department of Biochemistry, Carver College of Medicine, University of Iowa Iowa City IA USA .,Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa Iowa City IA USA
| | - Mimi Fang
- Department of Biochemistry, Carver College of Medicine, University of Iowa Iowa City IA USA
| | - Bintou Doumbia
- Department of Chemistry, Butler University Indianapolis IN USA
| | - Alexis Neyman
- Department of Chemistry, Butler University Indianapolis IN USA
| | - Ji Hyeon Cha
- Department of Chemistry, Butler University Indianapolis IN USA
| | - Michael Thomas
- Department of Chemistry, Butler University Indianapolis IN USA
| | | | - Meng Wu
- Department of Biochemistry, Carver College of Medicine, University of Iowa Iowa City IA USA .,University of Iowa High Throughput Screening (UIHTS) Core USA.,Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa USA
| | - Anne M Wilson
- Department of Chemistry, Butler University Indianapolis IN USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa Iowa City IA USA
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17
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Karra AG, Tziortziou M, Kylindri P, Georgatza D, Gorgogietas VA, Makiou A, Krokida A, Tsialtas I, Kalousi FD, Papadopoulos GE, Papadopoulou KΚ, Psarra AMG. Boswellic acids and their derivatives as potent regulators of glucocorticoid receptor actions. Arch Biochem Biophys 2020; 695:108656. [PMID: 33127380 DOI: 10.1016/j.abb.2020.108656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 12/20/2022]
Abstract
Glucocorticoid (GCs) hormones exert their actions via their cognate steroid receptors the Glucocorticoid Receptors (GR), by genomic or non-genomic mechanisms of actions. GCs regulate many cellular functions among them growth, metabolism, immune response and apoptosis. Due to their cell type specific induction of apoptosis GCs are used for the treatment of certain type of cancer. In addition, due to their anti-inflammatory actions, GCs are among the most highly prescribed drug to treat chronic inflammatory disorders, albeit to the many adverse side effects arising by their long term and high doses use. Thus, there is a high need for selective glucocorticoid receptor agonist - modulators (SEGRA- SGRMs) as effective as classic GCs, but with a reduced side effect profile. Boswellic acids (BAs) are triterpenes that show structural similarities with GCs and exhibit anti-inflammatory and anti-cancer activities. In this study we examined whether BA alpha and beta and certain BAs derivatives exert their actions, at least in part, through the regulation of GR activities. Applying docking analysis we found that BAs can bind stably into the deacylcortivazol (DAC) accommodation pocket of GR. Moreover we showed that certain boswellic acids derivatives induce glucocorticoid receptor nuclear translocation, no activation of GRE dependent luciferase gene expression, and suppression of the TNF-α induced NF-κB transcriptional activation in GR positive HeLa and HEK293 cells, but not in low GR level COS-7 cells. Furthermore, certain boswellic acids compounds exert antagonistic effect on the DEX-induced GR transcriptional activation and induce cell type specific mitochondrial dependent apoptosis. Our results indicate that certain BAs are potent selective glucocorticoid receptor regulators and could have great potential for therapeutic use.
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Affiliation(s)
- Aikaterini G Karra
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Maria Tziortziou
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Paraskevi Kylindri
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Dimitra Georgatza
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Vyron A Gorgogietas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Anthi Makiou
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Afroditi Krokida
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Ioannis Tsialtas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Foteini D Kalousi
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | | | | | - Anna-Maria G Psarra
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
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18
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Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment. Proc Natl Acad Sci U S A 2020; 117:24285-24293. [PMID: 32917814 DOI: 10.1073/pnas.2006890117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy is a genetic disorder that shows chronic and progressive damage to skeletal and cardiac muscle leading to premature death. Antiinflammatory corticosteroids targeting the glucocorticoid receptor (GR) are the current standard of care but drive adverse side effects such as deleterious bone loss. Through subtle modification to a steroidal backbone, a recently developed drug, vamorolone, appears to preserve beneficial efficacy but with significantly reduced side effects. We use combined structural, biophysical, and biochemical approaches to show that loss of a receptor-ligand hydrogen bond drives these remarkable therapeutic effects. Moreover, vamorolone uniformly weakens coactivator associations but not corepressor associations, implicating partial agonism as the main driver of its dissociative properties. Additionally, we identify a critical and evolutionarily conserved intramolecular network connecting the ligand to the coregulator binding surface. Interruption of this allosteric network by vamorolone selectively reduces GR-driven transactivation while leaving transrepression intact. Our results establish a mechanistic understanding of how vamorolone reduces side effects, guiding the future design of partial agonists as selective GR modulators with an improved therapeutic index.
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19
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Köhler C, Carlström G, Gunnarsson A, Weininger U, Tångefjord S, Ullah V, Lepistö M, Karlsson U, Papavoine T, Edman K, Akke M. Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor. SCIENCE ADVANCES 2020; 6:eabb5277. [PMID: 32832645 PMCID: PMC7439413 DOI: 10.1126/sciadv.abb5277] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/05/2020] [Indexed: 05/07/2023]
Abstract
Allosteric communication within proteins is a hallmark of biochemical signaling, but the dynamic transmission pathways remain poorly characterized. We combined NMR spectroscopy and surface plasmon resonance to reveal these pathways and quantify their energetics in the glucocorticoid receptor, a transcriptional regulator controlling development, metabolism, and immune response. Our results delineate a dynamic communication network of residues linking the ligand-binding pocket to the activation function-2 interface, where helix 12, a switch for transcriptional activation, exhibits ligand- and coregulator-dependent dynamics coupled to graded activation. The allosteric free energy responds to variations in ligand structure: subtle changes gradually tune allostery while preserving the transmission pathway, whereas substitution of the entire pharmacophore leads to divergent allosteric control by apparently rewiring the communication network. Our results provide key insights that should aid in the design of mechanistically differentiated ligands.
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Affiliation(s)
- C. Köhler
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - G. Carlström
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - A. Gunnarsson
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - U. Weininger
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P. O. Box 124, 221 00 Lund, Sweden
| | - S. Tångefjord
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - V. Ullah
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - M. Lepistö
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - U. Karlsson
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - T. Papavoine
- Respiratory, Inflammation and Autoimmunity, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - K. Edman
- Discovery Sciences, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - M. Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P. O. Box 124, 221 00 Lund, Sweden
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20
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Toporova L, Balaguer P. Nuclear receptors are the major targets of endocrine disrupting chemicals. Mol Cell Endocrinol 2020; 502:110665. [PMID: 31760044 DOI: 10.1016/j.mce.2019.110665] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022]
Abstract
Endocrine disrupting chemicals (EDCs) are exogenous substances that are suspected to cause adverse effects in the endocrine system mainly by acting through their interaction with nuclear receptors such as the estrogen receptors α and β (ERα and ERβ), the androgen receptor (AR), the pregnan X receptor (PXR), the peroxisome proliferator activated receptors α and γ (PPARα, PPARγ) and the thyroid receptors α and β (TRα and TRβ). More recently, the retinoid X receptors (RXRα, RXRβ and RXRγ), the constitutive androstane receptor (CAR) and the estrogen related receptor γ (ERRγ) have also been identified as targets of EDCs. Finally, nuclear receptors still poorly studied for their interaction with environmental ligands such as the progesterone receptor (PR), the mineralocorticoid receptor (MR), the glucocorticoid receptor (GR), the retinoic acid receptors (RAR α, RARβ and RARγ), the farnesoid X receptor (FXR) and the liver X receptors α and β (LXRα and LXβ) as well are suspected targets of EDCs. Humans are generally exposed to low doses of pollutants, therefore the aim of current research is to identify the targets of EDCs at environmental concentrations. In this review, we analyze recent works referring that nuclear receptors are targets of EDCs and we highlight which EDCs are able to act at low concentrations.
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Affiliation(s)
- Lucia Toporova
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, ICM, Univ Montpellier, 34090, Montpellier, France.
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, ICM, Univ Montpellier, 34090, Montpellier, France.
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21
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Liu X, Wang Y, Ortlund EA. First High-Resolution Crystal Structures of the Glucocorticoid Receptor Ligand-Binding Domain-Peroxisome Proliferator-Activated γ Coactivator 1- α Complex with Endogenous and Synthetic Glucocorticoids. Mol Pharmacol 2019; 96:408-417. [PMID: 31391291 PMCID: PMC6724573 DOI: 10.1124/mol.119.116806] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/30/2019] [Indexed: 11/22/2022] Open
Abstract
Both synthetic and endogenous glucocorticoids are important pharmaceutic drugs known to bind to the ligand-binding domain (LBD) of glucocorticoid receptor (GR), a member of the nuclear receptor (NR) superfamily. Ligand binding induces conformational changes within GR, resulting in subsequent DNA binding and differential coregulator recruitment, ultimately activating or repressing target gene expression. One of the most crucial coregulators is peroxisome proliferator-activated γ coactivator 1-α (PGC1α), which acts to regulate energy metabolism by directly interacting with GR to modulate gene expression. However, the mechanisms through which PGC1α senses GR conformation to drive transcription are not completely known. Here, an ancestral variant of the GR (AncGR2) LBD was used as a tool to produce stable protein for biochemical and structural studies. PGC1α is found to interact more tightly and form a more stable complex with AncGR2 LBD than nuclear receptor coactivator 2. We report the first high-resolution X-ray crystal structures of AncGR2 LBD in complex with PGC1α and dexamethasone (DEX) or hydrocortisone (HCY). Structural analyses reveal how distinct steroid drugs bind to GR with different affinities by unique hydrogen bonds and hydrophobic interactions. Important charge clamps are formed between the activation function 2 and PGC1α to mediate their specific interactions. These interactions lead to a high level of protection from hydrogen-deuterium exchange at the coregulator interaction site and strong intramolecular allosteric communication to ligand binding site. This is the first structure detailing the GR-PGC1α interaction providing a foundation for future design of specific therapeutic agents targeting these critical metabolic regulators. SIGNIFICANCE STATEMENT: High-resolution structures of AncGR2 LBD bound to DEX and HCY in complex with PGC1α reveal the molecular mechanism of PGC1α binding to AncGR2 LBD as well as the distinct affinities between DEX and HCY binding. Identifying the structural mechanisms that drive drug affinity is of pharmacologic interest to the glucocorticoid receptor field as an avenue to guide future drug design targeting GR-PGC1α signaling, which plays a crucial role in controlling hepatic glucose output.
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Affiliation(s)
- Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta Georgia (X.L., Y.W., E.A.O.) and College of Life Sciences, Qingdao University, Qingdao, People's Republic of China (Y.W.)
| | - Yashuo Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta Georgia (X.L., Y.W., E.A.O.) and College of Life Sciences, Qingdao University, Qingdao, People's Republic of China (Y.W.)
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta Georgia (X.L., Y.W., E.A.O.) and College of Life Sciences, Qingdao University, Qingdao, People's Republic of China (Y.W.)
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22
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Louw A. GR Dimerization and the Impact of GR Dimerization on GR Protein Stability and Half-Life. Front Immunol 2019; 10:1693. [PMID: 31379877 PMCID: PMC6653659 DOI: 10.3389/fimmu.2019.01693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/14/2022] Open
Abstract
Pharmacologically, glucocorticoids, which mediate their effects via the glucocorticoid receptor (GR), are a most effective therapy for inflammatory diseases despite the fact that chronic use causes side-effects and acquired GC resistance. The design of drugs with fewer side-effects and less potential for the development of resistance is therefore considered crucial for improved therapy. Dimerization of the GR is an integral step in glucocorticoid signaling and has been identified as a possible molecular site to target for drug development of anti-inflammatory drugs with an improved therapeutic index. Most of the current understanding regarding the role of GR dimerization in GC signaling derives for dimerization deficient mutants, although the role of ligands biased toward monomerization has also been described. Even though designing for loss of dimerization has mostly been applied for reduction of side-effect profile, designing for loss of dimerization may also be a fruitful strategy for the development of GC drugs with less potential to develop GC resistance. GC-induced resistance affects up to 30% of users and is due to a reduction in the GR functional pool. Several molecular mechanisms of GC-mediated reductions in GR pool have been described, one of which is the autologous down-regulation of GR density by the ubiquitin-proteasome-system (UPS). Loss of GR dimerization prevents autologous down-regulation of the receptor through modulation of interactions with components of the UPS and post-translational modifications (PTMs), such as phosphorylation, which prime the GR for degradation. Rational design of conformationally biased ligands that select for a monomeric GR conformation, which increases GC sensitivity through improving GR protein stability and increasing half-life, may be a productive avenue to explore. However, potential drawbacks to this approach should be considered as well as the advantages and disadvantages in chronic vs. acute treatment regimes.
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Affiliation(s)
- Ann Louw
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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23
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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24
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Development of highly potent glucocorticoids for steroid-resistant severe asthma. Proc Natl Acad Sci U S A 2019; 116:6932-6937. [PMID: 30894497 DOI: 10.1073/pnas.1816734116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Clinical application of inhaled glucocorticoids (GCs) has been hampered in the case of steroid-resistant severe asthma. To overcome this limitation, we have developed a series of highly potent GCs, including VSGC12, VSG158, and VSG159 based on the structural insight into the glucocorticoid receptor (GR). Particularly, VSG158 exhibits a maximal repression of lung inflammation and is 10 times more potent than the currently most potent clinical GC, Fluticasone Furoate (FF), in a murine model of asthma. More importantly, VSG158 displays a unique property to reduce neutrophilic inflammation in a steroid-resistant airway inflammation model, which is refractory to clinically available GCs, including dexamethasone and FF. VSG158 and VSG159 are able to deliver effective treatments with reduced off-target and side effects. In addition, these GCs also display pharmacokinetic properties that are suitable for the inhalation delivery method for asthma treatment. Taken together, the excellent therapeutic and side-effect profile of these highly potent GCs holds promise for treating steroid-resistant severe asthma.
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25
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Potamitis C, Siakouli D, Papavasileiou KD, Boulaka A, Ganou V, Roussaki M, Calogeropoulou T, Zoumpoulakis P, Alexis MN, Zervou M, Mitsiou DJ. Discovery of New non-steroidal selective glucocorticoid receptor agonists. J Steroid Biochem Mol Biol 2019; 186:142-153. [PMID: 30321666 DOI: 10.1016/j.jsbmb.2018.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 09/19/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022]
Abstract
Glucocorticoids (GCs) are widely used as potent anti-inflammatory drugs; however, GC therapy is often accompanied by adverse side effects. The anti-inflammatory action of GCs is exerted through the glucocorticoid receptor (GR) in part by antagonizing the pro-inflammatory nuclear factor k B (NF-kB) whereas the majority of side effects are assumed to be mediated by transactivation of GR target genes. We set out to identify novel non-steroidal selective GR agonists (SEGRA) favoring transrepression of NF-kB target genes over transactivation of genes associated with undesirable effects. Our virtual screening protocol was driven by a pharmacophore model based on a pyrrolidinone amide analogue (named as 'compound 12' in Biggadike et al 2009, PNAS USA 106, 18,114) bound to the extended binding pocket of the GR ligand binding domain (GR-LBD). Ambinter library (7.8 million compounds) was queried by our validated pharmacophore hypothesis and the prioritized compounds were biologically evaluated using a series of well-established screening assays. Two structurally similar hits (1 and 13) were identified that bind to GR, induce its translocation to the nucleus, do not mediate transactivation of GR target genes whereas partially repress a number of pro-inflammatory NF-kB target genes, in a GR-dependent manner. Explanatory molecular dynamics (MD) calculations could detail the per-residue interactions accounting for the binding of 1 and 13 to the extended binding pocket of GR. The discovered 1,3-benzothiazole analogs introduce a new class of genuine SEGRA paving the way for hit-to-lead optimization.
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Affiliation(s)
- Constantinos Potamitis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Dimitra Siakouli
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Konstantinos D Papavasileiou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece; National Center for Scientific Research "Demokritos", Institute of Nanoscience and Nanotechnology, Molecular Thermodynamics and Modelling of Materials Laboratory, GR-15310 Aghia Paraskevi Attikis, Greece
| | - Athina Boulaka
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Vassiliki Ganou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Marina Roussaki
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Theodora Calogeropoulou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Panagiotis Zoumpoulakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Michael N Alexis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
| | - Maria Zervou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece.
| | - Dimitra J Mitsiou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece.
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26
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Potential Dissociative Glucocorticoid Receptor Activity for Protopanaxadiol and Protopanaxatriol. Int J Mol Sci 2018; 20:ijms20010094. [PMID: 30591629 PMCID: PMC6337468 DOI: 10.3390/ijms20010094] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
Glucocorticoids are steroid hormones that regulate inflammation, growth, metabolism, and apoptosis via their cognate receptor, the glucocorticoid receptor (GR). GR, acting mainly as a transcription factor, activates or represses the expression of a large number of target genes, among them, many genes of anti-inflammatory and pro-inflammatory molecules, respectively. Transrepression activity of glucocorticoids also accounts for their anti-inflammatory activity, rendering them the most widely prescribed drug in medicine. However, chronic and high-dose use of glucocorticoids is accompanied with many undesirable side effects, attributed predominantly to GR transactivation activity. Thus, there is a high need for selective GR agonist, capable of dissociating transrepression from transactivation activity. Protopanaxadiol and protopanaxatriol are triterpenoids that share structural and functional similarities with glucocorticoids. The molecular mechanism of their actions is unclear. In this study applying induced-fit docking analysis, luciferase assay, immunofluorescence, and Western blot analysis, we showed that protopanaxadiol and more effectively protopanaxatriol are capable of binding to GR to activate its nuclear translocation, and to suppress the nuclear factor-kappa beta activity in GR-positive HeLa and HEK293 cells, but not in GR-low level COS-7 cells. Interestingly, no transactivation activity was observed, whereas suppression of the dexamethasone-induced transactivation of GR and induction of apoptosis in HeLa and HepG2 cells were observed. Thus, our results indicate that protopanaxadiol and protopanaxatriol could be considered as potent and selective GR agonist.
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27
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de Vera IMS, Munoz-Tello P, Zheng J, Dharmarajan V, Marciano DP, Matta-Camacho E, Giri PK, Shang J, Hughes TS, Rance M, Griffin PR, Kojetin DJ. Defining a Canonical Ligand-Binding Pocket in the Orphan Nuclear Receptor Nurr1. Structure 2018; 27:66-77.e5. [PMID: 30416039 DOI: 10.1016/j.str.2018.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/17/2018] [Accepted: 10/05/2018] [Indexed: 01/12/2023]
Abstract
Nuclear receptor-related 1 protein (Nurr1/NR4A2) is an orphan nuclear receptor (NR) that is considered to function without a canonical ligand-binding pocket (LBP). A crystal structure of the Nurr1 ligand-binding domain (LBD) revealed no physical space in the conserved region where other NRs with solvent accessible apo-protein LBPs bind synthetic and natural ligands. Using solution nuclear magnetic resonance spectroscopy, hydrogen/deuterium exchange mass spectrometry, and molecular dynamics simulations, we show that the putative canonical Nurr1 LBP is dynamic with high solvent accessibility, exchanges between two or more conformations on the microsecond-to-millisecond timescale, and can expand from the collapsed crystallized conformation to allow binding of unsaturated fatty acids. These findings should stimulate future studies to probe the ligandability and druggability of Nurr1 for both endogenous and synthetic ligands, which could lead to new therapeutics for Nurr1-related diseases, including Parkinson's disease and schizophrenia.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - David P Marciano
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Edna Matta-Camacho
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Pankaj Kumar Giri
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Travis S Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
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28
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Single-molecule force spectroscopy reveals folding steps associated with hormone binding and activation of the glucocorticoid receptor. Proc Natl Acad Sci U S A 2018; 115:11688-11693. [PMID: 30366952 DOI: 10.1073/pnas.1807618115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The glucocorticoid receptor (GR) is a prominent nuclear receptor linked to a variety of diseases and an important drug target. Binding of hormone to its ligand binding domain (GR-LBD) is the key activation step to induce signaling. This process is tightly regulated by the molecular chaperones Hsp70 and Hsp90 in vivo. Despite its importance, little is known about GR-LBD folding, the ligand binding pathway, or the requirement for chaperone regulation. In this study, we have used single-molecule force spectroscopy by optical tweezers to unravel the dynamics of the complete pathway of folding and hormone binding of GR-LBD. We identified a "lid" structure whose opening and closing is tightly coupled to hormone binding. This lid is located at the N terminus without direct contacts to the hormone. Under mechanical load, apo-GR-LBD folds stably and readily without the need of chaperones with a folding free energy of [Formula: see text] The folding pathway is largely independent of the presence of hormone. Hormone binds only in the last step and lid closure adds an additional [Formula: see text] of free energy, drastically increasing the affinity. However, mechanical double-jump experiments reveal that, at zero force, GR-LBD folding is severely hampered by misfolding, slowing it to less than 1·s-1 From the force dependence of the folding rates, we conclude that the misfolding occurs late in the folding pathway. These features are important cornerstones for understanding GR activation and its tight regulation by chaperones.
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29
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Liu B, Fu XQ, Li T, Su T, Guo H, Zhu PL, Tse AKW, Liu SM, Yu ZL. Computational and experimental prediction of molecules involved in the anti-melanoma action of berberine. JOURNAL OF ETHNOPHARMACOLOGY 2017; 208:225-235. [PMID: 28729227 DOI: 10.1016/j.jep.2017.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/07/2017] [Accepted: 07/15/2017] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGIC RELEVANCE Berberine (BBR) is a naturally occurring alkaloid compound that can be found in Chinese medicinal herbs such as Rhizoma Coptidis and Phellodendri Cortex. These BBR containing herbs are commonly used by Chinese medicine doctors to treat cancers including melanoma. In this study, we explored proteins potentially involved in the anti-melanoma effects of BBR using computational and experimental approaches. MATERIALS AND METHODS Target proteins of BBR were predicted using the reverse pharmacophore screening, molecular docking and molecular dynamics. Anti-melanoma activities of BBR in melanoma cells were examined by MTT and EdU proliferation assays. Effects of BBR on activities of target proteins in melanoma cells were examined by Western blotting or fluorescence assay. RESULTS Ten proteins implicated in cancer and with high fit-score in the reverse pharmacophore screening were selected as potential targets of BBR. Molecular docking and molecular dynamics revealed that BBR could stably bind to four of the ten proteins, namely 3-phosphoinositide-dependent protein kinase 1 (PDK1), glucocorticoid receptor (GR), p38 mitogen-activated protein kinase (p38) and dihydroorotate dehydrogenase (DHODH). Cellular experiments showed that BBR inhibited cell proliferation, increased the phosphorylation of GR and p38, and inhibited the activity of DHODH in A375 human melanoma cells. CONCLUSIONS These findings suggest that p38, GR and DHODH are potentially involved in the anti-melanoma action of BBR. This study provided a chemical and pharmacological justification for the clinical use of BBR-containing herbs in melanoma treatment.
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Affiliation(s)
- Bin Liu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China; Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiu-Qiong Fu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Ting Li
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Tao Su
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Hui Guo
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Pei-Li Zhu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Anfernee Kai-Wing Tse
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Shi-Ming Liu
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Zhi-Ling Yu
- Center for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China; Consun Chinese Medicines Research Centre for Renal Diseases, Hong Kong Baptist University, Hong Kong, China; HKBU Shenzhen Research Institute and Continuing Education, Shenzhen, China.
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30
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Jin Z, Lin H, Srinivasan S, Nwachukwu JC, Bruno N, Griffin PR, Nettles KW, Kamenecka TM. Synthesis of novel steroidal agonists, partial agonists, and antagonists for the glucocorticoid receptor. Bioorg Med Chem Lett 2016; 27:347-353. [PMID: 27919657 DOI: 10.1016/j.bmcl.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/01/2023]
Abstract
Adverse effects of glucocorticoids could be limited by developing new compounds that selectively modulate anti-inflammatory activity of the glucocorticoid receptor (GR). We have synthesized a novel series of steroidal GR ligands, including potent agonists, partial agonists and antagonists with a wide range of effects on inhibiting secretion of interleukin-6. Some of these new ligands were designed to directly impact conformational stability of helix-12, in the GR ligand-binding domain (LBD). These compounds modulated GR activity and glucocorticoid-induced gene expression in a manner that was inversely correlated to the degree of inflammatory response. In contrast, compounds designed to directly modulate LBD epitopes outside helix-12, led to dissociated levels of GR-mediated gene expression and inflammatory response. Therefore, these new series of compounds and their derivatives will be useful to dissect the ligand-dependent features of GR signaling specificity.
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Affiliation(s)
- Zhuang Jin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hua Lin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Nelson Bruno
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA.
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31
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Discovery and structural optimization of 4-(4-(benzyloxy)phenyl)-3,4-dihydropyrimidin-2(1H)-ones as RORc inverse agonists. Acta Pharmacol Sin 2016; 37:1516-1524. [PMID: 27374490 DOI: 10.1038/aps.2016.32] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/05/2016] [Indexed: 01/01/2023] Open
Abstract
AIM Retinoic acid receptor-related orphan nuclear receptors (RORs) are orphan nuclear receptors that show constitutive activity in the absence of ligands. Among 3 subtypes of RORs, RORc is a promising therapeutic target for the treatment of Th17-mediated autoimmune diseases. Here, we report novel RORc inverse agonists discovered through structure-based drug design. METHODS Based on the structure of compound 8, a previously described agonist of RORa, a series of 4-(4-(benzyloxy)phenyl)-3,4-dihydropyrimidin-2(1H)-one derivatives were designed and synthesized. The interaction between the compounds and RORc was detected at molecular level using AlphaScreen assay. The compounds were further examined in 293T cells transfected with RORc and luciferase reporter gene. Thermal stability shift assay was used to evaluate the effects of the compounds on protein stability. RESULTS A total of 27 derivatives were designed and synthesized. Among them, the compound 22b was identified as the most potent RORc inverse agonist. Its IC50 values were 2.39 μmol/L in AlphaScreen assay, and 0.82 μmol/L in inhibition of the cell-based luciferase reporter activity. Furthermore, the compound 22b displayed a 120-fold selectivity for RORc over other nuclear receptors. Moreover, a molecular docking study showed that the structure-activity relationship was consistent with the binding mode of compound 22b in RORc. CONCLUSION 4-(4-(Benzyloxy)phenyl)-3,4-dihydropyrimidin-2(1H)-one derivatives are promising candidates for the treatment of Th17-mediated autoimmune diseases, such as rheumatoid arthritis, psoriasis, and multiple sclerosis.
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Georgatza D, Gorgogietas VA, Kylindri P, Charalambous MC, Papadopoulou KK, Hayes JM, Psarra AMG. The triterpene echinocystic acid and its 3-O-glucoside derivative are revealed as potent and selective glucocorticoid receptor agonists. Int J Biochem Cell Biol 2016; 79:277-287. [DOI: 10.1016/j.biocel.2016.08.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/19/2016] [Accepted: 08/29/2016] [Indexed: 12/20/2022]
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Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations. MONATSHEFTE FUR CHEMIE 2016; 147:553-563. [PMID: 27069282 PMCID: PMC4785218 DOI: 10.1007/s00706-016-1674-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/14/2016] [Indexed: 01/23/2023]
Abstract
ABSTRACT Pharmacophore modeling is a widely used technique in computer-aided drug discovery. Structure-based pharmacophore models of a ligand in complex with a protein have proven to be useful for supporting in silico hit discovery, hit to lead expansion, and lead optimization. As a structure-based approach it depends on the correct interpretation of ligand-protein interactions. There are legitimate concerns about the fidelity of the bound ligand and about non-physiological contacts with parts of the crystal and the solvent effects that influence the protein structure. A possible way to refine the structure of a protein-ligand system is to use the final structure of a given MD simulation. In this study we compare pharmacophore models built using the initial protein-ligand structure obtained from the protein data bank (PDB) with pharmacophore models built with the final structure of a molecular dynamics simulation. We show that the pharmacophore models differ in feature number and feature type and that the pharmacophore models built from the last structure of a MD simulation shows in some cases better ability to distinguish between active and decoy ligand structures. GRAPHICAL ABSTRACT
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Hurt DE, Suzuki S, Mayama T, Charmandari E, Kino T. Structural Analysis on the Pathologic Mutant Glucocorticoid Receptor Ligand-Binding Domains. Mol Endocrinol 2016; 30:173-88. [PMID: 26745667 DOI: 10.1210/me.2015-1177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Glucocorticoid receptor (GR) gene mutations may cause familial or sporadic generalized glucocorticoid resistance syndrome. Most of the missense forms distribute in the ligand-binding domain and impair its ligand-binding activity and formation of the activation function (AF)-2 that binds LXXLL motif-containing coactivators. We performed molecular dynamics simulations to ligand-binding domain of pathologic GR mutants to reveal their structural defects. Several calculated parameters including interaction energy for dexamethasone or the LXXLL peptide indicate that destruction of ligand-binding pocket (LBP) is a primary character. Their LBP defects are driven primarily by loss/reduction of the electrostatic interaction formed by R611 and T739 of the receptor to dexamethasone and a subsequent conformational mismatch, which deacylcortivazol resolves with its large phenylpyrazole moiety and efficiently stimulates transcriptional activity of the mutant receptors with LBP defect. Reduced affinity of the LXXLL peptide to AF-2 is caused mainly by disruption of the electrostatic bonds to the noncore leucine residues of this peptide that determine the peptide's specificity to GR, as well as by reduced noncovalent interaction against core leucines and subsequent exposure of the AF-2 surface to solvent. The results reveal molecular defects of pathologic mutant receptors and provide important insights to the actions of wild-type GR.
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Affiliation(s)
- Darrell E Hurt
- Bioinformatics and Computational Biosciences Branch (D.E.H.), Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852; Program in Reproductive and Adult Endocrinology (S.S., T.M., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Endocrinology, Metabolism and Diabetes (E.C.), First Department of Pediatrics, University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens 11527, Greece; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha, Qatar
| | - Shigeru Suzuki
- Bioinformatics and Computational Biosciences Branch (D.E.H.), Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852; Program in Reproductive and Adult Endocrinology (S.S., T.M., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Endocrinology, Metabolism and Diabetes (E.C.), First Department of Pediatrics, University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens 11527, Greece; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha, Qatar
| | - Takafumi Mayama
- Bioinformatics and Computational Biosciences Branch (D.E.H.), Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852; Program in Reproductive and Adult Endocrinology (S.S., T.M., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Endocrinology, Metabolism and Diabetes (E.C.), First Department of Pediatrics, University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens 11527, Greece; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha, Qatar
| | - Evangelia Charmandari
- Bioinformatics and Computational Biosciences Branch (D.E.H.), Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852; Program in Reproductive and Adult Endocrinology (S.S., T.M., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Endocrinology, Metabolism and Diabetes (E.C.), First Department of Pediatrics, University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens 11527, Greece; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha, Qatar
| | - Tomoshige Kino
- Bioinformatics and Computational Biosciences Branch (D.E.H.), Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852; Program in Reproductive and Adult Endocrinology (S.S., T.M., T.K.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892; Department of Pediatrics (S.S.), Asahikawa Medical University, Asahikawa 078-8510, Japan; Division of Endocrinology, Metabolism and Diabetes (E.C.), First Department of Pediatrics, University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens 11527, Greece; and Department of Experimental Therapeutics (T.K.), Division of Experimental Biology, Sidra Medical and Research Center, Doha, Qatar
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Ultrafast protein structure-based virtual screening with Panther. J Comput Aided Mol Des 2015; 29:989-1006. [PMID: 26407559 DOI: 10.1007/s10822-015-9870-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/19/2015] [Indexed: 12/31/2022]
Abstract
Molecular docking is by far the most common method used in protein structure-based virtual screening. This paper presents Panther, a novel ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of the possible ligands are then compared to the model by using a similarity search algorithm. On average, one ligand can be processed in a few minutes by using classical docking methods, whereas using Panther processing takes <1 s. The presented Panther protocol can be used in several applications, such as speeding up the early phases of drug discovery projects, reducing the number of failures in the clinical phase of the drug development process, and estimating the environmental toxicity of chemicals. Panther-code is available in our web pages (http://www.jyu.fi/panther) free of charge after registration.
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Synergistic activation of human pregnane X receptor by binary cocktails of pharmaceutical and environmental compounds. Nat Commun 2015; 6:8089. [PMID: 26333997 PMCID: PMC4569708 DOI: 10.1038/ncomms9089] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 07/15/2015] [Indexed: 12/19/2022] Open
Abstract
Humans are chronically exposed to multiple exogenous substances, including environmental pollutants, drugs and dietary components. Many of these compounds are suspected to impact human health, and their combination in complex mixtures could exacerbate their harmful effects. Here we demonstrate that a pharmaceutical oestrogen and a persistent organochlorine pesticide, both exhibiting low efficacy when studied separately, cooperatively bind to the pregnane X receptor, leading to synergistic activation. Biophysical analysis shows that each ligand enhances the binding affinity of the other, so the binary mixture induces a substantial biological response at doses at which each chemical individually is inactive. High-resolution crystal structures reveal the structural basis for the observed cooperativity. Our results suggest that the formation of ‘supramolecular ligands' within the ligand-binding pocket of nuclear receptors contributes to the synergistic toxic effect of chemical mixtures, which may have broad implications for the fields of endocrine disruption, toxicology and chemical risk assessment. Endocrine-disrupting chemicals act on nuclear hormone receptors, such as PXR. Here, Delfosse et al. show how two such chemicals interact with each other in the PXR ligand-binding pocket, forming a so-called supramolecular ligand that is a more potent PXR activator than each of the two chemicals alone.
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Liu YL, Jang S, Wang SM, Chen CH, Li FY. Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1074113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Luz JG, Carson MW, Condon B, Clawson D, Pustilnik A, Kohlman DT, Barr RJ, Bean JS, Dill MJ, Sindelar DK, Maletic M, Coghlan MJ. Indole Glucocorticoid Receptor Antagonists Active in a Model of Dyslipidemia Act via a Unique Association with an Agonist Binding Site. J Med Chem 2015. [PMID: 26218343 DOI: 10.1021/acs.jmedchem.5b00736] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To further elucidate the structural activity correlation of glucocorticoid receptor (GR) antagonism, the crystal structure of the GR ligand-binding domain (GR LBD) complex with a nonsteroidal antagonist, compound 8, was determined. This novel indole sulfonamide shows in vitro activity comparable to known GR antagonists such as mifepristone, and notably, this molecule lowers LDL (-74%) and raises HDL (+73%) in a hamster model of dyslipidemia. This is the first reported crystal structure of the GR LBD bound to a nonsteroidal antagonist, and this article provides additional elements for the design and pharmacology of clinically relevant nonsteroidal GR antagonists that may have greater selectivity and fewer side effects than their steroidal counterparts.
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Affiliation(s)
- John G Luz
- Eli Lilly Biotechnology Center , 10300 Campus Point Drive, Suite 200, San Diego, California 92121 United States
| | - Matthew W Carson
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - Bradley Condon
- Eli Lilly Biotechnology Center , 10300 Campus Point Drive, Suite 200, San Diego, California 92121 United States
| | - David Clawson
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - Anna Pustilnik
- Eli Lilly Biotechnology Center , 10300 Campus Point Drive, Suite 200, San Diego, California 92121 United States
| | - Daniel T Kohlman
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - Robert J Barr
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - James S Bean
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - M Joelle Dill
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - Dana K Sindelar
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
| | - Milan Maletic
- Eli Lilly Biotechnology Center , 10300 Campus Point Drive, Suite 200, San Diego, California 92121 United States
| | - Michael J Coghlan
- Lilly Research Laboratories, A Division of Eli Lilly & Co. , Lilly Corporate Center, Indianapolis, Indiana 46285 United States
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Schoch GA, Sammito M, Millán C, Usón I, Rudolph MG. Structure of a 13-fold superhelix (almost) determined from first principles. IUCRJ 2015; 2:177-87. [PMID: 25866655 PMCID: PMC4392412 DOI: 10.1107/s2052252515000238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2). For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.
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Affiliation(s)
- Guillaume A. Schoch
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Massimo Sammito
- Instituto de Biología Molecular de Barcelona (IBMB), CSIC, Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Instituto de Biología Molecular de Barcelona (IBMB), CSIC, Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB), CSIC, Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys, 23, 08010 Barcelona, Spain
| | - Markus G. Rudolph
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
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40
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Harcken C, Riether D, Liu P, Razavi H, Patel U, Lee T, Bosanac T, Ward Y, Ralph M, Chen Z, Souza D, Nelson RM, Kukulka A, Fadra-Khan TN, Zuvela-Jelaska L, Patel M, Thomson DS, Nabozny GH. Optimization of drug-like properties of nonsteroidal glucocorticoid mimetics and identification of a clinical candidate. ACS Med Chem Lett 2014; 5:1318-23. [PMID: 25516791 DOI: 10.1021/ml500387y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/17/2014] [Indexed: 01/15/2023] Open
Abstract
A series of nonsteroidal "dissociated" glucocorticoid receptor agonists was optimized for drug-like properties such as cytochrome P450 inhibition, metabolic stability, aqueous solubility, and hERG ion channel inhibition. This effort culminated in the identification of the clinical candidate compound ( R )-39.
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Affiliation(s)
- Christian Harcken
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Doris Riether
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Pingrong Liu
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Hossein Razavi
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Usha Patel
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Thomas Lee
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Todd Bosanac
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Yancey Ward
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Mark Ralph
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Zhidong Chen
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Donald Souza
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Richard M. Nelson
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Alison Kukulka
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Tazmeen N. Fadra-Khan
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Ljiljana Zuvela-Jelaska
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Mita Patel
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - David S. Thomson
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Gerald H. Nabozny
- Department of Medicinal
Chemistry
and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
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Dobričić V, Marković B, Milenković N, Savić V, Jaćević V, Rančić N, Vladimirov S, Čudina O. Design, Synthesis, and Local Anti-Inflammatory Activity of 17β-Carboxamide Derivatives of Glucocorticoids. Arch Pharm (Weinheim) 2014; 347:786-97. [DOI: 10.1002/ardp.201400165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Vladimir Dobričić
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; University of Belgrade; Belgrade Serbia
| | - Bojan Marković
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; University of Belgrade; Belgrade Serbia
| | - Nikola Milenković
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; University of Belgrade; Belgrade Serbia
| | - Vladimir Savić
- Faculty of Pharmacy, Department of Organic Chemistry; University of Belgrade; Belgrade Serbia
| | - Vesna Jaćević
- National Poison Control Centre; Military Medical Academy; Belgrade Serbia
| | - Nemanja Rančić
- Centre for Clinical Pharmacology; Medical Faculty Military Medical Academy; University of Defence; Belgrade Serbia
| | - Sote Vladimirov
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; University of Belgrade; Belgrade Serbia
| | - Olivera Čudina
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; University of Belgrade; Belgrade Serbia
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Gong H, Yang M, Xiao Z, Doweyko AM, Cunningham M, Wang J, Habte S, Holloway D, Burke C, Shuster D, Gao L, Carman J, Somerville JE, Nadler SG, Salter-Cid L, Barrish JC, Weinstein DS. Discovery of acylurea isosteres of 2-acylaminothiadiazole in the azaxanthene series of glucocorticoid receptor agonists. Bioorg Med Chem Lett 2014; 24:3268-73. [DOI: 10.1016/j.bmcl.2014.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 01/27/2023]
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Blackford JA, Brimacombe KR, Dougherty EJ, Pradhan M, Shen M, Li Z, Auld DS, Chow CC, Austin CP, Simons SS. Research resource: modulators of glucocorticoid receptor activity identified by a new high-throughput screening assay. Mol Endocrinol 2014; 28:1194-206. [PMID: 24850414 DOI: 10.1210/me.2014-1069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoid steroids affect almost every type of tissue and thus are widely used to treat a variety of human pathological conditions. However, the severity of numerous side effects limits the frequency and duration of glucocorticoid treatments. Of the numerous approaches to control off-target responses to glucocorticoids, small molecules and pharmaceuticals offer several advantages. Here we describe a new, extended high-throughput screen in intact cells to identify small molecule modulators of dexamethasone-induced glucocorticoid receptor (GR) transcriptional activity. The novelty of this assay is that it monitors changes in both GR maximal activity (A(max)) and EC(50) (the position of the dexamethasone dose-response curve). Upon screening 1280 chemicals, 10 with the greatest changes in the absolute value of A(max) or EC(50) were selected for further examination. Qualitatively identical behaviors for 60% to 90% of the chemicals were observed in a completely different system, suggesting that other systems will be similarly affected by these chemicals. Additional analysis of the 10 chemicals in a recently described competition assay determined their kinetically defined mechanism and site of action. Some chemicals had similar mechanisms of action despite divergent effects on the level of the GR-induced product. These combined assays offer a straightforward method of identifying numerous new pharmaceuticals that can alter GR transactivation in ways that could be clinically useful.
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Affiliation(s)
- John A Blackford
- Steroid Hormones Section (J.A.B., E.J.D., M.P., S.S.S.), Laboratory of Endocrinology and Receptor Biology, and Laboratory of Biological Modeling (C.C.C.), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892; and National Center for Advancing Translational Sciences (K.R.B., M.S., Z.L., D.S.A., C.P.A.), National Institutes of Health, Rockville, Maryland 20892
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He Y, Yi W, Suino-Powell K, Zhou XE, Tolbert WD, Tang X, Yang J, Yang H, Shi J, Hou L, Jiang H, Melcher K, Xu HE. Structures and mechanism for the design of highly potent glucocorticoids. Cell Res 2014; 24:713-26. [PMID: 24763108 DOI: 10.1038/cr.2014.52] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 02/28/2014] [Accepted: 03/12/2014] [Indexed: 02/07/2023] Open
Abstract
The evolution of glucocorticoid drugs was driven by the demand of lowering the unwanted side effects, while keeping the beneficial anti-inflammatory effects. Potency is an important aspect of this evolution as many undesirable side effects are associated with use of high-dose glucocorticoids. The side effects can be minimized by highly potent glucocorticoids that achieve the same treatment effects at lower doses. This demand propelled the continuous development of synthetic glucocorticoids with increased potencies, but the structural basis of their potencies is poorly understood. To determine the mechanisms underlying potency, we solved the X-ray structures of the glucocorticoid receptor (GR) ligand-binding domain (LBD) bound to its endogenous ligand, cortisol, which has relatively low potency, and a highly potent synthetic glucocorticoid, mometasone furoate (MF). The cortisol-bound GR LBD revealed that the flexibility of the C1-C2 single bond in the steroid A ring is primarily responsible for the low affinity of cortisol to GR. In contrast, we demonstrate that the very high potency of MF is achieved by its C-17α furoate group completely filling the ligand-binding pocket, thus providing additional anchor contacts for high-affinity binding. A single amino acid in the ligand-binding pocket, Q642, plays a discriminating role in ligand potency between MF and cortisol. Structure-based design led to synthesis of several novel glucocorticoids with much improved potency and efficacy. Together, these results reveal key structural mechanisms of glucocorticoid potency and provide a rational basis for developing novel highly potent glucocorticoids.
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Affiliation(s)
- Yuanzheng He
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Wei Yi
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kelly Suino-Powell
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - X Edward Zhou
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - W David Tolbert
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Xiaobo Tang
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Yang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huaiyu Yang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingjing Shi
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Li Hou
- VARI-SIMM Center, Center for Structure and Function of Drug Targets, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - H Eric Xu
- 1] Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA [2] VARI-SIMM Center, Center for Structure and Function of Drug Targets, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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45
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Lagarde N, Ben Nasr N, Jérémie A, Guillemain H, Laville V, Labib T, Zagury JF, Montes M. NRLiSt BDB, the manually curated nuclear receptors ligands and structures benchmarking database. J Med Chem 2014; 57:3117-25. [PMID: 24666037 DOI: 10.1021/jm500132p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nuclear receptors (NRs) constitute an important class of drug targets. We created the most exhaustive NR-focused benchmarking database to date, the NRLiSt BDB (NRs ligands and structures benchmarking database). The 9905 compounds and 339 structures of the NRLiSt BDB are ready for structure-based and ligand-based virtual screening. In the present study, we detail the protocol used to generate the NRLiSt BDB and its features. We also give some examples of the errors that we found in ChEMBL that convinced us to manually review all original papers. Since extensive and manually curated experimental data about NR ligands and structures are provided in the NRLiSt BDB, it should become a powerful tool to assess the performance of virtual screening methods on NRs, to assist the understanding of NR's function and modulation, and to support the discovery of new drugs targeting NRs. NRLiSt BDB is freely available online at http://nrlist.drugdesign.fr .
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Affiliation(s)
- Nathalie Lagarde
- Laboratoire Génomique, Bioinformatique et Applications, EA 4627, Conservatoire National des Arts et Métiers , 292 Rue Saint Martin, 75003 Paris, France
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46
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Rahman GM, Das J. Modeling studies on the structural determinants for the DAG/phorbol ester binding to C1 domain. J Biomol Struct Dyn 2014; 33:219-32. [DOI: 10.1080/07391102.2014.895679] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Zhang Y, Xue X, Jin X, Song Y, Li J, Luo X, Song M, Yan W, Song H, Xu Y. Discovery of 2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide derivatives as new RORγ inhibitors using virtual screening, synthesis and biological evaluation. Eur J Med Chem 2014; 78:431-41. [PMID: 24704616 DOI: 10.1016/j.ejmech.2014.03.065] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/19/2014] [Accepted: 03/22/2014] [Indexed: 01/22/2023]
Abstract
Retinoic acid receptor-related orphan receptor γ (RORγ), a member of the nuclear hormone receptor superfamily, is a promising therapeutic target for treating Th17-mediated autoimmune diseases. We performed structure-based virtual screening targeting the RORγ ligand-binding domain. Among the tested compounds, s4 demonstrated RORγ antagonistic activities with micromolar IC50 values in both an AlphaScreen assay (20.27 μM) and a cell-based reporter gene assay (11.84 μM). Optimization of the s4 compound led to the identification of compounds 7j, 8c, 8k, and 8p, all of which displayed significantly enhanced RORγ inhibition with IC50 values of 40-140 nM. These results represent a promising starting point for developing potent small molecule RORγ inhibitors.
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Affiliation(s)
- Yan Zhang
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China
| | - Xiaoqian Xue
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China; School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Xiangyu Jin
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China; Department of Bioengineering, School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Yu Song
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China; Department of Bioengineering, School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Jing Li
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China
| | - Xiaoyu Luo
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China
| | - Ming Song
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China
| | - Weiqun Yan
- Department of Bioengineering, School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Hongrui Song
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, No. 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Yong Xu
- Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, China.
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48
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Scior T, Verhoff M, Gutierrez-Aztatzi I, Ammon HPT, Laufer S, Werz O. Interference of boswellic acids with the ligand binding domain of the glucocorticoid receptor. J Chem Inf Model 2014; 54:978-86. [PMID: 24512031 DOI: 10.1021/ci400666a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Boswellic acids (BAs) possess anti-inflammatory properties in various biological models with similar features to those of glucocorticoids (GCs), such as suppression of the release of pro-inflammatory cytokines. Hence, the molecular mechanism of BAs responsible for their anti-inflammatory features might be attributable to interference with the human glucocorticoid receptor (GR). Due to obvious structural similarities with GCs, we conducted pharmacophore studies as well as molecular docking simulations of BAs as putative ligands at the ligand binding site (LBS) of the GR in distinct functional states. In order to verify receptor binding and functional activation of the GR by BAs, radiometric binding assays as well as GR response element-dependent luciferase reporter assay were performed with dexamethasone (DEX) as a functional positive control. With respect to the observed position of GCs in GR crystal complexes in the active antagonist state, BAs docked in a flipped orientation with estimated binding constants reflecting nanomolar affinities. For validation, DEX and other steroids were successfully redocked into their crystal poses in similar ranges as reported in the literature. In line with the pharmacophore and docking models, the BAs were strong GR binders (radiometric binding assay), albeit none of the BAs activated the GR in the reporter gene assay, when compared to the GC agonist DEX. The flipped scaffolds of all BAs dislodge the known C-11 function from its receiving amino acid (Asn564), which may explain the silencing effects of receptor-bound BAs in the reporter gene assay. Together, our results constitute a compelling example of rigid keys acting in an adaptable lock qualifying as a reversed induced fit mechanism, thereby extending the hitherto published knowledge about molecular target interactions of BAs.
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Affiliation(s)
- Thomas Scior
- Department of Pharmacy, Benemérita Universidad Autónoma de Puebla , C.P. 72570 Puebla México
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49
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Harcken C, Riether D, Kuzmich D, Liu P, Betageri R, Ralph M, Emmanuel M, Reeves JT, Berry A, Souza D, Nelson RM, Kukulka A, Fadra TN, Zuvela-Jelaska L, Dinallo R, Bentzien J, Nabozny GH, Thomson DS. Identification of Highly Efficacious Glucocorticoid Receptor Agonists with a Potential for Reduced Clinical Bone Side Effects. J Med Chem 2014; 57:1583-98. [DOI: 10.1021/jm4019178] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian Harcken
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Doris Riether
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Daniel Kuzmich
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Pingrong Liu
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Raj Betageri
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Mark Ralph
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Michel Emmanuel
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Jonathan T. Reeves
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Angela Berry
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Donald Souza
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Richard M. Nelson
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Alison Kukulka
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Tazmeen N. Fadra
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Ljiljana Zuvela-Jelaska
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Roger Dinallo
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Jörg Bentzien
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Gerald H. Nabozny
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - David S. Thomson
- Department of Medicinal Chemistry,
Department of Immunology and Inflammation, Department of Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
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50
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Carson MW, Luz JG, Suen C, Montrose C, Zink R, Ruan X, Cheng C, Cole H, Adrian MD, Kohlman DT, Mabry T, Snyder N, Condon B, Maletic M, Clawson D, Pustilnik A, Coghlan MJ. Glucocorticoid Receptor Modulators Informed by Crystallography Lead to a New Rationale for Receptor Selectivity, Function, and Implications for Structure-Based Design. J Med Chem 2014; 57:849-60. [DOI: 10.1021/jm401616g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Matthew W. Carson
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - John G. Luz
- Eli Lilly Biotechnology
Center, 10300 Campus Point Drive, Suite
200, San Diego, California 92121, United States
| | - Chen Suen
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Chahrzad Montrose
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Richard Zink
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Xiaoping Ruan
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Christine Cheng
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Harlan Cole
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Mary D. Adrian
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Dan T. Kohlman
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Thomas Mabry
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Nancy Snyder
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Brad Condon
- Eli Lilly Biotechnology
Center, 10300 Campus Point Drive, Suite
200, San Diego, California 92121, United States
| | - Milan Maletic
- Eli Lilly Biotechnology
Center, 10300 Campus Point Drive, Suite
200, San Diego, California 92121, United States
| | - David Clawson
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Anna Pustilnik
- Eli Lilly Biotechnology
Center, 10300 Campus Point Drive, Suite
200, San Diego, California 92121, United States
| | - Michael J. Coghlan
- Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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