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Liu H, Hu B, Luan J, Sun Y, Wang S, Li W, Chen L, Wang H, Gao Y, Wang J. Structural requirement of RARγ agonism through computational aspects. J Mol Model 2023; 29:108. [PMID: 36964229 DOI: 10.1007/s00894-023-05507-6] [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: 11/18/2022] [Accepted: 03/09/2023] [Indexed: 03/26/2023]
Abstract
CONTEXT RARγ is a therapeutic target for many skin diseases and has potential in cancer treatment. In the current study, we put forward a comprehensive structure-activity relationship study of third and fourth generations of RARγ agonists, addressing multiple crystal structures of RARγ complexes and approved drugs. Adapalene and Trifarotene, through hybrid strategies including protein contacts Atlas analysis, molecular docking, dynamics simulations, MM-GBSA, ASM, and pharmacophore modeling. Our result revealed crucial amino acids Arg267, Ser278, Phe288, Phe230, Met272, Leu271, and Leu268 within the RARγ pocket, as well as pharmacophore features such as two hydrophobic groups, two aromatic rings, and negative ionic features, which are essential for the binding of RARγ agonists. Based on this study, the binding mechanism of RARγ agonists was elucidated, which will be helpful for the rational design of new RARγ agonists for skin diseases and cancer treatment. METHODS In this study, Schrödinger suite 2021-2 with OPLS_4 force field, Discovery Studio program 3.0, LigandScout 4.3, and PyMOL are utilized in the investigation.
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Affiliation(s)
- Haihan Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Jiasi Luan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yuqing Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Shizun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Weixai Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Lu Chen
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yinli Gao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, 110016, China.
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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Golla S, Kokatla HP. Rongalite-Mediated Transition Metal- and Hydride-Free Chemoselective Reduction of α-Keto Esters and α-Keto Amides. J Org Chem 2022; 87:9915-9925. [PMID: 35839148 DOI: 10.1021/acs.joc.2c00936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A transition metal- and hydride-free protocol has been developed for the chemoselective reduction of α-keto esters and α-keto amides using rongalite as a reducing agent. Here, rongalite acts as a hydride-free reducing agent via a radical mechanism. This protocol offers the synthesis of a wide range of α-hydroxy esters and α-hydroxy amides with 85-98% yields. This chemoselective method is compatible with other reducible functionalities such as halides, alkenes, amides, and nitriles. The use of inexpensive rongalite (ca. $0.03/1 g), mild reaction conditions, and gram-scale synthesis are some of the key features of this methodology. Also, cyclandelate, a vasodilator drug, has been synthesized in gram scale with 79% yield.
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Affiliation(s)
- Sivaparwathi Golla
- Department of Chemistry, National Institute of Technology Warangal, Warangal, Telangana 506004, India
| | - Hari Prasad Kokatla
- Department of Chemistry, National Institute of Technology Warangal, Warangal, Telangana 506004, India
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Zhang J, Zhao J, Sun Y, Liang Y, Zhao J, Zou H, Zhang T, Ren L. GR-mediated anti-inflammation of α-boswellic acid: Insights from in vitro and in silico studies. Food Chem Toxicol 2021; 155:112379. [PMID: 34197882 DOI: 10.1016/j.fct.2021.112379] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Although multiple bioactivities of α-boswellic acid have been reported, the molecular mechanism of its anti-inflammatory action is not yet clear. Hence, glucocorticoid receptor (GR)-mediated anti-inflammation of α-boswellic acid was investigated in this work. Fluorescence polarization assay suggested that α-boswellic acid bound to GR with IC50 value of 658.00 ± 0.21 μM. Upon binding to α-boswellic acid, GR translocated from cytoplasm into nucleus of HeLa cells, facilitating sequential transcriptional regulation of GR-related genes. Luciferase reporter assay suggested that α-boswellic acid lacked GR transcriptional activity, indicating its potential as a dissociative GR ligand. Interestingly, α-boswellic acid selectively modulated the anti-inflammatory gene CBG (marker for GR transrepression), while leaving the "side-effect" gene TAT (marker for GR transactivation) unaffected in HepG2 cells. Furthermore, α-boswellic acid inhibited lipopolysaccharide-stimulated cytokines production in U937 macrophages, confirming its anti-inflammation property in vitro. Molecular docking showed that both hydrogen-bonding and hydrophobic interactions helped to stabilize α-boswellic acid-GR binding. Their binding stability was further confirmed in a 70-ns dynamics simulation. In summary, α-boswellic acid could bind to and translocate GR but did not induce glucocorticoid response element-mediated transcription. Since α-boswellic acid showed the dissociated characteristic that separated transrepression from transactivation, it might be a selective GR modulator against inflammatory disorders.
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Affiliation(s)
- Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jiarui Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yantong Sun
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jingqi Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Haoyang Zou
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Li Ren
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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4
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Zhang S, Fairen‐Jimenez D, Zaworotko MJ. Structural Elucidation of the Mechanism of Molecular Recognition in Chiral Crystalline Sponges. Angew Chem Int Ed Engl 2020; 59:17600-17606. [PMID: 32589318 PMCID: PMC7540565 DOI: 10.1002/anie.202006438] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/25/2020] [Indexed: 11/11/2022]
Abstract
To gain insight into chiral recognition in porous materials we have prepared a family of fourth generation chiral metal-organic frameworks (MOFs) that have rigid frameworks and adaptable (flexible) pores. The previously reported parent material, [Co2 (S-mandelate)2 (4,4'-bipyridine)3 ](NO3 )2 , CMOM-1S, is a modular MOF; five new variants in which counterions (BF4- , CMOM-2S) or mandelate ligands are substituted (2-Cl, CMOM-11R; 3-Cl, CMOM-21R; 4-Cl, CMOM-31R; 4-CH3 , CMOM-41R) and the existing CF3 SO3- variant CMOM-3S are studied herein. Fine-tuning of pore size, shape, and chemistry afforded a series of distinct host-guest binding sites with variable chiral separation properties with respect to three structural isomers of phenylpropanol. Structural analysis of the resulting crystalline sponge phases revealed that host-guest interactions, guest-guest interactions, and pore adaptability collectively determine chiral discrimination.
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Affiliation(s)
- Shi‐Yuan Zhang
- Department of Chemical ScienceBernal InstitutionUniversity of LimerickLimerickV94 T9PXRepublic of Ireland
- Department of Chemical Engineering & BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - David Fairen‐Jimenez
- Department of Chemical Engineering & BiotechnologyUniversity of CambridgeCambridgeCB3 0ASUK
| | - Michael J. Zaworotko
- Department of Chemical ScienceBernal InstitutionUniversity of LimerickLimerickV94 T9PXRepublic of Ireland
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5
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Zhang S, Fairen‐Jimenez D, Zaworotko MJ. Structural Elucidation of the Mechanism of Molecular Recognition in Chiral Crystalline Sponges. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shi‐Yuan Zhang
- Department of Chemical Science Bernal Institution University of Limerick Limerick V94 T9PX Republic of Ireland
- Department of Chemical Engineering & Biotechnology University of Cambridge Cambridge CB3 0AS UK
| | - David Fairen‐Jimenez
- Department of Chemical Engineering & Biotechnology University of Cambridge Cambridge CB3 0AS UK
| | - Michael J. Zaworotko
- Department of Chemical Science Bernal Institution University of Limerick Limerick V94 T9PX Republic of Ireland
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Abstract
This chapter has been conceived as an introductory text to aid in the understanding of the key design strategies for the development of synthetic analogs of endogenous retinoids as ligands for the retinoic acid receptors (RARs) and retinoid X receptors (RXRs). The structure and binding characteristics of the endogenous retinoids are first explained to put the main chemical design challenges in context. Existing biochemical and structural data is then used to describe the guiding principles used to develop agonists and antagonists of the RARs and RXRs. In light of the increasing proliferation of biophysical methods that employ fluorescence measurements or molecular tags, we also examine the application of retinoids as probes and the chemical principles required to develop these tools.
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Affiliation(s)
| | - Andrew Whiting
- Department of Chemistry, Durham University, Lower Mountjoy, Durham, United Kingdom
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7
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Miro Estruch I, Melchers D, Houtman R, de Haan LHJ, Groten JP, Louisse J, Rietjens IMCM. Characterization of the differential coregulator binding signatures of the Retinoic Acid Receptor subtypes upon (ant)agonist action. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2017; 1865:1195-1206. [PMID: 28642153 DOI: 10.1016/j.bbapap.2017.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 06/02/2017] [Accepted: 06/17/2017] [Indexed: 10/19/2022]
Abstract
Retinoic Acid Receptor alpha (RARα/NR1B1), Retinoic Acid Receptor beta (RARβ/NR1B2) and Retinoic Acid Receptor gamma (RARγ/NR1B3) are transcription factors regulating gene expression in response to retinoids. Within the RAR genomic pathways, binding of RARs to coregulators is a key intermediate regulatory phase. However, ligand-dependent interactions between the wide variety of coregulators that may be present in a cell and the different RAR subtypes are largely unknown. The aim of this study is to characterize the coregulator binding profiles of RARs in the presence of the pan-agonist all-trans-Retinoic Acid (AtRA); the subtype-selective agonists Am80 (RARα), CD2314 (RARβ) and BMS961 (RARγ); and the antagonist Ro415253. To this end, we used a microarray assay for coregulator-nuclear receptor interactions to assess RAR binding to 154 motifs belonging to >60 coregulators. The results revealed a high number of ligand-dependent RAR-coregulator interactions among all RAR variants, including many binding events not yet described in literature. Next, this work confirmed a greater ligand-independent activity of RARβ compared to the other RAR subtypes based on both higher basal and lower ligand-driven coregulator binding. Further, several coregulator motifs showed selective binding to a specific RAR subtype. Next, this work showed that subtype-selective agonists can be successfully discriminated by using coregulator binding assays. Finally this study demonstrated the possible applications of a coregulator binding assay as a tool to discriminate between agonistic/antagonistic actions of ligands. The RAR-coregulator interactions found will be of use to direct further studies to better understand the mechanisms driving the eventual actions of retinoids.
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Affiliation(s)
- Ignacio Miro Estruch
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Diana Melchers
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - René Houtman
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - John P Groten
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Jochem Louisse
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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8
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Di Rocco A, Uchibe K, Larmour C, Berger R, Liu M, Barton ER, Iwamoto M. Selective Retinoic Acid Receptor γ Agonists Promote Repair of Injured Skeletal Muscle in Mouse. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:2495-504. [PMID: 26205250 PMCID: PMC4597269 DOI: 10.1016/j.ajpath.2015.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 04/16/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Retinoic acid signaling regulates several biological events, including myogenesis. We previously found that retinoic acid receptor γ (RARγ) agonist blocks heterotopic ossification, a pathological bone formation that mostly occurs in the skeletal muscle. Interestingly, RARγ agonist also weakened deterioration of muscle architecture adjacent to the heterotopic ossification lesion, suggesting that RARγ agonist may oppose skeletal muscle damage. To test this hypothesis, we generated a critical defect in the tibialis anterior muscle of 7-week-old mice with a cautery, treated them with RARγ agonist or vehicle corn oil, and examined the effects of RARγ agonist on muscle repair. The muscle defects were partially repaired with newly regenerating muscle cells, but also filled with adipose and fibrous scar tissue in both RARγ-treated and control groups. The fibrous or adipose area was smaller in RARγ agonist-treated mice than in the control. In addition, muscle repair was remarkably delayed in RARγ-null mice in both critical defect and cardiotoxin injury models. Furthermore, we found a rapid increase in retinoid signaling in lacerated muscle, as monitored by retinoid signaling reporter mice. Together, our results indicate that endogenous RARγ signaling is involved in muscle repair and that selective RARγ agonists may be beneficial to promote repair in various types of muscle injuries.
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Affiliation(s)
- Agnese Di Rocco
- Translational Research Program in Pediatric Orthopaedics, The Children's Hospital of Philadelphia Research Institute, Philadelphia
| | - Kenta Uchibe
- Translational Research Program in Pediatric Orthopaedics, The Children's Hospital of Philadelphia Research Institute, Philadelphia
| | - Colleen Larmour
- Translational Research Program in Pediatric Orthopaedics, The Children's Hospital of Philadelphia Research Institute, Philadelphia
| | - Rebecca Berger
- Translational Research Program in Pediatric Orthopaedics, The Children's Hospital of Philadelphia Research Institute, Philadelphia
| | - Min Liu
- Department of Physiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elisabeth R Barton
- Department of Anatomy and Cell Biology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Masahiro Iwamoto
- Translational Research Program in Pediatric Orthopaedics, The Children's Hospital of Philadelphia Research Institute, Philadelphia.
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Álvarez S, Lieb M, Martínez C, Khanwalkar H, Rodríguez-Barrios F, Álvarez R, Gronemeyer H, de Lera AR. Modulation of Retinoic Acid Receptor Subtypes by 5- and 8-Substituted (Naphthalen-2-yl)-based Arotinoids. ChemMedChem 2015; 10:1378-91. [PMID: 26012882 DOI: 10.1002/cmdc.201500150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 12/29/2022]
Abstract
Retinoid receptors (RARs and RXRs) transduce the signals of their natural and synthetic ligands (retinoids and rexinoids) to cellular transcriptional machinery to induce gene programs that control diverse biological and physiological effects on organisms. All-trans-retinoic acid, the natural ligand for RARs, is used therapeutically for the treatment of acute promyelocytic leukemia (APL), whereas the synthetic rexinoid bexarotene (a representative member of the aromatic retinoids or arotinoids) is approved for the treatment of cutaneous T-cell lymphoma (CTCL). Other retinoids have found applications in the topical treatment of skin disorders. In continuation of previous work on the naphthalene-based arotinoid scaffold, we synthesized a new series of (3-halo)benzoic acids connected to C5- or C8-substituted naphthyl rings via (E)-ethenyl and amide and, for the C5 series, (E)-chalcone linkers. These compounds were evaluated as RAR modulators in comparison with previously described dihydronaphthalene arotinoids with the same substitution pattern. Transactivation studies in this series revealed an absence of synergy between small halogen atoms (F, Cl) at C3 and the groups at C5 or C8, as had been observed on some of the dihydronaphthalene analogues. Instead, non-halogenated 4-(2-naphthamido)benzoic acid derivatives transactivated toward the RARβ subtype in preference to the paralogues. The derivatives with bulkier substituents at C8 were characterized as dual RARβ/RARα antagonists, and (E)-4-[(8-(phenylethynyl)naphthalene-2-yl)ethenyl]benzoic acid (11 c), with an ethenyl connector, was shown to be a potent antagonist of RARα.
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Affiliation(s)
- Susana Álvarez
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IBI, As Lagoas-Marcosende, 36310 Vigo (Spain)
| | - Michele Lieb
- Department of Cancer Biology, Institut de Génetique et de Biologie Moleculaire et Cellulaire (IGBMC)/CNRS/INSERM/ULP, BP 163, Ilkirch Cedex, C.U. de Strasbourg (France)
| | - Claudio Martínez
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IBI, As Lagoas-Marcosende, 36310 Vigo (Spain)
| | - Harshal Khanwalkar
- Department of Cancer Biology, Institut de Génetique et de Biologie Moleculaire et Cellulaire (IGBMC)/CNRS/INSERM/ULP, BP 163, Ilkirch Cedex, C.U. de Strasbourg (France)
| | - Fátima Rodríguez-Barrios
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IBI, As Lagoas-Marcosende, 36310 Vigo (Spain)
| | - Rosana Álvarez
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IBI, As Lagoas-Marcosende, 36310 Vigo (Spain).
| | - Hinrich Gronemeyer
- Department of Cancer Biology, Institut de Génetique et de Biologie Moleculaire et Cellulaire (IGBMC)/CNRS/INSERM/ULP, BP 163, Ilkirch Cedex, C.U. de Strasbourg (France).
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, CINBIO and IBI, As Lagoas-Marcosende, 36310 Vigo (Spain).
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di Masi A, Leboffe L, De Marinis E, Pagano F, Cicconi L, Rochette-Egly C, Lo-Coco F, Ascenzi P, Nervi C. Retinoic acid receptors: from molecular mechanisms to cancer therapy. Mol Aspects Med 2015; 41:1-115. [PMID: 25543955 DOI: 10.1016/j.mam.2014.12.003] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 02/07/2023]
Abstract
Retinoic acid (RA), the major bioactive metabolite of retinol or vitamin A, induces a spectrum of pleiotropic effects in cell growth and differentiation that are relevant for embryonic development and adult physiology. The RA activity is mediated primarily by members of the retinoic acid receptor (RAR) subfamily, namely RARα, RARβ and RARγ, which belong to the nuclear receptor (NR) superfamily of transcription factors. RARs form heterodimers with members of the retinoid X receptor (RXR) subfamily and act as ligand-regulated transcription factors through binding specific RA response elements (RAREs) located in target genes promoters. RARs also have non-genomic effects and activate kinase signaling pathways, which fine-tune the transcription of the RA target genes. The disruption of RA signaling pathways is thought to underlie the etiology of a number of hematological and non-hematological malignancies, including leukemias, skin cancer, head/neck cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer, renal cell carcinoma, pancreatic cancer, liver cancer, glioblastoma and neuroblastoma. Of note, RA and its derivatives (retinoids) are employed as potential chemotherapeutic or chemopreventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. In humans, retinoids reverse premalignant epithelial lesions, induce the differentiation of myeloid normal and leukemic cells, and prevent lung, liver, and breast cancer. Here, we provide an overview of the biochemical and molecular mechanisms that regulate the RA and retinoid signaling pathways. Moreover, mechanisms through which deregulation of RA signaling pathways ultimately impact on cancer are examined. Finally, the therapeutic effects of retinoids are reported.
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Affiliation(s)
- Alessandra di Masi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Loris Leboffe
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Elisabetta De Marinis
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Francesca Pagano
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Laura Cicconi
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS UMR 7104 - Inserm U 964, University of Strasbourg, 1 rue Laurent Fries, BP10142, Illkirch Cedex F-67404, France.
| | - Francesco Lo-Coco
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy.
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, Roma I-00146, Italy.
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100.
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Martínez C, Lieb M, Álvarez S, Rodríguez-Barrios F, Álvarez R, Khanwalkar H, Gronemeyer H, de Lera AR. Dual RXR Agonists and RAR Antagonists Based on the Stilbene Retinoid Scaffold. ACS Med Chem Lett 2014; 5:533-7. [PMID: 24900875 DOI: 10.1021/ml400521f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/19/2014] [Indexed: 01/24/2023] Open
Abstract
Arotinoids containing a C5,C8-diphenylnaphthalene-2-yl ring linked to a (C3-halogenated) benzoic acid via an ethenyl connector (but not the corresponding naphthamides), which are prepared by Horner-Wadsworth-Emmons reaction of naphthaldehydes and benzylphosphonates, display the rather unusual property of being RXR agonists (15-fold induction of the RXR reporter cell line was achieved at 3- to 10-fold lower concentration than 9-cis-retinoic acid) and RAR antagonists as shown by transient transactivation studies. The binding of such bulky ligands suggests that the RXR ligand-binding domain is endowed with some degree of structural elasticity.
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Affiliation(s)
- Claudio Martínez
- Departamento
de Química Orgánica, Facultade de Química, CINBIO, Universidade de Vigo, and Instituto de Investigación Biomédica de Vigo (IBIV), 36310 Vigo, Spain
| | - Michele Lieb
- Equipe
Labellisée Ligue Contre le Cancer, Department of Functional
Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/UdS, BP 10142, 67404 Illkirch,
Cedex, C. U. de Strasbourg, France
| | - Susana Álvarez
- Departamento
de Química Orgánica, Facultade de Química, CINBIO, Universidade de Vigo, and Instituto de Investigación Biomédica de Vigo (IBIV), 36310 Vigo, Spain
| | - Fátima Rodríguez-Barrios
- Departamento
de Química Orgánica, Facultade de Química, CINBIO, Universidade de Vigo, and Instituto de Investigación Biomédica de Vigo (IBIV), 36310 Vigo, Spain
| | - Rosana Álvarez
- Departamento
de Química Orgánica, Facultade de Química, CINBIO, Universidade de Vigo, and Instituto de Investigación Biomédica de Vigo (IBIV), 36310 Vigo, Spain
| | - Harshal Khanwalkar
- Equipe
Labellisée Ligue Contre le Cancer, Department of Functional
Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/UdS, BP 10142, 67404 Illkirch,
Cedex, C. U. de Strasbourg, France
| | - Hinrich Gronemeyer
- Equipe
Labellisée Ligue Contre le Cancer, Department of Functional
Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/UdS, BP 10142, 67404 Illkirch,
Cedex, C. U. de Strasbourg, France
| | - Angel R. de Lera
- Departamento
de Química Orgánica, Facultade de Química, CINBIO, Universidade de Vigo, and Instituto de Investigación Biomédica de Vigo (IBIV), 36310 Vigo, Spain
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12
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Affiliation(s)
- Pengxiang Huang
- Metabolic Signaling and Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Vikas Chandra
- Metabolic Signaling and Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Fraydoon Rastinejad
- Metabolic Signaling and Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
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13
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le Maire A, Bourguet W. Retinoic acid receptors: structural basis for coregulator interaction and exchange. Subcell Biochem 2014; 70:37-54. [PMID: 24962880 DOI: 10.1007/978-94-017-9050-5_3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the form of heterodimers with retinoid X receptors (RXRs), retinoic acid receptors (RARs) are master regulators of gene expression in humans and important drug targets. They act as ligand-dependent transcription factors that regulate a large variety of gene networks controlling cell growth, differentiation, survival and death. The biological functions of RARs rely on a dynamic series of coregulator exchanges controlled by ligand binding. Unliganded RARs exert a repressor activity by interacting with transcriptional corepressors which themselves serve as docking platforms for the recruitment of histone deacetylases that impose a higher order structure on chromatin which is not permissive to gene transcription. Upon ligand binding, the receptor undergoes conformational changes inducing corepressor release and the recruitment of coactivators with histone acetylase activities allowing chromatin decompaction and gene transcription. In the following, we review the structural determinants of the interaction between RAR and either type of coregulators both at the level of the individual receptor and in the context of the RAR-RXR heterodimers. We also discuss the molecular details of the fine tuning of these associations by the various pharmacological classes of ligands.
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Affiliation(s)
- Albane le Maire
- Inserm U1054, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090, Montpellier, France,
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14
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Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:144-54. [PMID: 24419387 PMCID: PMC3919266 DOI: 10.1107/s139900471302748x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.
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Affiliation(s)
- Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Herbert E. Klei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Jeffrey J. Headd
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Robert D. Oeffner
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | | | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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15
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Burris TP, Solt LA, Wang Y, Crumbley C, Banerjee S, Griffett K, Lundasen T, Hughes T, Kojetin DJ. Nuclear receptors and their selective pharmacologic modulators. Pharmacol Rev 2013; 65:710-78. [PMID: 23457206 PMCID: PMC11060414 DOI: 10.1124/pr.112.006833] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Nuclear receptors are ligand-activated transcription factors and include the receptors for steroid hormones, lipophilic vitamins, sterols, and bile acids. These receptors serve as targets for development of myriad drugs that target a range of disorders. Classically defined ligands that bind to the ligand-binding domain of nuclear receptors, whether they are endogenous or synthetic, either activate receptor activity (agonists) or block activation (antagonists) and due to the ability to alter activity of the receptors are often termed receptor "modulators." The complex pharmacology of nuclear receptors has provided a class of ligands distinct from these simple modulators where ligands display agonist/partial agonist/antagonist function in a tissue or gene selective manner. This class of ligands is defined as selective modulators. Here, we review the development and pharmacology of a range of selective nuclear receptor modulators.
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Affiliation(s)
- Thomas P Burris
- The Scripps Research Institute, 130 Scripps Way 2A1, Jupiter, FL 33458, USA.
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16
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Joharapurkar AA, Dhote VV, Jain MR. Selective Thyromimetics Using Receptor and Tissue Selectivity Approaches: Prospects for Dyslipidemia. J Med Chem 2012; 55:5649-75. [DOI: 10.1021/jm2004706] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Amit A. Joharapurkar
- Department of Pharmacology and Toxicology, Zydus Research Centre, Sarkhej Bavla NH 8A, Moraiya,
Ahmedabad 382210, India
| | - Vipin V. Dhote
- Department of Pharmacology and Toxicology, Zydus Research Centre, Sarkhej Bavla NH 8A, Moraiya,
Ahmedabad 382210, India
| | - Mukul R. Jain
- Department of Pharmacology and Toxicology, Zydus Research Centre, Sarkhej Bavla NH 8A, Moraiya,
Ahmedabad 382210, India
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17
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Singarapu KK, Zhu J, Tonelli M, Rao H, Assadi-Porter FM, Westler WM, DeLuca HF, Markley JL. Ligand-specific structural changes in the vitamin D receptor in solution. Biochemistry 2011; 50:11025-33. [PMID: 22112050 DOI: 10.1021/bi201637p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vitamin D receptor (VDR) is a member of the nuclear hormone receptor superfamily. When bound to a variety of vitamin D analogues, VDR manifests a wide diversity of physiological actions. The molecular mechanism by which different vitamin D analogues cause specific responses is not understood. The published crystallographic structures of the ligand binding domain of VDR (VDR-LBD) complexed with ligands that have differential biological activities have exhibited identical protein conformations. Here we report that rat VDR-LBD (rVDR-LBD) in solution exhibits differential chemical shifts when bound to three ligands that cause diverse responses: the natural hormone, 1,25-dihydroxyvitamin D(3) [1,25(OH)₂D₃], a potent agonist analogue, 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D₃ [2MD], and an antagonist, 2-methylene-(22E)-(24R)-25-carbobutoxy-26,27-cyclo-22-dehydro-1α,24-dihydroxy-19-norvitamin D₃ [OU-72]. Ligand-specific chemical shifts mapped not only to residues at or near the binding pocket but also to residues remote from the ligand binding site. The complexes of rVDR-LBD with native hormone and the potent agonist 2MD exhibited chemical shift differences in signals from helix-12, which is part of the AF2 transactivation domain that appears to play a role in the selective recruitment of coactivators. By contrast, formation of the complex of rVDR-LBD with the antagonist OU-72 led to disappearance of signals from residues in helices-11 and -12. We present evidence that disorder in this region of the receptor in the antagonist complex prevents the attachment of coactivators.
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Affiliation(s)
- Kiran K Singarapu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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18
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Barnard JH, Collings JC, Whiting A, Przyborski SA, Marder TB. Synthetic retinoids: structure-activity relationships. Chemistry 2010; 15:11430-42. [PMID: 19821467 DOI: 10.1002/chem.200901952] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Retinoid signalling pathways are involved in numerous processes in cells, particularly those mediating differentiation and apoptosis. The endogenous ligands that bind to the retinoid receptors, namely all-trans-retinoic acid (ATRA) and 9-cis-retinoic acid, are prone to double-bond isomerisation and to oxidation by metabolic enzymes, which can have significant and deleterious effects on their activities and selectivities. Many of these problems can be overcome through the use of synthetic retinoids, which are often much more stable, as well as being more active. Modification of their molecular structures can result in retinoids that act as antagonists, rather than agonists, or exhibit a large degree of selectivity for particular retinoid-receptor isotypes. Several such selective retinoids are likely to be of value as pharmaceutical agents with reduced toxicities, particularly in cancer therapy, as reagents for controlling cell differentiation, and as tools for elucidating the precise roles that specific retinoid signalling pathways play within cells.
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Affiliation(s)
- Jonathan H Barnard
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
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19
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Alvarez S, Khanwalkar H, Alvarez R, Erb C, Martínez C, Rodríguez-Barrios F, Germain P, Gronemeyer H, de Lera AR. C3 halogen and c8'' substituents on stilbene arotinoids modulate retinoic Acid receptor subtype function. ChemMedChem 2009; 4:1630-40. [PMID: 19670208 DOI: 10.1002/cmdc.200900214] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The synthesis and biological evaluation of the entire series of C3-halogenated derivatives and bulkier substituents at the C8'' position of the parent stilbene-based RARbeta-selective agonist BMS641 4 c was undertaken. The synthesis uses an E-selective Horner-Wadsworth-Emmons (HWE) condensation of C8-substituted C5-dimethyl dihydronaphthaldehyde and the benzylic phosphonates derived from the C3-halogenated benzoates to construct the stilbene skeleton. Transactivation studies revealed the synergistic effect of small halogen atoms at C3 (F, Cl) and the moderately bulky phenyl group at C8'' (in 4 b and 4 c) to achieve RARbeta selectivity. Our results, supported by computational studies, provide a structural rationale for the mixed agonist-antagonist activities of these arotinoids, which are potent agonists of the RARbeta subtype and antagonists of the RARalpha paralogue. Moreover, transitions from partial agonists to inverse agonists and antagonists can be accomplished with the incorporation of the same halogen atoms into the structures of known modulators BMS701 (5 a) and BMS493 (6 a), which have bulkier substituents than phenyl (p-tolyl and phenylethynyl, respectively) at C8''. Conversely, incorporation of halogen atoms in 6 a converted the ligand from an RARbeta inverse agonist (6 b) to an antagonist (6 c) or an agonist (6 d). Amazingly, 6 a-c commonly acted as inverse agonists for RARalpha, while 6 d and 6 e acted as regular RARalpha antagonists, not affecting co-repressor interaction. In the case of the mixed agonist/antagonist 5 a, C3-halogenation yields inverse RARalpha and RARbeta agonists (5 b-d) with the exception of iodinated 5 e, which is a regular antagonist for both these receptors. Because RARbeta gene expression is frequently deleted or epigenetically silenced in several tumor cells, the novel repertoire of receptor and function-selective RAR agonists, mixed agonist/antagonists, regular antagonists, and inverse agonists will be useful in the elucidation of the mechanism of tumor suppression by retinoids.
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Affiliation(s)
- Susana Alvarez
- Departamento de Química Orgánica, Facultade de Química, Universidade de Vigo, 36310 Vigo (Spain)
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20
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Mentel M, Blankenfeldt W, Breinbauer R. The Active Site of an Enzyme Can Host Both Enantiomers of a Racemic Ligand Simultaneously. Angew Chem Int Ed Engl 2009; 48:9084-7. [DOI: 10.1002/anie.200902997] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Mentel M, Blankenfeldt W, Breinbauer R. Gleichzeitige Bindung beider Enantiomere eines racemischen Wirkstoffs durch das aktive Zentrum eines Enzyms. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Alvarez S, Alvarez R, Khanwalkar H, Germain P, Lemaire G, Rodríguez-Barrios F, Gronemeyer H, de Lera AR. Retinoid receptor subtype-selective modulators through synthetic modifications of RARgamma agonists. Bioorg Med Chem 2009; 17:4345-59. [PMID: 19482478 DOI: 10.1016/j.bmc.2009.05.035] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 05/06/2009] [Accepted: 05/11/2009] [Indexed: 12/31/2022]
Abstract
A series of retinoids designed to interfere with the repositioning of H12 have been synthesized to identify novel RARgamma antagonists based on the structure of known RARgamma agonists. The transcriptional activities of the novel ligands were revealed by cell-based reporting assays, using engineered cells containg RAR subtype-selective fusions of the RAR ligand-binding domains with the yeast GAL4 activator DNA-binding domain and the cognate luciferase reporter gene. Whereas none of the ligands exhibited features of a selective RARgamma antagonist, some of them are endowed with interesting activities. In particular 24a acts as a pan-RAR agonist that induces at high concentration a higher transactivation potential on RARalpha than TTNPB and synergizes at low concentration with TTNPB-bound RARalpha but not RARbeta or RARgamma. Similarly, 24c synergizes with TTNPB-bound RARgamma and exhibits RARalpha,beta antagonist activity. Compounds 24b and 25b are strong RARalpha,beta-selective antagonists without agonist or antagonist activities for RARgamma. Compounds 24b and 24c display weak RXR antagonist activity. In addition several pan-antagonists and partial agonist/antagonists have been defined.
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Affiliation(s)
- Susana Alvarez
- Departamento de Química Orgánica, Universidade de Vigo, Vigo, Spain
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23
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Galdones E, Hales BF. Retinoic acid receptor gamma-induced misregulation of chondrogenesis in the murine limb bud in vitro. Toxicol Sci 2008; 106:223-32. [PMID: 18703560 DOI: 10.1093/toxsci/kfn169] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Vitamin A derivatives modulate gene expression through retinoic acid and rexinoid receptor (RAR/RXR) heterodimers and are indispensable for limb development. Of particular interest, RARgamma is highly expressed in cartilage, a target affected following retinoid-induced limb insult. The goal of this study was to examine how selective activation of RARgamma affects limb development. Forelimbs from E12.5 CD-1 mice were cultured for 6 days in the presence of all-trans RA (pan-RAR agonist; 0.1 or 1.0 microM) or BMS-189961 (BMS961, RARgamma-selective agonist; 0.01 or 0.1 microM) and limb morphology assessed. Untreated limbs developed normal cartilage elements whereas pan-RAR or RARgamma agonist-treated limbs exhibited reductive effects on chondrogenesis. Retinoid activity was assessed using RAREbeta2 (retinoic acid response element beta2)-lacZ reporter limbs; after 3 h of treatment, both drugs increased retinoid activity proximally. To elucidate the expression profiles of a subset of genes important for development, limbs were cultured for 3 h and cRNA hybridized to osteogenesis-focused microarrays. Two genes, matrix GLA protein (Mgp; chondrogenesis inhibitor) and growth differentiation factor-10 (Gdf10/Bmp3b) were induced by RA and BMS-189961. Real-time PCR was done to validate our results and whole mount in situ hybridizations against Mgp and Gdf10 localized their upregulation to areas of cartilage and programmed cell death, respectively. Thus, our results illustrate the importance of RARgamma in mediating the retinoid-induced upregulation of Mgp and Gdf10; determining their roles in chondrogenesis and cell death will help further unravel mechanisms underlying retinoid teratogenicity.
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Affiliation(s)
- Eugene Galdones
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada
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24
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CONFIRM: connecting fragments found in receptor molecules. J Comput Aided Mol Des 2008; 22:761-72. [DOI: 10.1007/s10822-008-9221-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 05/17/2008] [Indexed: 10/21/2022]
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25
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Moise AR, Domínguez M, Alvarez S, Alvarez R, Schupp M, Cristancho AG, Kiser PD, de Lera AR, Lazar MA, Palczewski K. Stereospecificity of retinol saturase: absolute configuration, synthesis, and biological evaluation of dihydroretinoids. J Am Chem Soc 2008; 130:1154-5. [PMID: 18179220 PMCID: PMC2621334 DOI: 10.1021/ja710487q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander R Moise
- Department of Pharmacology, Case School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA.
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26
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de Lera AR, Bourguet W, Altucci L, Gronemeyer H. Design of selective nuclear receptor modulators: RAR and RXR as a case study. Nat Rev Drug Discov 2007; 6:811-20. [PMID: 17906643 DOI: 10.1038/nrd2398] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) are members of the nuclear receptor superfamily whose effects on cell growth and survival can be modulated therapeutically by small-molecule ligands. Although compounds that target these receptors are powerful anticancer drugs, their use is limited by toxicity. An improved understanding of the structural biology of RXRs and RARs and recent advances in the chemical synthesis of modified retinoid and rexinoid ligands should enable the rational design of more selective agents that might overcome such problems. Here, we review structural data for RXRs and RARs, discuss strategies in the design of selective RXR and RAR modulators, and consider lessons that can be learned for the design of selective nuclear-receptor modulators in general.
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Affiliation(s)
- Angel R de Lera
- Universidade de Vigo, Departamento de Quimica Orgánica, Facultad de Quimica, 36310 Vigo, Spain
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27
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Altucci L, Leibowitz MD, Ogilvie KM, de Lera AR, Gronemeyer H. RAR and RXR modulation in cancer and metabolic disease. Nat Rev Drug Discov 2007; 6:793-810. [PMID: 17906642 DOI: 10.1038/nrd2397] [Citation(s) in RCA: 393] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Retinoic acid receptors (RARs) are ligand-controlled transcription factors that function as heterodimers with retinoid X receptors (RXRs) to regulate cell growth and survival. The success of RAR modulation in the treatment of acute promyelocytic leukaemia (APL) has stimulated considerable interest in the development of RAR and RXR modulators. This has been aided by recent advances in the understanding of the biological role of RARs and RXRs and in the design of selective receptor modulators that might overcome the limitations of current drugs. Here, we discuss the challenges and opportunities for therapeutic strategies based on RXR and RAR modulators, with a focus on cancer and metabolic diseases such as diabetes and obesity.
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Affiliation(s)
- Lucia Altucci
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, 80138 Napoli, Italy
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28
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Dawson MI, Xia Z, Liu G, Ye M, Fontana JA, Farhana L, Patel BB, Arumugarajah S, Bhuiyan M, Zhang XK, Han YH, Stallcup WB, Fukushi JI, Mustelin T, Tautz L, Su Y, Harris DL, Waleh N, Hobbs PD, Jong L, Chao WR, Schiff LJ, Sani BP. An adamantyl-substituted retinoid-derived molecule that inhibits cancer cell growth and angiogenesis by inducing apoptosis and binds to small heterodimer partner nuclear receptor: effects of modifying its carboxylate group on apoptosis, proliferation, and protein-tyrosine phosphatase activity. J Med Chem 2007; 50:2622-39. [PMID: 17489579 PMCID: PMC2528874 DOI: 10.1021/jm0613323] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Apoptotic and antiproliferative activities of small heterodimer partner (SHP) nuclear receptor ligand (E)-4-[3'-(1-adamantyl)-4'-hydroxyphenyl]-3-chlorocinnamic acid (3-Cl-AHPC), which was derived from 6-[3'-(1-adamantyl)-4'-hydroxyphenyl]-2-naphthalenecarboxylic acid (AHPN), and several carboxyl isosteric or hydrogen bond-accepting analogues were examined. 3-Cl-AHPC continued to be the most effective apoptotic agent, whereas tetrazole, thiazolidine-2,4-dione, methyldinitrile, hydroxamic acid, boronic acid, 2-oxoaldehyde, and ethyl phosphonic acid hydrogen bond-acceptor analogues were inactive or less efficient inducers of KG-1 acute myeloid leukemia and MDA-MB-231 breast, H292 lung, and DU-145 prostate cancer cell apoptosis. Similarly, 3-Cl-AHPC was the most potent inhibitor of cell proliferation. 4-[3'-(1-adamantyl)-4'-hydroxyphenyl]-3-chlorophenyltetrazole, (2E)-5-{2-[3'-(1-adamantyl)-2-chloro-4'-hydroxy-4-biphenyl]ethenyl}-1H-tetrazole, 5-{4-[3'-(1-adamantyl)-4'-hydroxyphenyl]-3-chlorobenzylidene}thiazolidine-2,4-dione, and (3E)-4-[3'-(1-adamantyl)-2-chloro-4'-hydroxy-4-biphenyl]-2-oxobut-3-enal were very modest inhibitors of KG-1 proliferation. The other analogues were minimal inhibitors. Fragment-based QSAR analyses relating the polar termini with cancer cell growth inhibition revealed that length and van der Waals electrostatic surface potential were the most influential features on activity. 3-Cl-AHPC and the 3-chlorophenyltetrazole and 3-chlorobenzylidenethiazolidine-2,4-dione analogues were also able to inhibit SHP-2 protein-tyrosine phosphatase, which is elevated in some leukemias. 3-Cl-AHPC at 1.0 microM induced human microvascular endothelial cell apoptosis but did not inhibit cell migration or tube formation.
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Affiliation(s)
- Marcia I Dawson
- Cancer Center, Burnham Institute for Medical Research, La Jolla, California 92037, USA.
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29
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Germain P, Chambon P, Eichele G, Evans RM, Lazar MA, Leid M, De Lera AR, Lotan R, Mangelsdorf DJ, Gronemeyer H. International Union of Pharmacology. LX. Retinoic acid receptors. Pharmacol Rev 2007; 58:712-25. [PMID: 17132850 DOI: 10.1124/pr.58.4.4] [Citation(s) in RCA: 285] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Retinoid is a term for compounds that bind to and activate retinoic acid receptors (RARalpha, RARbeta, and RARgamma), members of the nuclear hormone receptor superfamily. The most important endogenous retinoid is all-trans-retinoic acid. Retinoids regulate a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, cell growth arrest, differentiation and apoptosis, and homeostasis, as well as their disorders. This review summarizes the considerable amount of knowledge generated on these receptors.
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Affiliation(s)
- Pierre Germain
- Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, Illkirch, Communauté Urbaine de Strasbourg, France.
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30
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Sreekanth R, Rajan SS. The study of helical distortions due to environmental changes: choice of parameters. Biophys Chem 2007; 125:191-200. [PMID: 16919383 DOI: 10.1016/j.bpc.2006.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 07/28/2006] [Accepted: 07/29/2006] [Indexed: 10/24/2022]
Abstract
Parameters like interhelical angles, helical parameters, levels of distortions, etc., have been analysed to test their sensitivity to environmental changes using a method developed in this laboratory. This analysis was done on protein structures solved under different environmental conditions like temperature and pH, and ligand binding. The study reveals that the helical parameters are not sensitive enough to study the effect of environmental changes on protein helices. On the other hand the helical distortions as well as changes in the interhelical angles are more sensitive to these changes. The study also provides with additional information like the origin of distortions in a helix when a ligand binds to a protein, bending in helical axis, identification and extent of domain movements, etc.
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Affiliation(s)
- R Sreekanth
- Deparment of Crystallography and Biophysics, University of Madras, Chennai, India
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31
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Stjernschantz E, Marelius J, Medina C, Jacobsson M, Vermeulen NPE, Oostenbrink C. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method. J Chem Inf Model 2006; 46:1972-83. [PMID: 16995728 DOI: 10.1021/ci0601214] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An extensive evaluation of the linear interaction energy (LIE) method for the prediction of binding affinity of docked compounds has been performed, with an emphasis on its applicability in lead optimization. An automated setup is presented, which allows for the use of the method in an industrial setting. Calculations are performed for four realistic examples, retinoic acid receptor gamma, matrix metalloprotease 3, estrogen receptor alpha, and dihydrofolate reductase, focusing on different aspects of the procedure. The obtained LIE models are evaluated in terms of the root-mean-square (RMS) errors from experimental binding free energies and the ability to rank compounds appropriately. The results are compared to the best empirical scoring function, selected from a set of 10 scoring functions. In all cases, good LIE models can be obtained in terms of free-energy RMS errors, although reasonable ranking of the ligands of dihydrofolate reductase proves difficult for both the LIE method and scoring functions. For the other proteins, the LIE model results in better predictions than the best performing scoring function. These results indicate that the LIE approach, as a tool to evaluate docking results, can be a valuable asset in computational lead optimization programs.
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Affiliation(s)
- Eva Stjernschantz
- Leiden/Amsterdam Center for Drug Research, Division of Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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32
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Mezzetti A, Schrag JD, Cheong CS, Kazlauskas RJ. Mirror-Image Packing in Enantiomer Discrimination. ACTA ACUST UNITED AC 2005; 12:427-37. [PMID: 15850979 DOI: 10.1016/j.chembiol.2005.01.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 12/30/2004] [Accepted: 01/28/2005] [Indexed: 11/22/2022]
Abstract
Synthetic chemists often exploit the high enantioselectivity of lipases to prepare pure enantiomers of primary alcohols, but the molecular basis for this enantioselectivity is unknown. The crystal structures of two phosphonate transition-state analogs bound to Burkholderia cepacia lipase reveal this molecular basis for a typical primary alcohol: 2-methyl-3-phenyl-1-propanol. The enantiomeric alcohol moieties adopt surprisingly similar orientations, with only subtle differences that make it difficult to predict how to alter enantioselectivity. These structures, along with a survey of previous structures of enzyme bound enantiomers, reveal that binding of enantiomers does not involve an exchange of two substituent positions as most researchers assumed. Instead, the enantiomers adopt mirror-image packing, where three of the four substituents at the stereocenter lie in similar positions. The fourth substituent, hydrogen, points in opposite directions.
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Affiliation(s)
- Alessandra Mezzetti
- Department of Chemistry, McGill University, Montréal, Québec H3A 2K6, Canada
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33
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Abstract
Nuclear receptors modulate transcription through ligand-mediated recruitment of transcriptional coregulator proteins. The structural connection between ligand and coregulator is mediated by a molecular switch, made up of the most carboxy-terminal helix in the ligand-binding domain, helix 12. The dynamics of this switch are thought to underlie ligand specificity of nuclear receptor signaling, but the details of this control mechanism have remained elusive. This review highlights recent structural work on how the ligand controls this molecular switch and the modulation of this signaling pathway by receptor subtype and dimer partner.
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Affiliation(s)
- Kendall W Nettles
- The University of Chicago, The Ben May Institute for Cancer Research, Chicago, Illinois 60637, USA.
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34
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Germain P, Kammerer S, Pérez E, Peluso-Iltis C, Tortolani D, Zusi FC, Starrett J, Lapointe P, Daris JP, Marinier A, de Lera AR, Rochel N, Gronemeyer H. Rational design of RAR-selective ligands revealed by RARbeta crystal stucture. EMBO Rep 2004; 5:877-82. [PMID: 15319780 PMCID: PMC1299136 DOI: 10.1038/sj.embor.7400235] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2004] [Revised: 07/22/2004] [Accepted: 07/27/2004] [Indexed: 11/08/2022] Open
Abstract
The crystal structure of the ligand-binding domain of RARbeta, a suspect tumour suppressor, reveals important features that distinguish it from the two other RAR isotypes. The most striking difference is an extra cavity allowing RARbeta to bind more bulky agonists. Accordingly, we identified a ligand that shows RARbeta selectivity with a 100-fold higher affinity to RARbeta than to alpha or gamma isotypes. The structural differences between the three RAR ligand-binding pockets revealed a rationale explaining how a single retinoid can be at the same time an RARalpha, gamma antagonist and an RARbeta agonist. In addition, we demonstrate how to generate an RARbeta antagonist by gradually modifying the bulkiness of a single substitution. Together, our results provide structural guidelines for the synthesis of RARbeta-selective agonists and antagonists, allowing for the first time to address pharmacologically the tumour suppressor role of RARbeta in vitro and in animal models.
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Affiliation(s)
- Pierre Germain
- Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
- These authors contributed equally to this work
| | - Sabrina Kammerer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
- These authors contributed equally to this work
| | - Efrén Pérez
- Universidade de Vigo, Facultade de Química, 36200 Vigo, Spain
| | - Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
| | - David Tortolani
- Bristol-Myers Squibb, Pharmaceutical Research Institute, PO Box 4000, Princeton, New Jersey 08543-4000, USA
| | - F Christopher Zusi
- Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, USA
| | - John Starrett
- Bristol-Myers Squibb, 5 Research Parkway, Wallingford, Connecticut 06492, USA
| | - Philippe Lapointe
- Bristol-Myers Squibb, 100 Boul de L'Industrie, Candiac, Quebec, Canada
| | - Jean-Paul Daris
- Bristol-Myers Squibb, 100 Boul de L'Industrie, Candiac, Quebec, Canada
| | - Anne Marinier
- Bristol-Myers Squibb, 100 Boul de L'Industrie, Candiac, Quebec, Canada
| | - Angel R de Lera
- Universidade de Vigo, Facultade de Química, 36200 Vigo, Spain
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
| | - Hinrich Gronemeyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
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35
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Liu S, Brown CW, Berlin KD, Dhar A, Guruswamy S, Brown D, Gardner GJ, Birrer MJ, Benbrook DM. Synthesis of flexible sulfur-containing heteroarotinoids that induce apoptosis and reactive oxygen species with discrimination between malignant and benign cells. J Med Chem 2004; 47:999-1007. [PMID: 14761202 DOI: 10.1021/jm030346v] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regulation of growth, differentiation, and apoptosis by synthetic retinoids can occur through mechanisms that are dependent and independent of their ability to bind and activate nuclear retinoic acid receptors. The objective of this study was to determine if increasing flexibility of the heteroarotinoid structure would affect the specificity of the synthetic retinoids for the receptors and for their regulation of cancerous and nonmalignant cells. Methods were developed to produce the first examples of heteroarotinoids 15a-15h, which contain urea and/or thiourea linking groups between two aryl rings. Substituents at the para position of the single phenyl ring were either an ester, a nitro group, or a sulfonamide group. Ovarian cancer cell lines Caov-3, OVCAR-3, SK-OV-3, UCI-101, and 222 were utilized, and the inhibitory prowess of the heteroarotinoids was referenced to that of 4-HPR (25). Similar to 4-HPR (25), the heteroarotinoids inhibited growth of all cell lines at micromolar concentrations. Although the heteroarotinoids did not activate retinoic acid receptors, the agents induced potent growth inhibition against the cancer cells with weak activity against normal and benign cells. The growth inhibition was associated with cell loss and induction of reactive oxygen species.
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Affiliation(s)
- Shengquan Liu
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078-3071, USA
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36
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Hoerer S, Schmid A, Heckel A, Budzinski RM, Nar H. Crystal structure of the human liver X receptor beta ligand-binding domain in complex with a synthetic agonist. J Mol Biol 2004; 334:853-61. [PMID: 14643652 DOI: 10.1016/j.jmb.2003.10.033] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LXRbeta belongs to the nuclear hormone receptor superfamily of ligand-activated transcription factors. Its natural ligands are supposed to be oxidised derivatives of cholesterol. Stimulation of LXRbeta by agonists activates a number of genes that are involved in the regulation of lipid metabolism and cholesterol efflux from cells. Therefore, LXRbeta may represent a novel therapeutic target for the treatment of dyslipidemia and atherosclerosis.Here, we report the X-ray crystal structure of the LXRbeta ligand-binding domain in complex with a synthetic agonist, T-0901317. This compound occupies the ligand-binding pocket of the receptor, forms numerous lipophilic contacts with the protein and one crucial hydrogen bond to His435 and stabilises the agonist conformation of the receptor ligand-binding domain. The recruitment of the AF2-region of the protein is not achieved via direct polar interactions of the ligand with protein side-chains of this helical segment, but rather via few hydrophobic contacts and probably more importantly via indirect effects involving the pre-orientation of side-chains that surround the ligand-binding pocket and form the interface to the AF2-helix. On the basis of these results we propose a binding mode and a mechanism of action for the putative natural ligands, oxidised derivatives of cholesterol.
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Affiliation(s)
- Stefan Hoerer
- Department of Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach/Riss, Germany
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37
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Klebe G. From structure to recognition principles: mining in crystal data as a prerequisite for drug design. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2003:103-26. [PMID: 12664538 DOI: 10.1007/978-3-662-05314-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- G Klebe
- Institut für Pharmazeutische, Chemie Philipps-Universität Marburg, 35032 Marburg, Germany.
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38
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Mizwicki MT, Norman AW. Two key proteins of the vitamin D endocrine system come into crystal clear focus: comparison of the X-ray structures of the nuclear receptor for 1alpha,25(OH)2 vitamin D3, the plasma vitamin D binding protein, and their ligands. J Bone Miner Res 2003; 18:795-806. [PMID: 12733718 DOI: 10.1359/jbmr.2003.18.5.795] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Mathew T Mizwicki
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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39
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Dussault I, Beard R, Lin M, Hollister K, Chen J, Xiao JH, Chandraratna R, Forman BM. Identification of gene-selective modulators of the bile acid receptor FXR. J Biol Chem 2003; 278:7027-33. [PMID: 12496277 DOI: 10.1074/jbc.m209863200] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BAR is a nuclear bile acid receptor (BAR) (FXR) receptor that regulates gene networks involved in cholesterol and bile acid homeostasis. We have identified two classes of synthetic compounds that differentially modulate BAR activity. The first class activates BAR target genes in the predicted fashion and is 25-fold more potent than endogenous bile acids. The second class, represented by AGN34, antagonizes BAR in transient reporter assays. Surprisingly, this compound acts in a gene-selective manner in vivo: it is an agonist on CYP7A1, an antagonist on IBABP, and is neutral on SHP. These findings indicate that synthetic BAR modulators can be developed to regulate transcription in a gene-specific fashion. Given the ability of BAR to regulate several lipid homeostatic pathways, the identification of gene-selective BAR modulators have important implications for the development of improved cholesterol lowering agents.
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Affiliation(s)
- Isabelle Dussault
- Division of Molecular Medicine, The Beckman Research Institute, the City of Hope National Medical Center, The Gonda Diabetes & Genetic Research Center, Duarte, California 91010, USA
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40
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Dischino DD, Lee CW, Belema M, Zusi C. Synthesis of carbon-14 labeled (R)-3-fluoro-4-(2?-(5??, 6??, 7??, 8??-tetrahydro-5??, 5??, 8??, 8??-tetramethyl-2??-naphthyl)-[2?-hydroxy-14C])[carbonyl-14C]acetamidobenzoic acid. J Labelled Comp Radiopharm 2003. [DOI: 10.1002/jlcr.654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Zusi FC, Lorenzi MV, Vivat-Hannah V. Selective retinoids and rexinoids in cancer therapy and chemoprevention. Drug Discov Today 2002; 7:1165-74. [PMID: 12547017 DOI: 10.1016/s1359-6446(02)02526-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural and synthetic retinoids are effective inhibitors of tumor cell growth in vitro and in vivo. However, the toxicity of natural derivatives of vitamin A limits their therapeutic use. Recently, synthetic compounds selective for the different retinoid receptor isotypes have been generated that circumvent pan-retinoid toxicity. The tumor-suppressive activity of selective retinoid and/or rexinoid ligands has been established preclinically, and emerging clinical trials are supportive of the chemotherapeutic and chemopreventive potential of these compounds in multiple oncology indications, with reduced toxicity. Moreover, the combination of retinoids and/or rexinoids with chemotherapeutic agents for the synergistic modulation of specific pathways could also be of benefit in cancer therapy.
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Affiliation(s)
- F Christopher Zusi
- Wallingford Discovery Chemistry, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, CT 03492-1996, USA
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42
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Klaholz B, Moras D. C-H...O hydrogen bonds in the nuclear receptor RARgamma--a potential tool for drug selectivity. Structure 2002; 10:1197-204. [PMID: 12220491 DOI: 10.1016/s0969-2126(02)00828-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen bonds between polarized atoms play a crucial role in protein interactions and are often used in drug design, which usually neglects the potential of C-H...O hydrogen bonds. The 1.4 A resolution crystal structure of the ligand binding domain of the retinoic acid receptor RARgamma complexed with the retinoid SR11254 reveals several types of C-H...O hydrogen bonds. A striking example is the hydroxyl group of the ligand that acts as an H bond donor and acceptor, leading to a synergy between classical and C-H...O hydrogen bonds. This interaction introduces both specificity and affinity within the hydrophobic ligand pocket. The similarity of intraprotein and protein-ligand C-H...O interactions suggests that such bonds should be considered in rational drug design approaches.
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Affiliation(s)
- Bruno Klaholz
- Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 163, F-67404 Illkirch Cédex, France
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43
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Abstract
The nuclear receptor RXR is an obligate partner in many signal transduction pathways. We report the high-resolution structures of two complexes of the human RXRalpha ligand-binding domain specifically bound to two different and chemically unrelated agonist compounds: docosa hexaenoic acid, a natural derivative of eicosanoic acid, present in mammalian cells and recently identified as a potential endogenous RXR ligand in the mouse brain, and the synthetic ligand BMS 649. In both structures the RXR-ligand-binding domain forms homodimers and exhibits the active conformation previously observed with 9-cis-RA. Analysis of the differences in ligand-protein contacts (predominantly van der Waals forces) and binding cavity geometries and volumes for the several agonist-bound RXR structures clarifies the structural features important for ligand recognition. The L-shaped ligand-binding pocket adapts to the diverse ligands, especially at the level of residue N306, which might thus constitute a new target for drug-design. Despite its highest affinity 9-cis-RA displays the lowest number of ligand-protein contacts. These structural results support the idea that docosa hexaenoic acid and related fatty acids could be natural agonists of RXRs and question the real nature of the endogenous ligand(s) in mammalian cells.
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Affiliation(s)
- Pascal F Egea
- Laboratoire de Biologie et Génomique Structurales, Université Louis Pasteur, Parc d'Innovation BP163, 67404 Illkirch cedex, France
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44
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Matias PM, Carrondo MA, Coelho R, Thomaz M, Zhao XY, Wegg A, Crusius K, Egner U, Donner P. Structural basis for the glucocorticoid response in a mutant human androgen receptor (AR(ccr)) derived from an androgen-independent prostate cancer. J Med Chem 2002; 45:1439-46. [PMID: 11906285 DOI: 10.1021/jm011072j] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The crystal structure of a mutant androgen receptor (AR) ligand-binding domain (LBD) in complex with the agonist 9alpha-fluorocortisol has been determined at 1.95 A resolution. This mutant AR contains two mutations (L701H and T877A) and was previously reported as a high-affinity cortisol/cortisone responsive AR (AR(ccr)) isolated from the androgen-independent human prostate cancer cell lines MDA PCa 2a and 2b (Zhao et al. Nature Med. 2000, 6, 703-6). The three-dimensional structure of the AR(ccr) LBD complexed with 9alpha-fluorocortisol shows the typical conformation of an agonist-bound nuclear receptor in which helix 12 is precisely positioned as a "lid" for the ligand-binding pocket. Binding of 9alpha-fluorocortisol to the AR(ccr) involves favorable hydrogen bond patterns on the C17 and C21 substituents of the ligand due to the mutations at 701 and 877 in the AR(ccr). Our studies provide the first structural explanation for the glucocorticoid activation of AR(ccr), which is important for the development of new therapeutic treatments for androgen-independent prostate cancer.
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MESH Headings
- Algorithms
- Anti-Inflammatory Agents/chemistry
- Anti-Inflammatory Agents/pharmacology
- Crystallography, X-Ray
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/metabolism
- Fludrocortisone/chemistry
- Fludrocortisone/pharmacology
- Glucocorticoids/chemistry
- Glucocorticoids/metabolism
- Humans
- Hydrogen Bonding
- Ligands
- Male
- Models, Chemical
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutation
- Phenotype
- Prostatic Neoplasms/drug therapy
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Tumor Cells, Cultured
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Affiliation(s)
- Pedro M Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780 Oeiras, Portugal
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45
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Patel RN, Chu L, Chidambaram R, Zhu J, Kant J. Enantioselective microbial reduction of 2-oxo-2-(1′,2′,3′,4′-tetrahydro-1′,1′,4′,4′-tetramethyl-6′-naphthalenyl)acetic acid and its ethyl ester. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0957-4166(02)00109-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Peterson VJ, Barofsky E, Deinzer ML, Dawson MI, Feng KC, Zhang XK, Madduru MR, Leid M. Mass-spectrometric analysis of agonist-induced retinoic acid receptor gamma conformational change. Biochem J 2002; 362:173-81. [PMID: 11829754 PMCID: PMC1222374 DOI: 10.1042/0264-6021:3620173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Apo and holo forms of retinoic acid receptors, and other nuclear receptors, display differential sensitivity to proteolytic digestion that likely reflects the distinct conformational states of the free and liganded forms of the receptor. We have developed a method for rapid peptide mapping of holo-retinoic acid receptor gamma that utilizes matrix-assisted laser-desorption-ionization time-of-flight MS to identify peptide fragments that are derived from the partially proteolysed holo-receptor. The peptide maps of retinoic acid receptor gamma bound by four different agonists were identical, suggesting that all four ligands induced a similar conformational change within the ligand-binding domain of the receptor. In all cases, this agonist-induced conformational change promoted the direct association of retinoic acid receptor gamma with the transcriptional co-activator p300 and inhibited interaction of the receptor with the nuclear receptor co-repressor. SR11253, a compound previously reported to exert mixed retinoic acid receptor gamma agonist/antagonist activities in cultured cells, was found to bind directly to, but only weakly altered the protease-sensitivity of, the receptor and failed to promote interaction of the receptor with p300 or induce dissociation of receptor-nuclear receptor co-repressor complexes. This technique should be generally applicable to other members of the nuclear receptor superfamily that undergo an induced structural alteration upon agonist or antagonist binding, DNA binding and/or protein-protein interaction.
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Affiliation(s)
- Valerie J Peterson
- Laboratory of Molecular Pharmacology, Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, U.S.A
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47
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Egner U, Heinrich N, Ruff M, Gangloff M, Mueller-Fahrnow A, Wurtz JM. Different ligands-different receptor conformations: modeling of the hER alpha LBD in complex with agonists and antagonists. Med Res Rev 2001; 21:523-39. [PMID: 11607933 DOI: 10.1002/med.1024] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The aim of this study is to compare crystal structures of nuclear receptor ligand binding domains in complex with different agonists and partial agonists to achieve a better understanding of the three-dimensional structures and their ligand-induced conformational changes. This led to the identification of structurally conserved "rigid" regions and more flexible parts of the proteins. The analysis was found to be of great value in fitting selected non-steroidal compounds into the human estrogen receptor alpha (hER alpha) ligand binding pocket. The experimentally determined binding affinities for a number of 2-aryl indoles and 2-aryl indenones are in good agreement with the subsequently modeled binding interactions. To date, no crystal structure is published for a complex with a pure antagonist. We therefore used the available structural information on complexes with partial agonists and the crystal structure of a mutant protein in complex with estradiol displaying a similar conformation to predict binding interactions for antagonists. The results are discussed in detail.
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Affiliation(s)
- U Egner
- Research Laboratories of Schering AG, D-13342 Berlin, Germany
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48
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Wurtz JM, Moras D. Molecular determinants for agonist and antagonist binding to steroid nuclear receptors. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2001:167-80. [PMID: 11394044 DOI: 10.1007/978-3-662-04645-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Humans
- Models, Molecular
- Molecular Sequence Data
- Protein Conformation
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Steroid/agonists
- Receptors, Steroid/antagonists & inhibitors
- Receptors, Steroid/chemistry
- Receptors, Steroid/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
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Affiliation(s)
- J M Wurtz
- Laboratoire de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de France, 1 rue Laurent Fries BP 163, 67404 Illkrich Cedex, France
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Steinmetz AC, Renaud JP, Moras D. Binding of ligands and activation of transcription by nuclear receptors. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:329-59. [PMID: 11340063 DOI: 10.1146/annurev.biophys.30.1.329] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nuclear receptors (NRs) form a superfamily of ligand-inducible transcription factors composed of several domains. Recent structural studies focused on domain E, which harbors the ligand-binding site and the ligand-dependent transcription activation function AF-2. Structures of single representatives in an increasing number of various complexes as well as new structures of further NRs addressed issues such as discrimination of ligands, superagonism, isotype specificity, and partial agonism. Until today, one unique transcriptionally active form of domain E was determined; however, divergent tertiary structures of apo-forms and transcriptionally inactive forms are known. Thus, recent results link the transformation of NRs upon ligand binding to principles of protein folding. Furthermore, the ensemble of NR structures, including those of DNA-binding domains, provides one of the foundations for the understanding of interactions with transcription intermediary factors up to the characterization of the link between NR complexes and the basal transcriptional machinery at the structural level.
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Affiliation(s)
- A C Steinmetz
- Laboratoire de Biologie et Génomique Structurales, CNRS UPR 9004, Institut de Génétique et de Biologie Moléclaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France
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Goto S, Kogure K, Abe K, Kimata Y, Kitahama K, Yamashita E, Terada H. Efficient radical trapping at the surface and inside the phospholipid membrane is responsible for highly potent antiperoxidative activity of the carotenoid astaxanthin. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1512:251-8. [PMID: 11406102 DOI: 10.1016/s0005-2736(01)00326-1] [Citation(s) in RCA: 210] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The effects of the carotenoids beta-carotene and astaxanthin on the peroxidation of liposomes induced by ADP and Fe(2+) were examined. Both compounds inhibited production of lipid peroxides, astaxanthin being about 2-fold more effective than beta-carotene. The difference in the modes of destruction of the conjugated polyene chain between beta-carotene and astaxanthin suggested that the conjugated polyene moiety and terminal ring moieties of the more potent astaxanthin trapped radicals in the membrane and both at the membrane surface and in the membrane, respectively, whereas only the conjugated polyene chain of beta-carotene was responsible for radical trapping near the membrane surface and in the interior of the membrane. The efficient antioxidant activity of astaxanthin is suggested to be due to the unique structure of the terminal ring moiety.
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Affiliation(s)
- S Goto
- Faculty of Pharmaceutical Sciences, University of Tokushima, Japan.
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