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Frkic RL, Pederick JL, Horsfall AJ, Jovcevski B, Crame EE, Kowalczyk W, Pukala TL, Chang MR, Zheng J, Blayo AL, Abell AD, Kamenecka TM, Harbort JS, Harmer JR, Griffin PR, Bruning JB. PPARγ Corepression Involves Alternate Ligand Conformation and Inflation of H12 Ensembles. ACS Chem Biol 2023; 18:1115-1123. [PMID: 37146157 DOI: 10.1021/acschembio.2c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Inverse agonists of peroxisome proliferator activated receptor γ (PPARγ) have emerged as safer alternatives to full agonists for their reduced side effects while still maintaining impressive insulin-sensitizing properties. To shed light on their molecular mechanism, we characterized the interaction of the PPARγ ligand binding domain with SR10221. X-ray crystallography revealed a novel binding mode of SR10221 in the presence of a transcriptionally repressing corepressor peptide, resulting in much greater destabilization of the activation helix, H12, than without corepressor peptide. Electron paramagnetic resonance provided in-solution complementary protein dynamic data, which revealed that for SR10221-bound PPARγ, H12 adopts a plethora of conformations in the presence of corepressor peptide. Together, this provides the first direct evidence for corepressor-driven ligand conformation for PPARγ and will allow the development of safer and more effective insulin sensitizers suitable for clinical use.
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Affiliation(s)
- Rebecca L Frkic
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Aimee J Horsfall
- ARC Centre of Excellence for Nanoscale Biophotonics, The Institute for Photonics and Advanced Sensing, and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elise E Crame
- Discipline of Physiology, School of Biomedicine, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Tara L Pukala
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mi Ra Chang
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Jie Zheng
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Anne-Laure Blayo
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale Biophotonics, The Institute for Photonics and Advanced Sensing, and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Joshua S Harbort
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - John B Bruning
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Gangadhariah M, Pardhi T, Ravilla J, Chandra S, Singh SA. Citrus nutraceutical eriocitrin and its metabolites are partial agonists of peroxisome proliferator-activated receptor gamma (PPARγ): a molecular docking and molecular dynamics study. J Biomol Struct Dyn 2022; 41:11373-11393. [PMID: 36576222 DOI: 10.1080/07391102.2022.2162127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) agonists are potent insulin sensitizers in treating type 2 diabetes. Despite being very effective in the fight against diabetes-mediated complications, PPARγ agonists are accompanied by severe side effects leading to complicated health problems, making the discovery of novel safe ligands highly pertinent. A significant intense research effort is in progress to explore the PPARγ activating potential of a wide range of natural compounds. Lemon (Citrus limon) contains various bioactive flavonoids, and eriocitrin is the major flavonoid. It possesses substantial antioxidant and anticancer, lipid-lowering activities and prevents obesity-associated metabolic diseases. Eriocitrin is metabolized to eriodictyol in the intestine, and the absorbed eriodictyol undergoes conversion to numerous metabolites in vivo. It is unclear if eriocitrin or its metabolites are responsible for their beneficial effects. We have used molecular docking, ADMET properties, drug-likeness score and molecular dynamics simulation study to find if eriocitrin and its metabolites are potent binders for PPARγ. Docking studies revealed that eriocitrin binds to PPARγ with the highest binding energy, but ADMET properties and in vivo studies show that the bioavailability of eriocitrin is very poor. Molecular dynamics studies were carried out to validate the docking results, and multiple parameters like RMSD, RMSF, Radius of gyration, SASA, hydrogen bond analysis, interaction energy, principal component analysis, Gibbs free energy and MM-PBSA were calculated. Based on our studies, eriodictyol, eriodictyol 7-O-glucuronide, eriodictyol 3'-O-glucuronide, homoeriodictyol and homoeriodictyol 7-O-glucuronide which are metabolites of eriocitrin appear to be potent partial agonists of PPARγ under physiological conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahesha Gangadhariah
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, India
| | - Triveni Pardhi
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland, OH, USA
| | - Jahnavi Ravilla
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory Department of Botany, Soban Singh Jeena University S.S.J. Campus, Almora, Uttarakhand, India
| | - Sridevi Annapurna Singh
- Department of Traditional Foods and Applied Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, India
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Frkic RL, Richter K, Bruning JB. The therapeutic potential of inhibiting PPARγ phosphorylation to treat type 2 diabetes. J Biol Chem 2021; 297:101030. [PMID: 34339734 PMCID: PMC8387755 DOI: 10.1016/j.jbc.2021.101030] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
A promising approach for treating type 2 diabetes mellitus (T2DM) is to target the Peroxisome Proliferator-Activated Receptor γ (PPARγ) transcription factor, which regulates the expression of proteins critical for T2DM. Mechanisms involved in PPARγ signaling are poorly understood, yet globally increasing T2DM prevalence demands improvements in drug design. Synthetic, nonactivating PPARγ ligands can abolish the phosphorylation of PPARγ at Ser273, a posttranslational modification correlated with obesity and insulin resistance. It is not understood how these ligands prevent phosphorylation, and the lack of experimental mechanistic information can be attributed to previous ambiguity in the field as well as to limitations in experimental approaches; in silico modeling currently provides the only insight into how ligands block Ser273 phosphorylation. The future availability of experimental evidence is critical for clarifying the mechanism by which ligands prevent phosphorylation and should be the priority of future T2DM-focused research. Following this, the properties of ligands that enable them to block phosphorylation can be improved upon to generate ligands tailored for blocking phosphorylation and therefore restoring insulin sensitivity. This would represent a significant step forward for treating T2DM. This review summarizes current knowledge of the roles of PPARγ in T2DM as well as the effects of synthetic ligands on the modulation of these roles. We hypothesize potential factors that contribute to the reduction in recent developments and summarize what has currently been done to shed light on this critical field of research.
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Affiliation(s)
- Rebecca L Frkic
- The Institute for Photonics and Advanced Sensing, and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Katharina Richter
- Richter Lab, Department of Surgery, Basil Hetzel Institute for Translational Health Research, The University of Adelaide, Adelaide, South Australia, Australia
| | - John B Bruning
- The Institute for Photonics and Advanced Sensing, and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
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Mai CT, Zheng DC, Li XZ, Zhou H, Xie Y. Liver X receptors conserve the therapeutic target potential for the treatment of rheumatoid arthritis. Pharmacol Res 2021; 170:105747. [PMID: 34186192 DOI: 10.1016/j.phrs.2021.105747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic multi-system autoimmune disease with extremely complex pathogenesis. Significantly altered lipid paradox related to the inflammatory burden is reported in RA patients, inducing 50% higher cardiovascular risks. Recent studies have also demonstrated that lipid metabolism can regulate many functions of immune cells in which metabolic pathways have altered. The nuclear liver X receptors (LXRs), including LXRα and LXRβ, play a central role in regulating lipid homeostasis and inflammatory responses. Undoubtedly, LXRs have been considered as an attractive therapeutic target for the treatment of RA. However, there are some contradictory effects of LXRs agonists observed in previous animal studies where both pro-inflammatory role and anti-inflammatory role were revealed for LXRs activation in RA. Therefore, in addition to updating the knowledge of LXRs as the prominent regulators of lipid homeostasis, the purpose of this review is to summarize the effects of LXRs agonists in RA-associated immune cells, to explore the underlying reasons for the contradictory therapeutic effects of LXRs agonists observed in RA animal models, and to discuss future strategy for the treatment of RA with LXRs modulators.
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Affiliation(s)
- Chu-Tian Mai
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau; Faculty of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - De-Chong Zheng
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau; Faculty of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Xin-Zhi Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau; Faculty of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Ying Xie
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau.
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Guillemot-Legris O, Muccioli GG. The oxysterome and its receptors as pharmacological targets in inflammatory diseases. Br J Pharmacol 2021; 179:4917-4940. [PMID: 33817775 DOI: 10.1111/bph.15479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Oxysterols have gained attention over the last decades and are now considered as fully fledged bioactive lipids. The study of their levels in several conditions, including atherosclerosis, obesity and neurodegenerative diseases, led to a better understanding of their involvement in (patho)physiological processes such as inflammation and immunity. For instance, the characterization of the cholesterol-7α,25-dihydroxycholesterol/GPR183 axis and its implication in immunity represents an important step in the oxysterome study. Besides this axis, others were identified as important in several inflammatory pathologies (such as colitis, lung inflammation and atherosclerosis). However, the oxysterome is a complex system notably due to a redundancy of metabolic enzymes and a wide range of receptors. Indeed, deciphering oxysterol roles and identifying the potential receptor(s) involved in a given pathology remain challenging. Oxysterol properties are very diverse, but most of them could be connected by a common component: inflammation. Here, we review the implication of oxysterol receptors in inflammatory diseases.
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Affiliation(s)
- Owein Guillemot-Legris
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Giulio G Muccioli
- Bioanalysis and Pharmacology of Bioactive Lipids Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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Schierle S, Chaikuad A, Lillich FF, Ni X, Woltersdorf S, Schallmayer E, Renelt B, Ronchetti R, Knapp S, Proschak E, Merk D. Oxaprozin Analogues as Selective RXR Agonists with Superior Properties and Pharmacokinetics. J Med Chem 2021; 64:5123-5136. [PMID: 33793232 DOI: 10.1021/acs.jmedchem.1c00235] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The retinoid X receptors (RXR) are ligand-activated transcription factors involved in multiple regulatory networks as universal heterodimer partners for nuclear receptors. Despite their high therapeutic potential in many pathologies, targeting of RXR has only been exploited in cancer treatment as the currently available RXR agonists suffer from exceptional lipophilicity, poor pharmacokinetics (PK), and adverse effects. Aiming to overcome the limitations and to provide improved RXR ligands, we developed a new potent RXR ligand chemotype based on the nonsteroidal anti-inflammatory drug oxaprozin. Systematic structure-activity relationship analysis enabled structural optimization toward low nanomolar potency similar to the well-established rexinoids. Cocrystal structures of the most active derivatives demonstrated orthosteric binding, and in vivo profiling revealed superior PK properties compared to current RXR agonists. The optimized compounds were highly selective for RXR activation and induced RXR-regulated gene expression in native cellular and in vivo settings suggesting them as excellent chemical tools to further explore the therapeutic potential of RXR.
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Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.,Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Felix F Lillich
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.,Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Stefano Woltersdorf
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Espen Schallmayer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Beatrice Renelt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Riccardo Ronchetti
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany.,Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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Sun N, Guo H, Wang Y. Retinoic acid receptor-related orphan receptor gamma-t (RORγt) inhibitors in clinical development for the treatment of autoimmune diseases: a patent review (2016-present). Expert Opin Ther Pat 2019; 29:663-674. [DOI: 10.1080/13543776.2019.1655541] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nannan Sun
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Huimin Guo
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
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3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns. Int J Mol Sci 2019; 20:ijms20133174. [PMID: 31261733 PMCID: PMC6651053 DOI: 10.3390/ijms20133174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/25/2023] Open
Abstract
Discovering conserved three-dimensional (3D) patterns among protein structures may provide valuable insights into protein classification, functional annotations or the rational design of multi-target drugs. Thus, several computational tools have been developed to discover and compare protein 3D-patterns. However, most of them only consider previously known 3D-patterns such as orthosteric binding sites or structural motifs. This fact makes necessary the development of new methods for the identification of all possible 3D-patterns that exist in protein structures (allosteric sites, enzyme-cofactor interaction motifs, among others). In this work, we present 3D-PP, a new free access web server for the discovery and recognition all similar 3D amino acid patterns among a set of proteins structures (independent of their sequence similarity). This new tool does not require any previous structural knowledge about ligands, and all data are organized in a high-performance graph database. The input can be a text file with the PDB access codes or a zip file of PDB coordinates regardless of the origin of the structural data: X-ray crystallographic experiments or in silico homology modeling. The results are presented as lists of sequence patterns that can be further analyzed within the web page. We tested the accuracy and suitability of 3D-PP using two sets of proteins coming from the Protein Data Bank: (a) Zinc finger containing and (b) Serotonin target proteins. We also evaluated its usefulness for the discovering of new 3D-patterns, using a set of protein structures coming from in silico homology modeling methodologies, all of which are overexpressed in different types of cancer. Results indicate that 3D-PP is a reliable, flexible and friendly-user tool to identify conserved structural motifs, which could be relevant to improve the knowledge about protein function or classification. The web server can be freely utilized at https://appsbio.utalca.cl/3d-pp/.
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