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Hazarika S, Yu T, Biswas A, Dube N, Villalona P, Okafor CD. Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579785. [PMID: 38405809 PMCID: PMC10888817 DOI: 10.1101/2024.02.10.579785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (> 10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein-protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full length nuclear receptors.
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Affiliation(s)
- Saurov Hazarika
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tracy Yu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Arumay Biswas
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Namita Dube
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Priscilla Villalona
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - C. Denise Okafor
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
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Hazarika S, Fehrle M, Okafor CD. How nuclear receptors transition between active and inactive forms: An energetic perspective. J Chem Phys 2024; 160:115102. [PMID: 38501469 DOI: 10.1063/5.0189234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Nuclear receptors regulate transcriptional programs in response to the binding of natural and synthetic ligands. These ligands modulate the receptor by inducing dynamic changes in the ligand binding domain that shift the C-terminal helix (H12) between active and inactive conformations. Despite decades of study, many questions persist regarding the nature of the inactive state and how ligands shift receptors between different states. Here, we use molecular dynamics (MD) simulations to investigate the timescale and energetic landscape of the conformational transition between inactive and active forms of progesterone receptor (PR) bound to a partial agonist. We observe that the microsecond timescale is insufficient to observe any transitions; only at millisecond timescales achieved via accelerated MD simulations do we find the inactive PR switches to the active state. Energetic analysis reveals that both active and inactive PR states represent energy minima separated by a barrier that can be traversed. In contrast, little or no transition is observed between active and inactive states when an agonist or antagonist is bound, confirming that ligand identity plays a key role in defining the energy landscape of nuclear receptor conformations.
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Affiliation(s)
- Saurov Hazarika
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Matthew Fehrle
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - C Denise Okafor
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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3
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Irani S, Tan W, Li Q, Toy W, Jones C, Gadiya M, Marra A, Katzenellenbogen JA, Carlson KE, Katzenellenbogen BS, Karimi M, Segu Rajappachetty R, Del Priore IS, Reis-Filho JS, Shen Y, Chandarlapaty S. Somatic estrogen receptor α mutations that induce dimerization promote receptor activity and breast cancer proliferation. J Clin Invest 2024; 134:e163242. [PMID: 37883178 PMCID: PMC10760953 DOI: 10.1172/jci163242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
Physiologic activation of estrogen receptor α (ERα) is mediated by estradiol (E2) binding in the ligand-binding pocket of the receptor, repositioning helix 12 (H12) to facilitate binding of coactivator proteins in the unoccupied coactivator binding groove. In breast cancer, activation of ERα is often observed through point mutations that lead to the same H12 repositioning in the absence of E2. Through expanded genetic sequencing of breast cancer patients, we identified a collection of mutations located far from H12 but nonetheless capable of promoting E2-independent transcription and breast cancer cell growth. Using machine learning and computational structure analyses, this set of mutants was inferred to act distinctly from the H12-repositioning mutants and instead was associated with conformational changes across the ERα dimer interface. Through both in vitro and in-cell assays of full-length ERα protein and isolated ligand-binding domain, we found that these mutants promoted ERα dimerization, stability, and nuclear localization. Point mutations that selectively disrupted dimerization abrogated E2-independent transcriptional activity of these dimer-promoting mutants. The results reveal a distinct mechanism for activation of ERα function through enforced receptor dimerization and suggest dimer disruption as a potential therapeutic strategy to treat ER-dependent cancers.
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Affiliation(s)
- Seema Irani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wuwei Tan
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Qing Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Weiyi Toy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Catherine Jones
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mayur Gadiya
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio Marra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John A. Katzenellenbogen
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathryn E. Carlson
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Benita S. Katzenellenbogen
- Department of Chemistry and Molecular and Integrative Physiology, and the Cancer Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Ramya Segu Rajappachetty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Isabella S. Del Priore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
- Department of Computer Science and Engineering and
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
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4
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Khan SH, Braet SM, Koehler SJ, Elacqua E, Anand GS, Okafor CD. Ligand-induced shifts in conformational ensembles that describe transcriptional activation. eLife 2022; 11:80140. [PMID: 36222302 PMCID: PMC9555869 DOI: 10.7554/elife.80140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
Nuclear receptors function as ligand-regulated transcription factors whose ability to regulate diverse physiological processes is closely linked with conformational changes induced upon ligand binding. Understanding how conformational populations of nuclear receptors are shifted by various ligands could illuminate strategies for the design of synthetic modulators to regulate specific transcriptional programs. Here, we investigate ligand-induced conformational changes using a reconstructed, ancestral nuclear receptor. By making substitutions at a key position, we engineer receptor variants with altered ligand specificities. We combine cellular and biophysical experiments to characterize transcriptional activity, as well as elucidate mechanisms underlying altered transcription in receptor variants. We then use atomistic molecular dynamics (MD) simulations with enhanced sampling to generate ensembles of wildtype and engineered receptors in combination with multiple ligands, followed by conformational analysis and correlation of MD-based predictions with functional ligand profiles. We determine that conformational ensembles accurately describe ligand responses based on observed population shifts. These studies provide a platform which will allow structural characterization of physiologically-relevant conformational ensembles, as well as provide the ability to design and predict transcriptional responses in novel ligands.
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Affiliation(s)
- Sabab Hasan Khan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
| | - Sean M Braet
- Department of Chemistry, Pennsylvania State University
| | | | | | | | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
- Department of Chemistry, Pennsylvania State University
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5
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Sinyani A, Idowu K, Shunmugam L, Kumalo HM, Khan R. A molecular dynamics perspective into estrogen receptor inhibition by selective flavonoids as alternative therapeutic options. J Biomol Struct Dyn 2022; 41:4093-4105. [PMID: 35477414 DOI: 10.1080/07391102.2022.2062786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Zearalenone is an estrogenic mycotoxin which is a common food contaminant and has been implicated in increasing the incidence of carcinogenesis and other reproductive health ailments through the estrogen receptor alpha (ERα) pathway. Competitive ERα blockers such as 4-Hydroxytamoxifen (OHT), are synthetic FDA approved drugs which, albeit being an effective anticancer agent, induces life altering side effects. For this reason, there is an increased interest in the use of naturally occurring medicinal plant products such as flavonoids. This study aimed to identity flavonoid ERα inhibitors and provide insights into the mechanism of inhibition using computational techniques. The Molecular Mechanics/Generalized Born Surface Area calculations revealed that quercetrin, hesperidin, epigallocatechin 3-gallate and kaempferol 7-O-glucoside out of 14 flavonoids had higher binding affinity for ERα than OHT. The structural analysis revealed that the binding of the compounds to the receptor lead to dynamic alterations, which induced conformational shift in the structure and orientation of the receptor resulting in stabilised, compact and low energy systems. The results of this study provide imperative information that supports the use of flavonoids in the inhibition of ERα to prevent or ameliorate the consequential adverse effects associated with zearalenone exposure.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Angela Sinyani
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kehinde Idowu
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP)/Genomics Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Letitia Shunmugam
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel Mathambo Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rene Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Zhang F, Chen X, Chen J, Xu Y, Li S, Guo Y, Pu X. Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation. J Chem Inf Model 2021; 62:5120-5135. [PMID: 34779608 DOI: 10.1021/acs.jcim.1c00650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The residue located at 15 positions before the most conserved residue in TM7 (7.35 of Ballesteros-Weinstein number) plays important roles in ligand binding and the receptor activity for class A GPCRs. Nevertheless, its regulation mechanism has not been clearly clarified in experiments, and some controversies also exist for its impact on μ-opioid receptors (μOR) bound by agonists. Thus, we chose the μ-opioid receptor (μOR) of class A GPCRs as a representative and utilized a microsecond accelerated molecular dynamics simulation (aMD) coupled with a protein structure network (PSN) to explore the effect of W3187.35 on its functional activity induced by the agonist endomorphin2 mainly by a comparison of the wild system and its W7.35A mutant. When endomorphin2 binds to the wild-type μOR, TM6 in μOR moves outward to form an open intracellular conformation that is beneficial to accommodating the β-arrestin transducer, rather than the G-protein transducer due to the clash with the α5 helix of G-protein, thus acting as a β-arrestin biased agonist. However, the W318A mutation induces the intracellular part of μOR to form a closed state, which disfavors coupling with either G-protein or β-arrestin. The allosteric pathway analysis further reveals that the binding of endomorphin2 to the wild-type μOR transmits more activation signals to the β-arrestin binding site while the W318A mutation induces more structural signals to transmit to common binding residues of the G protein and β-arrestin. More interestingly, the residue at the 7.35 position regulates the shortest allosteric pathway in indirect ways by influencing the interactions between other ligand-binding residues and endomorphin2. W2936.48 and F2896.44 are important for regulating the different activities of μOR induced either by the agonist or by the mutation. Y3367.53, F3438.50, and D3408.47 play crucial roles in activating the β-arrestin biased signal induced by the agonist endomorphin2, while L1583.43 and V2866.41 devote important contributions to the change in the activity of endomorphin2 from the β-arrestin biased agonist to the antagonist upon the W318A mutation.
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Affiliation(s)
- Fuhui Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yanjiani Xu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shiqi Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China
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Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations. Int J Mol Sci 2021; 22:ijms22179371. [PMID: 34502280 PMCID: PMC8431471 DOI: 10.3390/ijms22179371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.
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Marroqui L, Martinez-Pinna J, Castellano-Muñoz M, Dos Santos RS, Medina-Gali RM, Soriano S, Quesada I, Gustafsson JA, Encinar JA, Nadal A. Bisphenol-S and Bisphenol-F alter mouse pancreatic β-cell ion channel expression and activity and insulin release through an estrogen receptor ERβ mediated pathway. CHEMOSPHERE 2021; 265:129051. [PMID: 33250229 DOI: 10.1016/j.chemosphere.2020.129051] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Bisphenol-S (BPS) and Bisphenol-F (BPF) are current Bisphenol-A (BPA) substitutes. Here we used pancreatic β-cells from wild type (WT) and estrogen receptor β (ERβ) knockout (BERKO) mice to investigate the effects of BPS and BPF on insulin secretion, and the expression and activity of ion channels involved in β-cell function. BPS or BPF rapidly increased insulin release and diminished ATP-sensitive K+ (KATP) channel activity. Similarly, 48 h treatment with BPS or BPF enhanced insulin release and decreased the expression of several ion channel subunits in β-cells from WT mice, yet no effects were observed in cells from BERKO mice. PaPE-1, a ligand designed to preferentially trigger extranuclear-initiated ER pathways, mimicked the effects of bisphenols, suggesting the involvement of extranuclear-initiated ERβ pathways. Molecular dynamics simulations indicated differences in ERβ ligand-binding domain dimer stabilization and solvation free energy among different bisphenols and PaPE-1. Our data suggest a mode of action involving ERβ whose activation alters three key cellular events in β-cell, namely ion channel expression and activity, and insulin release. These results may help to improve the hazard identification of bisphenols.
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Affiliation(s)
- Laura Marroqui
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Juan Martinez-Pinna
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Manuel Castellano-Muñoz
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Reinaldo S Dos Santos
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Regla M Medina-Gali
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Sergi Soriano
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Ivan Quesada
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain
| | - Jan-Ake Gustafsson
- Department of Cell Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, USA; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - José A Encinar
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain
| | - Angel Nadal
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain.
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9
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Pokhrel R, Tang T, Holub JM. Monitoring ligand-mediated helix 12 transitions within the human estrogen receptor α using bipartite tetracysteine display. Org Biomol Chem 2020; 18:6063-6071. [PMID: 32724950 DOI: 10.1039/d0ob01234c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Estrogen receptor α ligand-binding domains (ERα-LBD) expressing tetracysteine motifs bind FlAsH-EDT2 upon transition of helix 12 (H12) to a folded state. Changes in fluorescence intensity allowed surveillance of ligand-mediated H12 transitions and facilitated the determination of FlAsH association rates (kon) and apparent equilibrium dissociation constants (Kapp) to ERα-LBDs in the presence of estrogenic ligands.
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Affiliation(s)
- Ranju Pokhrel
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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10
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Rewiring Ancient Residue Interaction Networks Drove the Evolution of Specificity in Steroid Receptors. Structure 2020; 28:196-205.e3. [DOI: 10.1016/j.str.2019.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
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11
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Shtaiwi A, Adnan R, Khairuddean M, Khan SU. Computational investigations of the binding mechanism of novel benzophenone imine inhibitors for the treatment of breast cancer. RSC Adv 2019; 9:35401-35416. [PMID: 35541022 PMCID: PMC9082406 DOI: 10.1039/c9ra04759j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/10/2019] [Indexed: 12/31/2022] Open
Abstract
4-Hydroxytamoxifen (4-OHT), the most common hormone used for the treatment of breast cancer, is a selective estrogen receptor modulator (SERM) inhibitor that acts as an antagonist in breast tissue and a partial agonist in the endometrium. However, the detailed molecular mechanism of 4-OHT structure modification has not been well investigated to date. Herein, molecular docking, molecular dynamics simulations and free energy calculations were performed to explore the mechanisms of the molecular interactions between newly designed benzophenone imines (BIs) and the three forms apo, antagonist and agonist of the human estrogen receptor hERα. The proposed inhibitors were designed by replacing the triarylethylene estrogenic scaffold found in 4-OHT with Schiff base triarylimine derivatives. The antiestrogen scaffold i.e. the O-alkyl side chain in 4-OHT was developed by incorporating an alanine amino acid side chain functionality into the triarylimine scaffold. Docking results reveal that the newly designed BIs bind to the hydrophobic open pocket of the apo and antagonist hERα conformations with higher affinity as compared to the natural and synthetic estrogen estradiol (E2) and 4-OHT. The analysis of the molecular dynamics simulation results based on six different systems of the best docked BI (5c) with hERα receptors demonstrates stable interactions, and the complex undergoes fewer conformational fluctuations in the open apo/antagonist hERα receptors as compared to the case of the closed agonist. In addition, the calculated binding free energies indicate that the main factor that contributes to the stabilization of the receptor-inhibitor complexes is hydrophobic interactions. This study suggests that the development of these Schiff base derivatives may be worth exploring for the preparation of new 4-OHT analogues.
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Affiliation(s)
- Amneh Shtaiwi
- School of Pharmacy, Middle East University Queen Alia Airport Street 11118 Amman Jordan
- School of Chemical Sciences, Universiti Sains Malaysia 11800 Penang Malaysia +6046533262
| | - Rohana Adnan
- School of Chemical Sciences, Universiti Sains Malaysia 11800 Penang Malaysia +6046533262
| | - Melati Khairuddean
- School of Chemical Sciences, Universiti Sains Malaysia 11800 Penang Malaysia +6046533262
| | - Shafi Ullah Khan
- School of Pharmacy, Monash University Malaysia Jalan Lagoon Selatan, Bandar Sunway 47500 Subang Jaya Malaysia
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12
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Cao H, Wang L, Cao M, Ye T, Sun Y. Computational insights on agonist and antagonist mechanisms of estrogen receptor α induced by bisphenol A analogues. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:536-545. [PMID: 30831350 DOI: 10.1016/j.envpol.2019.02.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Structural analogues of bisphenol A (BPA) have become widely used as alternatives in BPA-free products. Most toxicological investigations have focused on the estrogenic activities of these analogues, which have been considered as potential environmental estrogens. However, recent studies revealed that certain BPA analogues could dramatically inhibit the proliferation of breast cancer cells, and exhibited strong anti-estrogenic effects compared with the antagonist 4-hydroxytamoxifen (OHT). Thus, we adopted computational models combining molecular dynamics simulations and binding free energy calculations to explore the underlying molecular basis of BPA analogues binding to estrogen receptor α (ERα). We also evaluated ligand-induced structural rearrangements of ERα at the atomic level. Conformational analyses showed that induced-fit H-bonding recognition by Thr347 was an important factor distinguishing antagonist from agonist BPA analogues. Moreover, antagonists of BPA analogues could indirectly induce the structural reposition of key helix 12 and produce an antagonistic conformation of ERα. Compared with OHT, the binding affinity of BPA analogues is stronger for antagonists than agonists. Taken together, we therefore propose computational indicators for screening of anti-estrogenic activities of BPA analogues, which may be beneficial for predicting the estrogenic or anti-estrogenic effects of BPA alternatives.
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Affiliation(s)
- Huiming Cao
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056, China; Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Ling Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056, China; Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Mengxi Cao
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056, China; Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Tong Ye
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056, China; Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Yuzhen Sun
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056, China; Institute of Environment and Health, Jianghan University, Wuhan, 430056, China.
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13
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Okafor CD, Colucci JK, Ortlund EA. Ligand-Induced Allosteric Effects Governing SR Signaling. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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14
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Adhikari S, Daftardar S, Fratev F, Rivera M, Sirimulla S, Alexander K, Boddu SH. Elucidation of the orientation of selected drugs with 2-hydroxylpropyl-β-cyclodextrin using 2D-NMR spectroscopy and molecular modeling. Int J Pharm 2018; 545:357-365. [DOI: 10.1016/j.ijpharm.2018.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 01/30/2023]
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15
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Molecular dynamics simulation of human estrogen receptor free and bound to morpholine ether benzophenone inhibitor. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2277-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Fratev F, Steinbrecher T, Jónsdóttir SÓ. Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies. ACS OMEGA 2018; 3:4357-4371. [PMID: 31458661 PMCID: PMC6641415 DOI: 10.1021/acsomega.8b00123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/04/2018] [Indexed: 05/30/2023]
Abstract
Estimating the correct binding modes of ligands in protein-ligand complexes is crucial not only in the drug discovery process but also for elucidating potential toxicity mechanisms. In the current paper, we propose a computational modeling workflow using the combination of docking, classical molecular dynamics (cMD), accelerated molecular dynamics (aMD) and free-energy perturbation (FEP+ protocol) for identification of possible ligand binding modes. It was applied for investigation of selected perfluorocarboxyl acids (PFCAs) in the PPARγ nuclear receptor. Although both regular and induced fit docking failed to reproduce the experimentally determined binding mode of the ligands when docked into a non-native X-ray structure, cMD and aMD simulations successfully identified the most probable binding conformations. Moreover, multiple binding modes were identified for all of these compounds and the shorter-chain PFCAs continuously moved between a few energetically favorable binding conformations. On the basis of MD predictions of binding conformations, we applied the default and also redesigned FEP+ sampling protocols, which accurately reproduced experimental differences in the binding energies. Thus, the preliminary MD simulations can also provide helpful information about correct setup of the FEP+ calculations. These results show that the PFCA binding modes were accurately predicted and that the FEP+ protocol can be used to estimate free energies of binding of flexible ligands that are not typical druglike compounds. Our in silico workflow revealed the specific ligand-residue interactions within the ligand binding domain and the main characteristics of the PFCAs, and it was concluded that these compounds are week PPARγ partial agonists. This work also suggests a common pipeline for identification of ligand binding modes, ligand-protein dynamics description, and relative free-energy calculations.
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Affiliation(s)
- Filip Fratev
- Department
of Pharmaceutical Sciences, School of Pharmacy, The University of Texas at El Paso, 1101 N Campbell Street, El Paso, Texas 79902, United
States
- Micar21
Ltd., Persenk 34B, 1407 Sofia, Bulgaria
| | - Thomas Steinbrecher
- Schrödinger
GmbH, Dynamostrasse 13, 68165 Mannheim, Baden-Württemberg, Germany
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17
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Pavlin M, Spinello A, Pennati M, Zaffaroni N, Gobbi S, Bisi A, Colombo G, Magistrato A. A Computational Assay of Estrogen Receptor α Antagonists Reveals the Key Common Structural Traits of Drugs Effectively Fighting Refractory Breast Cancers. Sci Rep 2018; 8:649. [PMID: 29330437 PMCID: PMC5766519 DOI: 10.1038/s41598-017-17364-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/20/2017] [Indexed: 01/14/2023] Open
Abstract
Somatic mutations of the Estrogen Receptor α (ERα) occur with an up to 40% incidence in ER sensitive breast cancer (BC) patients undergoing prolonged endocrine treatments. These polymorphisms are implicated in acquired resistance, disease relapse, and increased mortality rates, hence representing a current major clinical challenge. Here, multi-microseconds (12.5 µs) molecular dynamics simulations revealed that recurrent ERα polymorphisms (i. e. L536Q, Y537S, Y537N, D538G) (mERα) are constitutively active in their apo form and that they prompt the selection of an agonist (active)-like conformation even upon antagonists binding. Interestingly, our simulations rationalize, for the first time, the efficacy profile of (pre)clinically used Selective Estrogen Receptor Modulators/Downregulators (SERMs/SERDs) against these variants, enlightening, at atomistic level of detail, the key common structural traits needed by drugs able to effectively fight refractory BC types. This knowledge represents a key advancement for mechanism-based therapeutics targeting resistant ERα isoforms, potentially allowing the community to move a step closer to ‘precision medicine’ calibrated on patients’ genetic profiles and disease progression.
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Affiliation(s)
- Matic Pavlin
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Angelo Spinello
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy
| | - Marzia Pennati
- Fondazione IRCSS Istituto Nazionale dei Tumori, via Amadeo 42, 20113, Milano, Italy
| | - Nadia Zaffaroni
- Fondazione IRCSS Istituto Nazionale dei Tumori, via Amadeo 42, 20113, Milano, Italy
| | - Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, via Belmeloro 6, 40126, Bologna, Italy
| | | | - Alessandra Magistrato
- CNR-IOM-Democritos c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
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18
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Souza PCT, Textor LC, Melo DC, Nascimento AS, Skaf MS, Polikarpov I. An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position. Sci Rep 2017; 7:3509. [PMID: 28615710 PMCID: PMC5471280 DOI: 10.1038/s41598-017-03774-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/12/2017] [Indexed: 02/04/2023] Open
Abstract
The natural ligand 17β-estradiol (E2) is so far believed to induce a unique agonist-bound active conformation in the ligand binding domain (LBD) of the estrogen receptors (ERs). Both subtypes, ERα and ERβ, are transcriptionally activated in the presence of E2 with ERβ being somewhat less active than ERα under similar conditions. The molecular bases for this intriguing behavior are mainly attributed to subtype differences in the amino-terminal domain of these receptors. However, structural details that confer differences in the molecular response of ER LBDs to E2 still remain elusive. In this study, we present a new crystallographic structure of the ERβ LBD bound to E2 in which H12 assumes an alternative conformation that resembles antagonist ERs structures. Structural observations and molecular dynamics simulations jointly provide evidence that alternative ERβ H12 position could correspond to a stable conformation of the receptor under physiological pH conditions. Our findings shed light on the unexpected role of LBD in the lower functional response of ERβ subtype.
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Affiliation(s)
- Paulo C T Souza
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box, 6154, Campinas, SP, Brazil.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Larissa C Textor
- São Carlos Institute of Physics, University of São Paulo - USP, P.O. Box 396, São Carlos, SP, Brazil
| | - Denise C Melo
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box, 6154, Campinas, SP, Brazil
| | - Alessandro S Nascimento
- São Carlos Institute of Physics, University of São Paulo - USP, P.O. Box 396, São Carlos, SP, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box, 6154, Campinas, SP, Brazil.
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo - USP, P.O. Box 396, São Carlos, SP, Brazil.
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19
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Fratev F. PPARγ non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study. J Biomol Struct Dyn 2016; 35:476-485. [DOI: 10.1080/07391102.2016.1151830] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Filip Fratev
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
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20
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Abstract
PPARγ activation helix 12 can exist in an antagonist form: evidence from high-throughput accelerated molecular dynamics and metadynamics.
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Affiliation(s)
- Filip Fratev
- Institute of Biophysics and Biomedical Engineering
- Bulgarian Academy of Sciences
- Block 105
- Bulgaria
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21
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Li F, Sun X, Cai Y, Fan D, Li W, Tang Y, Liu G. Computational investigation of the interaction mechanism between the estrogen related receptor α and its agonists. RSC Adv 2016. [DOI: 10.1039/c6ra19536a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The agonists may promote the binding of coactivator PGC-1α to ERRα by stabilizing the conformation and the site of H12.
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Affiliation(s)
- Fuxing Li
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Xianqiang Sun
- Department of Biochemistry & Molecular Biophysics
- Washington University School of Medicine
- St. Louis
- USA
| | - Yingchun Cai
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Defang Fan
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
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22
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Batista MRB, Martínez L. Conformational Diversity of the Helix 12 of the Ligand Binding Domain of PPARγ and Functional Implications. J Phys Chem B 2015; 119:15418-29. [DOI: 10.1021/acs.jpcb.5b09824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mariana R. B. Batista
- Department of Physical Chemistry,
Institute of Chemistry, University of Campinas, CP 6154-13083-970, Campinas, SP Brazil
| | - Leandro Martínez
- Department of Physical Chemistry,
Institute of Chemistry, University of Campinas, CP 6154-13083-970, Campinas, SP Brazil
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23
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Fratev F, Tsakovska I, Al Sharif M, Mihaylova E, Pajeva I. Structural and Dynamical Insight into PPARγ Antagonism: In Silico Study of the Ligand-Receptor Interactions of Non-Covalent Antagonists. Int J Mol Sci 2015; 16:15405-24. [PMID: 26184155 PMCID: PMC4519905 DOI: 10.3390/ijms160715405] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 01/14/2023] Open
Abstract
The structural and dynamical properties of the peroxisome proliferator-activated receptor γ (PPARγ) nuclear receptor have been broadly studied in its agonist state but little is known about the key features required for the receptor antagonistic activity. Here we report a series of molecular dynamics (MD) simulations in combination with free energy estimation of the recently discovered class of non-covalent PPARγ antagonists. Their binding modes and dynamical behavior are described in details. Two key interactions have been detected within the cavity between helices H3, H11 and the activation helix H12, as well as with H12. The strength of the ligand-amino acid residues interactions has been analyzed in relation to the specificity of the ligand dynamical and antagonistic features. According to our results, the PPARγ activation helix does not undergo dramatic conformational changes, as seen in other nuclear receptors, but rather perturbations that occur through a significant ligand-induced reshaping of the ligand-receptor and the receptor-coactivator binding pockets. The H12 residue Tyr473 and the charge clamp residue Glu471 play a central role for the receptor transformations. Our results also demonstrate that MD can be a helpful tool for the compound phenotype characterization (full agonists, partial agonists or antagonists) when insufficient experimental data are available.
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Affiliation(s)
- Filip Fratev
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
- Micar21 Ltd., 1407 Sofia, Bulgaria.
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Merilin Al Sharif
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | | | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
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