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Nolte TM. Calculating toxic pressure for mixtures of endocrine disruptors. Heliyon 2024; 10:e34501. [PMID: 39149076 PMCID: PMC11325677 DOI: 10.1016/j.heliyon.2024.e34501] [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: 02/23/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 08/17/2024] Open
Abstract
Incidence of autoimmune disorders, birth defects, and neurological diseases rose over the past 50 years due to increasing variety and quantity of pollutants. To date, there appear few methods capable to evaluate and predict mixture effects by endocrine disruptors (EDs). For the first time, we have developed calculus to determine mixture effects by all kinds of EDs. Our method uses the golden ratio ϕ and draws from bifurcation and chaos theory. Using also the concept of molecular mimicry, we developed the equation: e f f e c t = 100 % 1 + e 5 · ∑ K i C i - n i ϕ 3 . We successfully tested the equation using a range of cohort studies and biomarkers, and for different pollutants like heavy metals, thyroid hormone mimickants, chromate/chlorate, etc. The equation is simple enough to use with only minor prior knowledge and understanding of basic algebra. The method is universal and calculation is data 'light', requiring only pollutant concentrations [C], potencies K and an integer n for endocrinal involvement. This study offers a comprehensive framework to assess the health effects of pollutant exposure across diverse populations, envisioning far-reaching impact, and presenting practical examples and insights.
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Affiliation(s)
- Tom M Nolte
- Department of Environmental Science, Institute for Water and Wetland Research, Radboud University Nijmegen, 6500, GL Nijmegen, the Netherlands
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2
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Xiang S, Wang Z, Tang R, Wang L, Wang Q, Yu Y, Deng Q, Hou T, Hao H, Sun H. Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling. J Chem Inf Model 2023; 63:7529-7544. [PMID: 37983966 DOI: 10.1021/acs.jcim.3c01451] [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: 11/22/2023]
Abstract
It is well-known that the potency of a drug is heavily associated with its kinetic and thermodynamic properties with the target. Nuclear receptors (NRs), as an important target family, play important roles in regulating a variety of physiological processes in vivo. However, it is hard to understand the drug-NR interaction process because of the closed structure of the ligand-binding domain (LBD) of the NR proteins, which apparently hinders the rational design of drugs with controllable kinetic properties. Therefore, understanding the underlying mechanism of the ligand-NR interaction process seems necessary to help NR drug design. However, it is usually difficult for experimental approaches to interpret the kinetic process of drug-target interactions. Therefore, in silico methods were utilized to explore the optimal binding/dissociation pathways of the NR ligands. Specifically, farnesoid X receptor (FXR) is considered here as the target system since it has been an important target for the treatment of bile acid metabolism-associated diseases, and a series of structures cocrystallized with diverse scaffold ligands were resolved. By using random acceleration molecular dynamics (RAMD) simulation and umbrella sampling (US), 5 main dissociation pathways (pathways I-V) were identified in 11 representative FXR ligands, with most of them (9/11) preferring to go through Pathway III and the remaining two favoring escaping from Pathway I and IV. Furthermore, key residues functioning in the three main dissociation pathways were revealed by the kinetic residue energy analysis (KREA) based on the US trajectories, which may serve as road-marker residues for rapid identification of the (un)binding pathways of FXR ligands. Moreover, the preferred pathways explored by RAMD simulations are in good agreement with the minimum free energy path identified by the US simulations with the Pearson R = 0.76 between the predicted binding affinity and the experimental data, suggesting that RAMD is suitable for applying in large-scale (un)binding-pathway exploration in the case of ligands with obscure binding tunnels to the target.
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Affiliation(s)
- Sutong Xiang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Rongfan Tang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qinghua Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Yang Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qirui Deng
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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3
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Zhou Y, Li J, Baryshnikov G, Tu Y. Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4. J Chem Inf Model 2022; 62:6172-6181. [PMID: 36457253 PMCID: PMC9749025 DOI: 10.1021/acs.jcim.2c01035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Suicide inhibition of the CYP3A4 enzyme by a drug inactivates the enzyme in the drug biotransformation process and often shows safety concerns about the drug. Despite extensive experimental studies, the abnormal molecular mechanism of a suicide inhibitor that forms a covalent bond with the residue far away from the catalytically active center of CYP3A4 inactivating the enzyme remains elusive. Here, the authors used molecular simulation approaches to study in detail how diquinone methide (DQR), the metabolite product of raloxifene, unbinds from CYP3A4 and inactivates the enzyme at the atomistic level. The results clearly indicate that in one of the intermediate states formed in its unbinding process, DQR covalently binds to Cys239, a residue far away from the catalytically active center of CYP3A4, and hinders the substrate from entering or leaving the enzyme. This work therefore provides an unprecedented way of clarifying the abnormal mechanism of suicide inhibition of the CYP3A4 enzyme.
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Affiliation(s)
- Yang Zhou
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou510632, China.,Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
| | - Junhao Li
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
| | - Glib Baryshnikov
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, 60174Norrköping, Sweden
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, 114 28Stockholm, Sweden
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4
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Bera I, Payghan PV. Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery. Curr Pharm Des 2020; 25:3339-3349. [PMID: 31480998 DOI: 10.2174/1381612825666190903153043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/01/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. OBJECTIVE The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. METHOD This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. RESULTS This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. CONCLUSION The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.
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Affiliation(s)
- Indrani Bera
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, United States
| | - Pavan V Payghan
- Structural Biology and Bioinformatics Department, CSIR-IICB, Kolkata, India.,Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
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5
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Schneider M, Pons JL, Labesse G, Bourguet W. In Silico Predictions of Endocrine Disruptors Properties. Endocrinology 2019; 160:2709-2716. [PMID: 31265055 PMCID: PMC6804484 DOI: 10.1210/en.2019-00382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/26/2019] [Indexed: 01/12/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) are a broad class of molecules present in our environment that are suspected to cause adverse effects in the endocrine system by interfering with the synthesis, transport, degradation, or action of endogenous ligands. The characterization of the harmful interaction between environmental compounds and their potential cellular targets and the development of robust in vivo, in vitro, and in silico screening methods are important for assessment of the toxic potential of large numbers of chemicals. In this context, computer-aided technologies that will allow for activity prediction of endocrine disruptors and environmental risk assessments are being developed. These technologies must be able to cope with diverse data and connect chemistry at the atomic level with the biological activity at the cellular, organ, and organism levels. Quantitative structure-activity relationship methods became popular for toxicity issues. They correlate the chemical structure of compounds with biological activity through a number of molecular descriptors (e.g., molecular weight and parameters to account for hydrophobicity, topology, or electronic properties). Chemical structure analysis is a first step; however, modeling intermolecular interactions and cellular behavior will also be essential. The increasing number of three-dimensional crystal structures of EDCs' targets has provided a wealth of structural information that can be used to predict their interactions with EDCs using docking and scoring procedures. In the present review, we have described the various computer-assisted approaches that use ligands and targets properties to predict endocrine disruptor activities.
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Affiliation(s)
- Melanie Schneider
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Jean-Luc Pons
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
- Correspondence: Gilles Labesse, PhD, or William Bourguet, PhD, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France. E-mail: or
| | - William Bourguet
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
- Correspondence: Gilles Labesse, PhD, or William Bourguet, PhD, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France. E-mail: or
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6
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Abstract
Nuclear receptors (NRs) are ligand-inducible transcription factors that play an essential role in a multitude of physiological processes as well as diseases, rendering them attractive drug targets. Crystal structures revealed the binding site of NRs to be buried in the core of the protein, with no obvious route for ligands to access this cavity. The process of ligand binding is known to be an often-neglected contributor to the efficacy of drug candidates and is thought to influence the selectivity and specificity of NRs. While experimental methods generally fail to highlight the dynamic processes of ligand access or egress on the atomistic scale, computational methods have provided fundamental insight into the pathways connecting the buried binding pocket to the surrounding environment. Methods based on molecular dynamics (MD) and Monte Carlo simulations have been applied to identify pathways and quantify their capability to transport ligands. Here, we systematically review findings of more than 20 years of research in the field, including the applied methodology and controversies. Further, we establish a unified nomenclature to describe the pathways with respect to their location relative to protein secondary structure elements and summarize findings relevant to drug design. Lastly, we discuss the effect of NR interaction partners such as coactivators and corepressors, as well as mutations on the pathways.
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Affiliation(s)
- André Fischer
- Molecular Modeling, Pharmacenter of the University of Basel , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
| | - Martin Smieško
- Molecular Modeling, Pharmacenter of the University of Basel , University of Basel , Klingelbergstrasse 50 , 4056 Basel , Switzerland
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7
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Chitranshi N, Dheer Y, Kumar S, Graham SL, Gupta V. Molecular docking, dynamics, and pharmacology studies on bexarotene as an agonist of ligand-activated transcription factors, retinoid X receptors. J Cell Biochem 2019; 120:11745-11760. [PMID: 30746761 DOI: 10.1002/jcb.28455] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 01/24/2023]
Abstract
Retinoid X receptors (RXRs) belong to the nuclear receptor superfamily, and upon ligand activation, these receptors control gene transcription via either homodimerization with themselves or heterodimerization with the partner-nuclear receptor. The protective effects of RXRs and RXR agonists have been reported in several neurodegenerative diseases, including in the retina. This study was aimed to prioritize compounds from natural and synthetic origin retinoids as potential RXR agonists by molecular docking and molecular dynamic simulation strategies. The docking studies indicated bexarotene as a lead compound that can activate various RXR receptor isoforms (α, β, and γ) and has a strong binding affinity to the receptor protein than retinoic acid, which is known as a natural endogenous RXR agonist. Dynamic simulation studies confirmed that the hydrogen bonding and hydrophobic interactions were highly stable in all the three isoforms of the RXR-bexarotene complex. To further validate the significance of the RXR receptor in neurons, in vitro pharmacological treatment of neuronal SH-SY5Y cells with bexarotene was performed. In vitro data from SH-SY5Y cells confirmed that bexarotene activated RXR-simulated neurite outgrowth significantly. We conclude that bexarotene could be potentially used as an exogenous activator of RXRs and emerge as a good drug target for several neurodegenerative disorders.
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Affiliation(s)
- Nitin Chitranshi
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
| | - Yogita Dheer
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
| | - Sanjay Kumar
- Bioinformatics Centre, Biotech Park, Jankipuram, Lucknow, Uttar Pradesh, India
| | - Stuart L Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
- Save Sight Institute, Sydney University, Sydney, New South Wales, Australia
| | - Vivek Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales
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8
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Nunes-Alves A, Zuckerman DM, Arantes GM. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophys J 2019. [PMID: 29539393 DOI: 10.1016/j.bpj.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The T4 lysozyme L99A mutant is often used as a model system to study small-molecule binding to proteins, but pathways for ligand entry and exit from the buried binding site and the associated protein conformational changes have not been fully resolved. Here, molecular dynamics simulations were employed to model benzene exit from its binding cavity using the weighted ensemble (WE) approach to enhance sampling of low-probability unbinding trajectories. Independent WE simulations revealed four pathways for benzene exit, which correspond to transient tunnels spontaneously formed in previous simulations of apo T4 lysozyme. Thus, benzene unbinding occurs through multiple pathways partially created by intrinsic protein structural fluctuations. Motions of several α-helices and side chains were involved in ligand escape from metastable microstates. WE simulations also provided preliminary estimates of rate constants for each exit pathway. These results complement previous works and provide a semiquantitative characterization of pathway heterogeneity for binding of small molecules to proteins.
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Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon.
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9
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de Vera IMS, Munoz-Tello P, Zheng J, Dharmarajan V, Marciano DP, Matta-Camacho E, Giri PK, Shang J, Hughes TS, Rance M, Griffin PR, Kojetin DJ. Defining a Canonical Ligand-Binding Pocket in the Orphan Nuclear Receptor Nurr1. Structure 2018; 27:66-77.e5. [PMID: 30416039 DOI: 10.1016/j.str.2018.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/17/2018] [Accepted: 10/05/2018] [Indexed: 01/12/2023]
Abstract
Nuclear receptor-related 1 protein (Nurr1/NR4A2) is an orphan nuclear receptor (NR) that is considered to function without a canonical ligand-binding pocket (LBP). A crystal structure of the Nurr1 ligand-binding domain (LBD) revealed no physical space in the conserved region where other NRs with solvent accessible apo-protein LBPs bind synthetic and natural ligands. Using solution nuclear magnetic resonance spectroscopy, hydrogen/deuterium exchange mass spectrometry, and molecular dynamics simulations, we show that the putative canonical Nurr1 LBP is dynamic with high solvent accessibility, exchanges between two or more conformations on the microsecond-to-millisecond timescale, and can expand from the collapsed crystallized conformation to allow binding of unsaturated fatty acids. These findings should stimulate future studies to probe the ligandability and druggability of Nurr1 for both endogenous and synthetic ligands, which could lead to new therapeutics for Nurr1-related diseases, including Parkinson's disease and schizophrenia.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - David P Marciano
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Edna Matta-Camacho
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Pankaj Kumar Giri
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Travis S Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
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10
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Do PC, Lee EH, Le L. Steered Molecular Dynamics Simulation in Rational Drug Design. J Chem Inf Model 2018; 58:1473-1482. [DOI: 10.1021/acs.jcim.8b00261] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Eric H. Lee
- Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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11
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Magalhães J, Annunziato G, Franko N, Pieroni M, Campanini B, Bruno A, Costantino G. Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets. J Chem Inf Model 2018; 58:710-723. [DOI: 10.1021/acs.jcim.7b00733] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Joana Magalhães
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
| | | | - Nina Franko
- Food and Drug Department, Laboratory of Biochemistry and Molecular Biology, Parco Area Delle Scienze 23/A−43124, Parma, Italy
| | - Marco Pieroni
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
| | - Barbara Campanini
- Food and Drug Department, Laboratory of Biochemistry and Molecular Biology, Parco Area Delle Scienze 23/A−43124, Parma, Italy
| | - Agostino Bruno
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
- Experimental Therapeutics Program, IFOM−The FIRC Institute for Molecular Oncology Foundation, Via Adamello 16−20139, Milano, Italy
| | - Gabriele Costantino
- Food and Drug Department, P4T group, Parco Area Delle Scienze 27/A−43124, Parma, Italy
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12
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Nguyen MK, Jaillet L, Redon S. ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways. J Comput Chem 2018; 39:665-678. [DOI: 10.1002/jcc.25132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/30/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Minh Khoa Nguyen
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK; 38000 Grenoble France
| | - Léonard Jaillet
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK; 38000 Grenoble France
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK; 38000 Grenoble France
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13
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Tang Z, Roberts CC, Chang CEA. Understanding ligand-receptor non-covalent binding kinetics using molecular modeling. FRONT BIOSCI-LANDMRK 2017; 22:960-981. [PMID: 27814657 PMCID: PMC5470370 DOI: 10.2741/4527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kinetic properties may serve as critical differentiators and predictors of drug efficacy and safety, in addition to the traditionally focused binding affinity. However the quantitative structure-kinetics relationship (QSKR) for modeling and ligand design is still poorly understood. This review provides an introduction to the kinetics of drug binding from a fundamental chemistry perspective. We focus on recent developments of computational tools and their applications to non-covalent binding kinetics.
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Affiliation(s)
- Zhiye Tang
- Department of Chemistry, University of California, Riverside, CA 92521
| | | | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA 92521,
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14
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CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands. Int J Mol Sci 2016; 18:ijms18010015. [PMID: 28025495 PMCID: PMC5297650 DOI: 10.3390/ijms18010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023] Open
Abstract
The peroxisome proliferator-activated receptor γ (PPARγ) ligands are important therapeutic drugs for the treatment of type 2 diabetes, obesity and cardiovascular diseases. In particular, partial agonists and non-agonists are interesting targets to reduce glucose levels, presenting few side effects in comparison to full agonists. In this work, we present a set of CHARMM-based parameters of a molecular mechanics force field for two PPARγ ligands, GQ16 and SR1664. GQ16 belongs to the thiazolidinedione class of drugs and it is a PPARγ partial agonist that has been shown to promote the “browning” of white adipose tissue. SR1664 is the precursor of the PPARγ non-agonist class of ligands that activates PPARγ in a non-classical manner. Here, we use quantum chemical calculations consistent with the CHARMM protocol to obtain bonded and non-bonded parameters, including partial atomic charges and effective torsion potentials for both molecules. The newly parameterized models were evaluated by examining the behavior of GQ16 and SR1664 free in water and bound to the ligand binding pocket of PPARγ using molecular dynamics simulations. The potential parameters derived here are readily transferable to a variety of pharmaceutical compounds and similar PPARγ ligands.
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15
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Chen Q, Wang X, Shi W, Yu H, Zhang X, Giesy JP. Identification of Thyroid Hormone Disruptors among HO-PBDEs: In Vitro Investigations and Coregulator Involved Simulations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12429-12438. [PMID: 27737548 DOI: 10.1021/acs.est.6b02029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Some hydroxylated polybrominated diphenyl ethers (HO-PBDEs), that have been widely detected in the environment and tissues of humans and wildlife, bind to thyroid hormone (TH) receptor (TR) and can disrupt functioning of systems modulated by the TR. However, mechanisms of TH disrupting effects are still equivocal. Here, disruption of functions of TH modulated pathways by HO-PBDEs was evaluated by assays of competitive binding, coactivator recruitment, and proliferation of GH3 cells. In silico simulations considering effects of coregulators were carried out to investigate molecular mechanisms and to predict potencies for disrupting functions of the TH. Some HO-PBDEs were able to bind to TR with moderate affinities but were not agonists. In GH3 proliferation assays, 13 out of 16 HO-PBDEs were antagonists for the TH. In silico simulations of molecular dynamics revealed that coregulators were essential for identification of TH disruptors. Among HO-PBDEs, binding of passive antagonists induced repositioning of H12, blocking AF-2 (transactivation function 2) and preventing recruitment of the coactivator. Binding of active antagonists exposed the coregulator binding site, which tended to bind to the corepressor rather than the coactivator. By considering both passive and active antagonisms, anti-TH potencies of HO-PBDEs could be predicted from free energy of binding.
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Affiliation(s)
- Qinchang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Xiaoxiang Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
- Multiphase Chemistry Department, Max Planck Institute for Chemistry , 55128 Mainz, Germany
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - John P Giesy
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
- Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5B4, Canada
- Department of Zoology and Center for Integrative Toxicology, Michigan State University , East Lansing, Michigan 48824, United States
- School of Biological Sciences, University of Hong Kong , Hong Kong, SAR, China
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16
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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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17
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Tsuji M. A ligand-entry surface of the nuclear receptor superfamily consists of the helix H3 of the ligand-binding domain. J Mol Graph Model 2015; 62:262-275. [PMID: 26544573 DOI: 10.1016/j.jmgm.2015.10.002] [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: 06/29/2015] [Revised: 08/24/2015] [Accepted: 10/06/2015] [Indexed: 01/02/2023]
Abstract
We successfully simulated receptor-ligand complex holo-form formation using the human retinoid X receptor-α ligand-binding domain (LBD) and its natural ligand, 9-cis retinoic acid. The success of this simulation was strongly dependent on the findings for an initial structure between the apo-LBD and the ligand as well as the discovery of the driving forces underlying the ligand-trapping and subsequent ligand-induction processes. Here, we would like to propose the "helix H3 three-point initial-binding hypothesis," which was instrumental in simulating the nuclear receptor (NR) superfamily. Using this hypothesis, we also succeeded in simulating holo-form formation of the human retinoic acid receptor-γ LBD and its natural ligand, all-trans retinoic acid. It is hoped that this hypothesis will facilitate novel understanding of both the ligand-trapping mechanism and the simultaneous C-terminal folding process in NR LBDs, as well as provide a new approach to drug design using a structure-based perspective.
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Affiliation(s)
- Motonori Tsuji
- Institute of Molecular Function, 2-105-14 Takasu, Misato-shi, Saitama 341-0037, Japan.
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18
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Mottin M, Souza PCT, Skaf MS. Molecular Recognition of PPARγ by Kinase Cdk5/p25: Insights from a Combination of Protein–Protein Docking and Adaptive Biasing Force Simulations. J Phys Chem B 2015; 119:8330-9. [DOI: 10.1021/acs.jpcb.5b04269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Melina Mottin
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
| | - Paulo C. T. Souza
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
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19
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Meneksedag-Erol D, Tang T, Uludağ H. Probing the Effect of miRNA on siRNA–PEI Polyplexes. J Phys Chem B 2015; 119:5475-86. [DOI: 10.1021/acs.jpcb.5b00415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deniz Meneksedag-Erol
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
| | - Tian Tang
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department
of Mechanical Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
| | - Hasan Uludağ
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
- Faculty
of Pharmacy and Pharmaceutical Sciences, University of Alberta, Alberta, Canada
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20
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Rastinejad F, Ollendorff V, Polikarpov I. Nuclear receptor full-length architectures: confronting myth and illusion with high resolution. Trends Biochem Sci 2014; 40:16-24. [PMID: 25435400 DOI: 10.1016/j.tibs.2014.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 12/31/2022]
Abstract
The crystal structures of three nuclear receptor (NR) complexes have emerged to reveal their multidomain architectures on DNA. These pictures provide unprecedented views of interfacial couplings between the DNA-binding domains (DBDs) and ligand-binding domains (LBDs). The detailed pictures contrast with previous interpretations of low-resolution electron microscopy (EM) and small angle X-ray scattering (SAXS) data, which had suggested a common architecture with noninteracting DBDs and LBDs. Revisiting both historical and recent interpretations of NR architecture, we invoke new principles underlying higher-order quaternary organization and the allosteric transmission of signals between domains. We also discuss how NR architectures are being probed in living cells to understand dimerization and DNA-binding events in real time.
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Affiliation(s)
- Fraydoon Rastinejad
- Sanford-Burnham Medical Research Institute, Metabolic Disease Program, 6400 Sanger Road, Lake Nona, FL 32827, USA.
| | - Vincent Ollendorff
- INRA, UMR866 Dynamique Musculaire et Métabolisme, F-34060 Montpellier Université Montpellier 1, F-34000 Montpellier - Université Montpellier 2, F-34000 Montpellier, France
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense, 400, São Carlos, SP, 13560-970, Brazil
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21
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Mackinnon JAG, Gallastegui N, Osguthorpe DJ, Hagler AT, Estébanez-Perpiñá E. Allosteric mechanisms of nuclear receptors: insights from computational simulations. Mol Cell Endocrinol 2014; 393:75-82. [PMID: 24911885 DOI: 10.1016/j.mce.2014.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 01/07/2023]
Abstract
The traditional structural view of allostery defines this key regulatory mechanism as the ability of one conformational event (allosteric site) to initiate another in a separate location (active site). In recent years computational simulations conducted to understand how this phenomenon occurs in nuclear receptors (NRs) has gained significant traction. These results have yield insights into allosteric changes and communication mechanisms that underpin ligand binding, coactivator binding site formation, post-translational modifications, and oncogenic mutations. Moreover, substantial efforts have been made in understanding the dynamic processes involved in ligand binding and coregulator recruitment to different NR conformations in order to predict cell/tissue-selective pharmacological outcomes of drugs. They also have improved the accuracy of in silico screening protocols so that nowadays they are becoming part of optimisation protocols for novel therapeutics. Here we summarise the important contributions that computational simulations have made towards understanding the structure/function relationships of NRs and how these can be exploited for rational drug design.
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Affiliation(s)
- Jonathan A G Mackinnon
- Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri-Reixac 15-21, 08028 Barcelona, Spain
| | - Nerea Gallastegui
- Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri-Reixac 15-21, 08028 Barcelona, Spain
| | - David J Osguthorpe
- Shifa Biomedical, 1 Great Valley Parkway, Suite 8, Malvern, PA 19355, USA
| | - Arnold T Hagler
- Department of Chemistry, University of Massachusetts, 701 Lederle, Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003-9336, USA.
| | - Eva Estébanez-Perpiñá
- Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri-Reixac 15-21, 08028 Barcelona, Spain.
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22
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Determinants of protein–ligand complex formation in the thyroid hormone receptor α: A molecular dynamics simulation study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Batista MRB, Martínez L. Dynamics of nuclear receptor Helix-12 switch of transcription activation by modeling time-resolved fluorescence anisotropy decays. Biophys J 2014; 105:1670-80. [PMID: 24094408 DOI: 10.1016/j.bpj.2013.07.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 12/28/2022] Open
Abstract
Nuclear hormone receptors (NRs) are major targets for pharmaceutical development. Many experiments demonstrate that their C-terminal Helix (H12) is more flexible in the ligand-binding domains (LBDs) without ligand, this increased mobility being correlated with transcription repression and human diseases. Crystal structures have been obtained in which the H12 is extended, suggesting the possibility of large amplitude H12 motions in solution. However, these structures were interpreted as possible crystallographic artifacts, and thus the microscopic nature of H12 movements is not well known. To bridge the gap between experiments and molecular models and provide a definitive picture of H12 motions in solution, extensive molecular dynamics simulations of the peroxisome proliferator-activated receptor-γ LBD, in which the H12 was bound to a fluorescent probe, were performed. A direct comparison of the modeled anisotropy decays to time-resolved fluorescence anisotropy experiments was obtained. It is shown that the decay rates are dependent on the interactions of the probe with the surface of the protein, and display little correlation with the flexibility of the H12. Nevertheless, for the probe to interact with the surface of the LBD, the H12 must be folded over the body of the LBD. Therefore, the molecular mobility of the H12 should preserve the globularity of the LBD, so that ligand binding and dissociation occur by diffusion through the surface of a compact receptor. These results advance the comprehension of both ligand-bound and ligand-free receptor structures in solution, and also guide the interpretation of time-resolved anisotropy decays from a molecular perspective, particularly by the use of simulations.
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Affiliation(s)
- Mariana R B Batista
- Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil; Institute of Physics of São Carlos, University of São Paulo, São Carlos, SP, Brazil
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24
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Souza PCT, Puhl AC, Martínez L, Aparício R, Nascimento AS, Figueira ACM, Nguyen P, Webb P, Skaf MS, Polikarpov I. Identification of a new hormone-binding site on the surface of thyroid hormone receptor. Mol Endocrinol 2014; 28:534-45. [PMID: 24552590 DOI: 10.1210/me.2013-1359] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.
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Affiliation(s)
- P C T Souza
- Institute of Chemistry (P.C.T.S., L.M., R.A., M.S.S.), State University of Campinas-UNICAMP, Campinas, Sao Paulo, Brazil; Institute of Physics of São Carlos (A.C.P., A.S.N., P.W., I.P.), University of São Paulo-USP, São Carlos, Sao Paulo, Brazil; National Laboratory of Biosciences (A.C.M.F.), CNPEM, Campinas, Sao Paulo, Brazil; University of California Medical Center (P.N.), Diabetes Center, San Francisco, California; and Genomic Medicine (P.W.), Houston Methodist Research Institute, Houston, Texas
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25
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Capelli AM, Bruno A, Entrena Guadix A, Costantino G. Unbinding Pathways from the Glucocorticoid Receptor Shed Light on the Reduced Sensitivity of Glucocorticoid Ligands to a Naturally Occurring, Clinically Relevant Mutant Receptor. J Med Chem 2013; 56:7003-14. [DOI: 10.1021/jm400802b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anna Maria Capelli
- Chemistry Research and Drug
Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli, Parma, Italy
- Dipartimento di Farmacia, Universita’ degli Studi di Parma, viale Area
delle Scienze 27/A, Parma, Italy
| | - Agostino Bruno
- Dipartimento di Farmacia, Universita’ degli Studi di Parma, viale Area
delle Scienze 27/A, Parma, Italy
| | - Antonio Entrena Guadix
- Departamento de Quımica
Farmaceutica y Organica, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071 Granada, Spain
| | - Gabriele Costantino
- Dipartimento di Farmacia, Universita’ degli Studi di Parma, viale Area
delle Scienze 27/A, Parma, Italy
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26
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Zhuang S, Bao L, Linhananta A, Liu W. Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization. J Mol Graph Model 2013; 44:155-60. [PMID: 23831995 DOI: 10.1016/j.jmgm.2013.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 06/06/2013] [Accepted: 06/07/2013] [Indexed: 11/28/2022]
Abstract
Numerous ligands bind tightly to thyroid hormone receptors (TRs), and exploring the binding and dissociation of these ligands from TRs will increase our understanding of their mechanisms of action. TRs form transcriptionally active heterodimers with retinoid X receptor (RXR); whether this heterodimerization affects ligand dissociation is poorly understood. To investigate the effects of heterodimerization, classical molecular dynamics (MD) simulations and random acceleration molecular dynamics (RAMD) simulations were performed to probe the dissociation of triiodothyronine (T3) from a TRα-RXR ligand binding domain (LBD) heterodimer and the TRα and TRβ LBDs at the atomic level. Seven (I-VII) dissociation pathways were identified for T3. Heterodimerization inhibited pathway I in the TRα-RXR LBD heterodimer, which may block the proper orientation of the helix 12 (H12), therefore affecting the biological functions of TRs. Upon TR heterodimerization, the second most dominant dissociation pathway switched from pathway IV for TRα LBD to pathway II for TRα-RXR LBD. No significant effects of TR heterodimerization were observed on the dominant dissociation pathway III that was located between H3, the H1-H2 loop and the β-sheet. Our study revealed that TR heterodimerization significantly affects T3 dissociation, which provides important information for the study of other TR ligands.
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Affiliation(s)
- Shulin Zhuang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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27
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Bernardes A, Souza PCT, Muniz JRC, Ricci CG, Ayers SD, Parekh NM, Godoy AS, Trivella DBB, Reinach P, Webb P, Skaf MS, Polikarpov I. Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization. J Mol Biol 2013; 425:2878-93. [PMID: 23707408 DOI: 10.1016/j.jmb.2013.05.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 04/30/2013] [Accepted: 05/15/2013] [Indexed: 01/01/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of nuclear transcription factors. They are involved in mediating numerous physiological effects in humans, including glucose and lipid metabolism. PPARα ligands effectively treat dyslipidemia and have significant antiinflammatory and anti-atherosclerotic activities. These effects and their ligand-dependent activity make nuclear receptors obvious targets for drug design. Here, we present the structure of the human PPARα in complex with WY14643, a member of fibrate class of drug, and a widely used PPAR activator. The crystal structure of this complex suggests that WY14643 induces activation of PPARα in an unusual bipartite mechanism involving conventional direct helix 12 stabilization and an alternative mode that involves a second ligand in the pocket. We present structural observations, molecular dynamics and activity assays that support the importance of the second site in WY14643 action. The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand. We show that binding of WY14643 to PPARα was associated with antiinflammatory disease in a human corneal cell model, suggesting possible applications for PPARα ligands.
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Affiliation(s)
- Amanda Bernardes
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador Sãocarlense 400, São Carlos, SP 13560-970, Brazil
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28
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Design, synthesis, and structure–activity relationship (SAR) of N-[7-(4-hydroxyphenoxy)-6-methylindan-4-yl]malonamic acids as thyroid hormone receptor β (TRβ) selective agonists. Bioorg Med Chem 2013; 21:592-607. [DOI: 10.1016/j.bmc.2012.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 11/22/2022]
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29
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Li W, Fu J, Cheng F, Zheng M, Zhang J, Liu G, Tang Y. Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations. J Chem Inf Model 2012; 52:3043-52. [PMID: 23101941 DOI: 10.1021/ci300459k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Farnesoid X receptor (FXR, NR1H4) is a member of a nuclear receptor superfamily, which plays important roles in bile acid homeostasis, lipoprotein and glucose metabolism, and hepatic regeneration. GW4064 is a potent and selective FXR agonist and has become a tool compound to probe the physiological functions of FXR. Until now, the mechanism of GW4064 entering and leaving the FXR pocket is still poorly understood. Here, we report a computational study of GW4064 unbinding pathways from FXR by using several molecular dynamics (MD) simulation techniques. Based on the crystal structure of FXR in complex with GW4064, conventional MD was first used to refine the binding and check the stability of GW4064 in the FXR pocket. Random acceleration MD simulations were then performed to explore the possible unbinding pathways of GW4064 from FXR. Four main pathway clusters were found, among which three subpathways, namely Paths 2A, 2B, and 1B, were observed most frequently. Multiple steered MD simulations were further employed to estimate the maximum rupture force and the sum of the forces and to characterize the intermediate states of the ligand unbinding process. By comparing the average force profiles and structural changes, Paths 2A and 2B were identified to be the most favorable unbinding pathways. The former is located between the H1-H2 loop and the H5-H6 loop, and the latter is located in the cleft formed by the H5-H6 loop, H6, and H7. Moreover, the residues lining the pathways were analyzed for their roles in ligand unbinding. Based on our results, the possible structural modification strategies on GW4064 were also proposed.
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Affiliation(s)
- Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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30
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Spyrakis* F, Barril* X, Luque* FJ. Molecular Dynamics: a Tool to Understand Nuclear Receptors. COMPUTATIONAL APPROACHES TO NUCLEAR RECEPTORS 2012. [DOI: 10.1039/9781849735353-00060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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31
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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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32
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Jyrkkärinne J, Küblbeck J, Pulkkinen J, Honkakoski P, Laatikainen R, Poso A, Laitinen T. Molecular Dynamics Simulations for Human CAR Inverse Agonists. J Chem Inf Model 2012; 52:457-64. [DOI: 10.1021/ci200432k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johanna Jyrkkärinne
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jenni Küblbeck
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Juha Pulkkinen
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Paavo Honkakoski
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Reino Laatikainen
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Tuomo Laitinen
- University of Eastern Finland, Faculty of Health Sciences,
School of Pharmacy, P.O. Box 1627, FI-70211 Kuopio, Finland
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33
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Sun L, Cheng QH, Gao HJ, Zhang YW. Effect of loading conditions on the dissociation behaviour of catch bond clusters. J R Soc Interface 2011; 9:928-37. [PMID: 21937488 DOI: 10.1098/rsif.2011.0553] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Under increasing tensile load, the lifetime of a single catch bond counterintuitively increases up to a maximum and then decreases exponentially like a slip bond. So far, the characteristics of single catch bond dissociation have been extensively studied. However, it remains unclear how a cluster of catch bonds behaves under tensile load. We perform computational analysis on the following models to examine the characteristics of clustered catch bonds: (i) clusters of catch bonds with equal load sharing, (ii) clusters of catch bonds with linear load sharing, and (iii) clusters of catch bonds in micropipette-manipulated cell detachment. We focus on the differences between the slip and catch bond clusters, identifying the critical factors for exhibiting the characteristics of catch bond mechanism for the multiple-bond system. Our computation reveals that for a multiple-bond cluster, the catch bond behaviour could only manifest itself under relatively uniform loading conditions and at certain stages of decohesion, explaining the difficulties in observing the catch bond mechanism under real biological conditions.
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Affiliation(s)
- L Sun
- Department of Materials Science and Engineering, National University of Singapore, Singapore
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34
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Souza PCT, Barra GB, Velasco LFR, Ribeiro ICJ, Simeoni LA, Togashi M, Webb P, Neves FAR, Skaf MS, Martínez L, Polikarpov I. Helix 12 dynamics and thyroid hormone receptor activity: experimental and molecular dynamics studies of Ile280 mutants. J Mol Biol 2011; 412:882-93. [PMID: 21530542 DOI: 10.1016/j.jmb.2011.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 01/28/2023]
Abstract
Nuclear hormone receptors (NRs) form a family of transcription factors that mediate cellular responses initiated by hormone binding. It is generally recognized that the structure and dynamics of the C-terminal helix 12 (H12) of NRs' ligand binding domain (LBD) are fundamental to the recognition of coactivators and corepressors that modulate receptor function. Here we study the role of three mutations in the I280 residue of H12 of thyroid hormone receptors using site-directed mutagenesis, functional assays, and molecular dynamics simulations. Although residues at position 280 do not interact with coactivators or with the ligand, we show that its mutations can selectively block coactivator and corepressor binding, and affect hormone binding affinity differently. Molecular dynamics simulations suggest that ligand affinity is reduced by indirectly displacing the ligand in the binding pocket, facilitating water penetration and ligand destabilization. Mutations I280R and I280K link H12 to the LBD by forming salt bridges with E457 in H12, stabilizing H12 in a conformation that blocks both corepressor and coactivator recruitment. The I280M mutation, in turn, blocks corepressor binding, but appears to enhance coactivator affinity, suggesting stabilization of H12 in agonist conformation.
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Affiliation(s)
- Paulo C T Souza
- Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil
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Martínez L, Malliavin TE, Blondel A. Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study. Proteins 2011; 79:1649-61. [PMID: 21425348 DOI: 10.1002/prot.22991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/14/2010] [Accepted: 12/30/2010] [Indexed: 11/07/2022]
Abstract
The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.
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Affiliation(s)
- Leandro Martínez
- Unité de Bioinformatique Structurale, URA CNRS 2185, Institut Pasteur, 25, rue du Dr Roux, F-75015 Paris, France.
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Shyu C, Cavileer TD, Nagler JJ, Ytreberg FM. Computational estimation of rainbow trout estrogen receptor binding affinities for environmental estrogens. Toxicol Appl Pharmacol 2011; 250:322-6. [PMID: 21075131 PMCID: PMC3022107 DOI: 10.1016/j.taap.2010.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/19/2010] [Accepted: 11/05/2010] [Indexed: 11/21/2022]
Abstract
Environmental estrogens have been the subject of intense research due to their documented detrimental effects on the health of fish and wildlife and their potential to negatively impact humans. A complete understanding of how these compounds affect health is complicated because environmental estrogens are a structurally heterogeneous group of compounds. In this work, computational molecular dynamics simulations were utilized to predict the binding affinity of different compounds using rainbow trout (Oncorhynchus mykiss) estrogen receptors (ERs) as a model. Specifically, this study presents a comparison of the binding affinity of the natural ligand estradiol-17β to the four rainbow trout ER isoforms with that of three known environmental estrogens 17α-ethinylestradiol, bisphenol A, and raloxifene. Two additional compounds, atrazine and testosterone, that are known to be very weak or non-binders to ERs were tested. The binding affinity of these compounds to the human ERα subtype is also included for comparison. The results of this study suggest that, when compared to estradiol-17β, bisphenol A binds less strongly to all four receptors, 17α-ethinylestradiol binds more strongly, and raloxifene has a high affinity for the α subtype only. The results also show that atrazine and testosterone are weak or non-binders to the ERs. All of the results are in excellent qualitative agreement with the known in vivo estrogenicity of these compounds in the rainbow trout and other fishes. Computational estimation of binding affinities could be a valuable tool for predicting the impact of environmental estrogens in fish and other animals.
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Affiliation(s)
- Conrad Shyu
- Department of Physics, University of Idaho, Moscow, Idaho 83844-0903
| | - Timothy D. Cavileer
- Department of Biological Sciences and Center for Reproductive Biology, University of Idaho, Moscow, Idaho, 83844-3051
| | - James J. Nagler
- Department of Biological Sciences and Center for Reproductive Biology, University of Idaho, Moscow, Idaho, 83844-3051
| | - F. Marty Ytreberg
- Department of Physics, University of Idaho, Moscow, Idaho 83844-0903
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Figueira ACM, Saidemberg DM, Souza PCT, Martínez L, Scanlan TS, Baxter JD, Skaf MS, Palma MS, Webb P, Polikarpov I. Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange. Mol Endocrinol 2010; 25:15-31. [PMID: 21106879 DOI: 10.1210/me.2010-0202] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH3). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH3, increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH3. We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes.
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Affiliation(s)
- A C M Figueira
- Universidade de São Paulo, Departamento Física e Informática, Instituto de Física, Avenida Trabalhador Sãocarlense 400, São Carlos, SP, Brazil
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Arroyo-Mañez P, Bikiel DE, Boechi L, Capece L, Di Lella S, Estrin DA, Martí MA, Moreno DM, Nadra AD, Petruk AA. Protein dynamics and ligand migration interplay as studied by computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1054-64. [PMID: 20797453 DOI: 10.1016/j.bbapap.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/12/2010] [Accepted: 08/13/2010] [Indexed: 10/19/2022]
Abstract
Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Pau Arroyo-Mañez
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
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de Araujo AS, Martínez L, de Paula Nicoluci R, Skaf MS, Polikarpov I. Structural modeling of high-affinity thyroid receptor-ligand complexes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1523-36. [PMID: 20512645 DOI: 10.1007/s00249-010-0610-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 04/27/2010] [Accepted: 05/04/2010] [Indexed: 11/24/2022]
Abstract
Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors' ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.
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Affiliation(s)
- Alexandre Suman de Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av Trabalhador SaoCarlense 400, IFSC, Grupo de Cristalografia, PO Box 369, Sao Carlos, SP 13560-970, Brazil
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Colizzi F, Perozzo R, Scapozza L, Recanatini M, Cavalli A. Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors. J Am Chem Soc 2010; 132:7361-71. [DOI: 10.1021/ja100259r] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francesco Colizzi
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy, Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland, and Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Remo Perozzo
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy, Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland, and Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Leonardo Scapozza
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy, Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland, and Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Maurizio Recanatini
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy, Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland, and Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Andrea Cavalli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy, Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland, and Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
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Parravicini C, Abbracchio MP, Fantucci P, Ranghino G. Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach. BMC STRUCTURAL BIOLOGY 2010; 10:8. [PMID: 20233425 PMCID: PMC2850907 DOI: 10.1186/1472-6807-10-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 03/16/2010] [Indexed: 01/21/2023]
Abstract
Background GPR17 is a hybrid G-protein-coupled receptor (GPCR) activated by two unrelated ligand families, extracellular nucleotides and cysteinyl-leukotrienes (cysteinyl-LTs), and involved in brain damage and repair. Its exploitment as a target for novel neuro-reparative strategies depends on the elucidation of the molecular determinants driving binding of purinergic and leukotrienic ligands. Here, we applied docking and molecular dynamics simulations (MD) to analyse the binding and the forced unbinding of two GPR17 ligands (the endogenous purinergic agonist UDP and the leukotriene receptor antagonist pranlukast from both the wild-type (WT) receptor and a mutant model, where a basic residue hypothesized to be crucial for nucleotide binding had been mutated (R255I) to Ile. Results MD suggested that GPR17 nucleotide binding pocket is enclosed between the helical bundle and extracellular loop (EL) 2. The driving interaction involves R255 and the UDP phosphate moiety. To support this hypothesis, steered MD experiments showed that the energy required to unbind UDP is higher for the WT receptor than for R255I. Three potential binding sites for pranlukast where instead found and analysed. In one of its preferential docking conformations, pranlukast tetrazole group is close to R255 and phenyl rings are placed into a subpocket highly conserved among GPCRs. Pulling forces developed to break polar and aromatic interactions of pranlukast were comparable. No differences between the WT receptor and the R255I receptor were found for the unbinding of pranlukast. Conclusions These data thus suggest that, in contrast to which has been hypothesized for nucleotides, the lack of the R255 residue doesn't affect the binding of pranlukast a crucial role for R255 in binding of nucleotides to GPR17. Aromatic interactions are instead likely to play a predominant role in the recognition of pranlukast, suggesting that two different binding subsites are present on GPR17.
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Affiliation(s)
- Chiara Parravicini
- Department of Pharmacological Sciences, University of Milano, via Balzaretti 9, 20133 Milano, Italy
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Martínez L, Souza PCT, Garcia W, Batista FAH, Portugal RV, Nascimento AS, Nakahira M, Lima LMTR, Polikarpov I, Skaf MS. On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors. J Phys Chem B 2009; 114:1529-40. [DOI: 10.1021/jp911554p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Leandro Martínez
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Paulo C. T. Souza
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Wanius Garcia
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Fernanda A. H. Batista
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Rodrigo V. Portugal
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Alessandro S. Nascimento
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Marcel Nakahira
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Luis M. T. R. Lima
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Igor Polikarpov
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SaoCarlense 400-IFSC-Grupo de Crystalografia, P.O. Box 369, Sao Carlos, SP, 13560-970, Brazil, and Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, CCS, bloco B, subsolo, sala 34. Ilha do Fundão, Rio de Janeiro, RJ, 21941-590, Brazil
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Shen J, Li W, Liu G, Tang Y, Jiang H. Computational insights into the mechanism of ligand unbinding and selectivity of estrogen receptors. J Phys Chem B 2009; 113:10436-44. [PMID: 19583238 DOI: 10.1021/jp903785h] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Estrogen receptors (ER) belong to the nuclear receptor superfamily, and two subtypes, ERalpha and ERbeta, have been identified to date. The differentiated functions and receptor expressions of ERalpha and ERbeta made it attracted to discover subtype-specified ligands with high selectivity. However, these two subtypes are highly homologous and only two residues differ in the ligand binding pocket. Therefore, the mechanism of ligand selectivity has become an important issue in searching selective ligands of ER subtypes. In this study, steered molecular dynamics simulations were carried out to investigate the unbinding pathways of two selective ERbeta ligands from the binding pocket of both ERalpha and ERbeta, which demonstrated that the pathway between the H11 helix and the H7 approximately H8 loop was the most probable for ligand escaping. Then potentials of mean force for ligands unbinding along this pathway were calculated in order to gain insights into the molecular basis for energetics of ligand unbinding and find clues of ligand selectivity. The results indicated that His524/475 in ERalpha/ERbeta acted as a "gatekeeper" during the ligand unbinding. Especially, the H7 approximately H8 loop of ERbeta acted as a polar "transmitter" that controlled the ligand unbinding from the binding site and contributed to the ligand selectivity. Finally, the mechanism of ligand selectivity of ER subtypes was discussed from a kinetic perspective and suggestions for improving the ligand selectivity of ERbeta were also presented. These findings could be helpful for rational design of highly selective ERbeta ligands.
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Affiliation(s)
- Jie Shen
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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Wang XS, Roitberg AE, Richards NGJ. Computational Studies of Ammonia Channel Function in Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase. Biochemistry 2009; 48:12272-82. [DOI: 10.1021/bi901521d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiang S. Wang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435
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Gaining ligand selectivity in thyroid hormone receptors via entropy. Proc Natl Acad Sci U S A 2009; 106:20717-22. [PMID: 19926848 DOI: 10.1073/pnas.0911024106] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TRbeta) vs. TRalpha reduce cholesterol and fat without effects on heart rate; thus, it is important to understand TRbeta-selective binding. Binding of 3 selective ligands (GC-1, KB141, and GC-24) is characterized at the atomic level; preferential binding depends on a nonconserved residue (Asn-331beta) in the TRbeta ligand-binding cavity (LBC), and GC-24 gains extra selectivity from insertion of a bulky side group into an extension of the LBC that only opens up with this ligand. Here we report that the natural TH 3,5,3'-triodothyroacetic acid (Triac) exhibits a previously unrecognized mechanism of TRbeta selectivity. TR x-ray structures reveal better fit of ligand with the TRalpha LBC. The TRbeta LBC, however, expands relative to TRalpha in the presence of Triac (549 A(3) vs. 461 A(3)), and molecular dynamics simulations reveal that water occupies the extra space. Increased solvation compensates for weaker interactions of ligand with TRbeta and permits greater flexibility of the Triac carboxylate group in TRbeta than in TRalpha. We propose that this effect results in lower entropic restraint and decreases free energy of interactions between Triac and TRbeta, explaining subtype-selective binding. Similar effects could potentially be exploited in nuclear receptor drug design.
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Lima STC, Nguyen NH, Togashi M, Apriletti JW, Nguyen P, Polikarpov I, Scanlan TS, Baxter JD, Webb P. Differential effects of TR ligands on hormone dissociation rates: evidence for multiple ligand entry/exit pathways. J Steroid Biochem Mol Biol 2009; 117:125-31. [PMID: 19729063 PMCID: PMC2784034 DOI: 10.1016/j.jsbmb.2009.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 08/16/2009] [Accepted: 08/21/2009] [Indexed: 11/26/2022]
Abstract
Some nuclear receptor (NR) ligands promote dissociation of radiolabeled bound hormone from the buried ligand binding cavity (LBC) more rapidly than excess unlabeled hormone itself. This result was interpreted to mean that challenger ligands bind allosteric sites on the LBD to induce hormone dissociation, and recent findings indicate that ligands bind weakly to multiple sites on the LBD surface. Here, we show that a large fraction of thyroid hormone receptor (TR) ligands promote rapid dissociation (T(1/2)<2h) of radiolabeled T(3) vs. T(3) (T(1/2) approximately 5-7h). We cannot discern relationships between this effect and ligand size, activity or affinity for TRbeta. One ligand, GC-24, binds the TR LBC and (weakly) to the TRbeta-LBD surface that mediates dimer/heterodimer interaction, but we cannot link this interaction to rapid T(3) dissociation. Instead, several lines of evidence suggest that the challenger ligand must interact with the buried LBC to promote rapid T(3) release. Since previous molecular dynamics simulations suggest that TR ligands leave the LBC by several routes, we propose that a subset of challenger ligands binds and stabilizes a partially unfolded intermediate state of TR that arises during T(3) release and that this effect enhances hormone dissociation.
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Affiliation(s)
- Suzana T. Cunha Lima
- Department of General Biology, Biology Institute. Federal University of Bahia. 147, Barão de Geremoabo Street, - Campus of Ondina, Salvador, BA, 40170–290 Brazil
| | - Ngoc-Ha Nguyen
- Department of Biochemistry and Biophysics, University of California School of Medicine, San Francisco, CA 94143, USA
| | - Marie Togashi
- Health Science Institute. Brasilia University, Asa Norte, Brasilia, DF 70919–970, Brazil
| | - James W. Apriletti
- Diabetes Center, University of California School of Medicine, San Francisco, CA 94143, USA
| | - Phuong Nguyen
- Diabetes Center, University of California School of Medicine, San Francisco, CA 94143, USA
| | - Igor Polikarpov
- Physics Institute of São Carlos, University of São Paulo. 400, Trabalhador São Carlense Av., São Carlos, SP 13560–970, Brazil
| | - Thomas S. Scanlan
- Department of Physiology & Pharmacology, Oregon Health & Science University, Portland, OR97239
| | - John D. Baxter
- The Methodist Hospital Research Institute. 6565 Fannin St. Houston, TX 77030, USA
| | - Paul Webb
- The Methodist Hospital Research Institute. 6565 Fannin St. Houston, TX 77030, USA
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Ai N, Krasowski MD, Welsh WJ, Ekins S. Understanding nuclear receptors using computational methods. Drug Discov Today 2009; 14:486-94. [PMID: 19429508 DOI: 10.1016/j.drudis.2009.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 03/03/2009] [Accepted: 03/04/2009] [Indexed: 02/06/2023]
Abstract
Nuclear receptors (NRs) are important targets for therapeutic drugs. NRs regulate transcriptional activities through binding to ligands and interacting with several regulating proteins. Computational methods can provide insights into essential ligand-receptor and protein-protein interactions. These in turn have facilitated the discovery of novel agonists and antagonists with high affinity and specificity as well as have aided in the prediction of toxic side effects of drugs by identifying possible off-target interactions. Here, we review the application of computational methods toward several clinically important NRs (with special emphasis on PXR) and discuss their use for screening and predicting the toxic side effects of xenobiotics.
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Affiliation(s)
- Ni Ai
- Department of Pharmacology, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey, Piscataway, NJ 08854, USA
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48
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Peräkylä M. Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:185-98. [DOI: 10.1007/s00249-008-0369-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 08/25/2008] [Accepted: 08/28/2008] [Indexed: 02/04/2023]
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49
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Martínez L, Polikarpov I, Skaf MS. Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: simulations using a novel multipoint steered molecular dynamics approach. J Phys Chem B 2008; 112:10741-51. [PMID: 18681473 DOI: 10.1021/jp803403c] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor's biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXRalpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs.
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Affiliation(s)
- Leandro Martínez
- Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil
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50
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Sonoda MT, Martínez L, Webb P, Skaf MS, Polikarpov I. Ligand dissociation from estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations. Mol Endocrinol 2008; 22:1565-78. [PMID: 18403716 PMCID: PMC5419439 DOI: 10.1210/me.2007-0501] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 04/03/2008] [Indexed: 11/19/2022] Open
Abstract
Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17beta-estradiol (E(2)) and the selective ER modulator raloxifene (RAL)] from the human ERalpha ligand-binding domain in monomeric and dimeric forms. E(2) dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II'). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I'). Remarkably, ER dimerization strongly suppresses Paths II and II' for E(2) dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.
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Affiliation(s)
- Milton T Sonoda
- São Carlos Institute of Physics, University of São Paulo-USP, São Carlos, SP, Brazil
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