1
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Powała A, Żołek T, Brown G, Kutner A. Structure and the Anticancer Activity of Vitamin D Receptor Agonists. Int J Mol Sci 2024; 25:6624. [PMID: 38928329 DOI: 10.3390/ijms25126624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Vitamin D is a group of seco-steroidal fat-soluble compounds. The two basic forms, vitamin D2 (ergocalciferol) and vitamin D3 (cholecalciferol), do not have biological activity. They are converted in the body by a two-step enzymatic hydroxylation into biologically active forms, 1α,25-dihydroxyvitamin D2 [ercalcitriol, 1,25(OH)2D2] and 1α,25-dihydroxyvitamin D3 [calcitriol, 1,25(OH)2D3], which act as classical steroid hormones. 1,25(OH)2D3 exerts most of its physiological functions by binding to the nuclear vitamin D receptor (VDR), which is present in most body tissues to provide support to a broad range of physiological processes. Vitamin D-liganded VDR controls the expression of many genes. High levels of 1,25(OH)2D3 cause an increase in calcium in the blood, which can lead to harmful hypercalcemia. Several analogs of 1,25(OH)2D3 and 1,25(OH)2D2 have been designed and synthesized with the aim of developing compounds that have a specific therapeutic function, for example, with potent anticancer activity and a reduced toxic calcemic effect. Particular structural modifications to vitamin D analogs have led to increased anticancer activity and reduced calcemic action with the prospect of extending work to provide future innovative therapies.
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Affiliation(s)
- Agnieszka Powała
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Stefana Banacha, 02-097 Warsaw, Poland
| | - Teresa Żołek
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Stefana Banacha, 02-097 Warsaw, Poland
| | - Geoffrey Brown
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrzej Kutner
- Department of Drug Chemistry Pharmaceutical and Biomedical Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Stefana Banacha, 02-097 Warsaw, Poland
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2
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Garcia-Maldonado E, Huber AD, Chai SC, Nithianantham S, Li Y, Wu J, Poudel S, Miller DJ, Seetharaman J, Chen T. Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR. Nat Commun 2024; 15:4054. [PMID: 38744881 PMCID: PMC11094003 DOI: 10.1038/s41467-024-48472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.
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Affiliation(s)
- Efren Garcia-Maldonado
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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3
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Anderson KW, Hudgens JW. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2672-2679. [PMID: 37930109 PMCID: PMC10704588 DOI: 10.1021/jasms.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Chromatographic separations at subzero temperature significantly improve the precision of back-exchange-corrected hydrogen-deuterium exchange mass spectrometry (HDX-MS) determinations. Our previously reported dual-enzyme HDX-MS analysis instrument used reversed phase liquid chromatography (RPLC) at -30 °C, but high backpressures limited flow rates and required materials and equipment rated for very high pressures. Here, we report the design and performance of a dual-enzyme HDX-MS analysis instrument comprising a RPLC trap column and a hydrophilic interaction liquid chromatography (HILIC) analytical column in a two-dimensional RPLC-HILIC configuration at subzero temperature. During operation at -30 °C, the HILIC column manifests greatly reduced backpressure, which enables faster analytical flow rates and the use of materials rated for lower maximum pressures. The average peptide eluted from a HILIC column during a 40 min gradient at -30 °C contained ≈13% more deuterium than peptides eluted from a tandem RPLC-RPLC apparatus using a conventional 8 min gradient at 0 °C. A subset of peptides eluted from the HILIC apparatus contained ≈24% more deuterium.
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Affiliation(s)
- Kyle W. Anderson
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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4
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Kumari A, Mittal L, Srivastava M, Pathak DP, Asthana S. Deciphering the Structural Determinants Critical in Attaining the FXR Partial Agonism. J Phys Chem B 2023; 127:465-485. [PMID: 36609158 DOI: 10.1021/acs.jpcb.2c06325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Elucidation of structural determinants is pivotal for structure-based drug discovery. The Farnesoid X receptor (FXR) is a proven target for NASH; however, its full agonism causes certain clinical complications. Therefore, partial agonism (PA) appears as a viable alternative for improved therapeutics. Since the agonist and PA both share the same binding site, i.e., ligand-binding pocket (LBP), which is highly dynamic and has synergy with the substrate binding site, the selective designing of PA is challenging. The identification of structural and conformational determinants is critical for PA compared with an agonist. Furthermore, the mechanism by which PA modulates the structural dynamics of FXR at the residue level, a prerequisite for PA designing, is still elusive. Here, by using ∼4.5 μs of MD simulations and residue-wise communication network analysis, we identified the structural regions which are flexible with PA but frozen with an agonist. Also, the network analysis identified the considerable changes between an agonist and PA in biologically essential zones of FXR such as helix H10/H11 and loop L:H11/H12, which lead to the modulation of synergy between LBP and the substrate binding site. Furthermore, the thermodynamic profiling suggested the methionine residues, mainly M328, M365, and M450, seem to be responsible for the recruitment of PA. The other residues I357, Y361, L465, F308, Q316, and K321 are also identified, exclusively interacting with PA. This study offers novel structural and mechanistic insights that are critical for FXR targeted drug discovery for PA designing.
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Affiliation(s)
- Anita Kumari
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India.,Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi110017, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
| | - Dharam Pal Pathak
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), New Delhi110017, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
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5
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Nagamani S, Jaiswal L, Sastry GN. Deciphering the importance of MD descriptors in designing Vitamin D Receptor agonists and antagonists using machine learning. J Mol Graph Model 2023; 118:108346. [PMID: 36208593 DOI: 10.1016/j.jmgm.2022.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]
Abstract
The Vitamin D Receptor (VDR) ligand-binding domain undergoes conformation change upon the binding of VDR agonists/antagonists. Helix 12 ((H)12) is one of the important helices at VDR ligand binding and its conformational changes are controlled by the binding of agonists and antagonists molecules. Various molecular modeling studies are available to explain the agonistic and antagonistic activity of vitamin D analogs. In this work, for the first time, we attempted to generate a machine learning model with fingerprints, 2D, 3D and MD descriptors that are specific to Vitamin D analogs and VDR. Initially, 2D and 3D descriptors and fingerprints of 1003 vitamin D analogs were calculated using CDK and RDKit. The machine learning model was generated using descriptors and fingerprints. Further, 80 Vitamin D analogs (40 VDR agonists + 40 VDR antagonists) were docked in the VDR active site. 50ns MD simulation was performed for each protein-ligand complex. Different MD descriptors such as Solvent Accessible Surface Area (SASA), radius of gyration, PC1 and PC2 were calculated and considered along with CDK and RDKit descriptors as features for machine learning calculations. A few other descriptors that are related to VDR conformational changes such as conformation of the (H)12, the angle at kink were considered for machine learning model generation. It was observed that the descriptors calculated from VDR conformational changes i) were able to distinguish between agonists and antagonists ii) provide key and comprehensive information about the unique binding characteristics of agonists and antagonists iii) provide a strong basis for the machine learning model generation. Overall, this study attempts the utilization of descriptors that are specific to a protein conformation will be helpful for the generation of an efficient machine learning model.
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Affiliation(s)
- Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Lavi Jaiswal
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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6
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Rochel N. Vitamin D and Its Receptor from a Structural Perspective. Nutrients 2022; 14:nu14142847. [PMID: 35889804 PMCID: PMC9325172 DOI: 10.3390/nu14142847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
The activities of 1α,25-dihydroxyvitamin D3, 1,25D3, are mediated via its binding to the vitamin D receptor (VDR), a ligand-dependent transcription factor that belongs to the nuclear receptor superfamily. Numerous studies have demonstrated the important role of 1,25D3 and VDR signaling in various biological processes and associated pathologies. A wealth of information about ligand recognition and mechanism of action by structural analysis of the VDR complexes is also available. The methods used in these structural studies were mainly X-ray crystallography complemented by NMR, cryo-electron microscopy and structural mass spectrometry. This review aims to provide an overview of the current knowledge of VDR structures and also to explore the recent progress in understanding the complex mechanism of action of 1,25D3 from a structural perspective.
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Affiliation(s)
- Natacha Rochel
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
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7
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Feng P, Shu S, Zhao F. Anti-osteoporosis Effect of Fisetin against Ovariectomy Induced Osteoporosis in Rats: In silico, in vitro and in vivo Activity. J Oleo Sci 2022; 71:105-118. [PMID: 35013033 DOI: 10.5650/jos.ess21252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Osteoporosis is a bone related disease that is characterised by bone loss that further increases the susceptibility to bone fractures and bone frailty due to disturbances in the micro-architecture of bone tissue. Fisetin (flavonoids) exhibited anti-inflammatory and antioxidative stress effects against various diseases. In this protocol, we make an effort to comfort the anti-osteoporosis effect of fisetin against ovariectomy (OVX) induced osteoporosis. A docking study of fisetin and alendronate on the estrogen (α and β) and vitamin D receptors was carried out. SaOS-2 (osteoblast like human) cells were used for the estimation of cell proliferation. The OVX induced OVX model was used and three doses of fisetin and alendronate was given to rats till 16 weeks. The hormone levels, bone turnover markers and biochemical parameters were estimated. Fisetin was docked into estrogen (α and β) and vitamin D receptors, resulting in stable complexes with lower binding scores. Fisetin significantly (p < 0.001) exhibited the induction of cell proliferation against the SaOS-2 cells. OVX induced osteoporosis rats exhibited a suppression of body weight and uterus index, after the Fisetin treatment. Fisetin treatment significantly (p < 0.001) improved the level of bone mineral content (BMC), bone mineral density (BMD) and biochemical parameters such as energy, maximum load, stiffness, young modules, maximum stress and reduced the level of 1,25(OH) 2 D3 and E 2 . Fisetin treatment significantly (p < 0.001) declined the level of phosphorus (P), calcium (Ca) and boosted the level of VitD. Fisetin treatment significantly (p < 0.001) reduced the malonaldehyde (MDA) level and enhanced the glutathione (GSH), catalase (CAT), superoxide dismutase (SOD) level in the bone, intestine and hepatic tissue. Fisetin treatment suppressed the cytokines, RANKL/OPG ratio, receptor activator of nuclear factor-κB ligand (RANKL) and improved the level of osteoprotegerin (OPG). The findings suggest that fisetin could be a beneficial phytoconstituent for the treatment and prevention of postmenopausal osteoporotic complications.
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Affiliation(s)
- Peng Feng
- Department of Orthopedics, Tongchuan People's Hospital
| | - Shijun Shu
- Department of Orthopedics, Xiamen Fifth Hospital
| | - Feifei Zhao
- Department of Orthopedic, The Fourth Hospital of Hebei Medical University (Hebei Cancer Hospital)
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8
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Estes B, Sudom A, Gong D, Whittington DA, Li V, Mohr C, Li D, Riley TP, Shi SDH, Zhang J, Garces F, Wang Z. Next generation Fc scaffold for multispecific antibodies. iScience 2021; 24:103447. [PMID: 34877503 PMCID: PMC8633962 DOI: 10.1016/j.isci.2021.103447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/13/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Bispecific antibodies (Bispecifics) demonstrate exceptional clinical potential to address some of the most complex diseases. However, Bispecific production in a single cell often requires the correct pairing of multiple polypeptide chains for desired assembly. This is a considerable hurdle that hinders the development of many immunoglobulin G (IgG)-like bispecific formats. Our approach focuses on the rational engineering of charged residues to facilitate the chain pairing of distinct heavy chains (HC). Here, we deploy structure-guided protein design to engineer charge pair mutations (CPMs) placed in the CH3-CH3' interface of the fragment crystallizable (Fc) region of an antibody (Ab) to correctly steer heavy chain pairing. When used in combination with our stable effector functionless 2 (SEFL2.2) technology, we observed high pairing efficiency without significant losses in expression yields. Furthermore, we investigate the relationship between CPMs and the sequence diversity in the parental antibodies, proposing a rational strategy to deploy these engineering technologies.
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Affiliation(s)
- Bram Estes
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Athena Sudom
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., San Francisco, CA 94080, USA
| | - Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Douglas A. Whittington
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Cambridge, MA 02141, USA
| | - Vivian Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Christopher Mohr
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Timothy P. Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Stone D.-H. Shi
- Department of Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Jun Zhang
- Department of Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc., San Francisco, CA 94080, USA
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9
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Ekimoto T, Kudo T, Yamane T, Ikeguchi M. Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations. J Chem Inf Model 2021; 61:3625-3637. [PMID: 34189910 DOI: 10.1021/acs.jcim.1c00534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The vitamin D receptor ligand-binding domain (VDR-LBD) undergoes conformational changes upon ligand binding. In this nuclear receptor family, agonistic or antagonistic activities are controlled by the conformation of the helix (H)12. However, all crystal structures of VDR-LBD reported to date correspond to the active H12 conformation, regardless of agonist/antagonist binding. To understand the mechanism of VDR-LBD regulation structurally, conformational samplings of agonist- and antagonist-bound rat VDR-LBD were performed using the generalized replica exchange with solute tempering (gREST) method. The gREST simulations demonstrated different structural responses of rat VDR-LBD to agonist or antagonist binding, whereas in conventional molecular dynamics simulations, the conformation was the same as that of the crystal structures, regardless of agonist/antagonist binding. In the gREST simulations, a spontaneous conformational change of H12 was observed only for the antagonist complex. The different responses to agonist/antagonist binding were attributed to hydrophobic core formation at the ligand-binding pocket and cooperative rearrangements of H11. The gREST method can be applied to the examination of structure-activity relationships for multiple VDR-LBD ligands.
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Affiliation(s)
- Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takafumi Kudo
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsutomu Yamane
- Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Center for Computational Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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10
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Yang Z, Muccio DD, Melo N, Atigadda VR, Renfrow MB. Stability of the Retinoid X Receptor-α Homodimer in the Presence and Absence of Rexinoid and Coactivator Peptide. Biochemistry 2021; 60:1165-1177. [PMID: 33792309 PMCID: PMC9949482 DOI: 10.1021/acs.biochem.0c00865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Differential scanning calorimetry and differential scanning fluorimetry were used to measure the thermal stability of human retinoid X receptor-α ligand binding domain (RXRα LBD) homodimer in the absence or presence of rexinoid and coactivator peptide, GRIP-1. The apo-RXRα LBD homodimer displayed a single thermal unfolding transition with a Tm of 58.7 °C and an unfolding enthalpy (ΔH) of 673 kJ/mol (12.5 J/g), much lower than average value (35 J/g) of small globular proteins. Using a heat capacity change (ΔCp) of 15 kJ/(mol K) determined by measurements at different pH values, the free energy of unfolding (ΔG) of the native state was 33 kJ/mol at 37 °C. Rexinoid binding to the apo-homodimer increased Tm by 5 to 9 °C and increased the ΔG of the native homodimer by 12 to 20 kJ/mol at 37 °C, consistent with the nanomolar dissociation constant (Kd) of the rexinoids. GRIP-1 binding to holo-homodimers containing rexinoid resulted in additional increases in ΔG of 14 kJ/mol, a value that was the same for all three rexinoids. Binding of rexinoid and GRIP-1 resulted in a combined 50% increase in unfolding enthalpy, consistent with reduced structural fluidity and more compact folding observed in other published structural studies. The complexes of UAB110 and UAB111 are each more stable than the UAB30 complex by 8 kJ/mol due to enhanced hydrophobic interactions in the binding pocket because of their larger end groups. This increase in thermodynamic stability positively correlates with their improved RXR activation potency. Thermodynamic measurements are thus valuable in predicting agonist potency.
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Affiliation(s)
- Zhengrong Yang
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Donald D. Muccio
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Nathalia Melo
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Venkatram R. Atigadda
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Matthew B. Renfrow
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
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11
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Bianchetti L, Sinar D, Depenveiller C, Dejaegere A. Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study. Proteins 2021; 89:952-965. [PMID: 33713045 DOI: 10.1002/prot.26073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
Abstract
In vertebrates, the mineralocorticoid receptor (MR) is a steroid-activated nuclear receptor (NR) that plays essential roles in water-electrolyte balance and blood pressure homeostasis. It belongs to the group of oxo-steroidian NRs, together with the glucocorticoid (GR), progesterone (PR), and androgen (AR) receptors. Classically, these oxo-steroidian NRs homodimerize and bind to specific genomic sequences to activate gene expression. NRs are multi-domain proteins, and dimerization is mediated by both the DNA (DBD) and ligand binding domains (LBDs), with the latter thought to provide the largest dimerization interface. However, at the structural level, the dimerization of oxo-steroidian receptors LBDs has remained largely a matter of debate and, despite their sequence homology, there is currently no consensus on a common homodimer assembly across the four receptors, that is, GR, PR, AR, and MR. Here, we examined all available MR LBD crystals using different computational methods (protein common interface database, proteins, interfaces, structures and assemblies, protein-protein interaction prediction by structural matching, and evolutionary protein-protein interface classifier, and the molecular mechanics Poisson-Boltzmann surface area method). A consensus is reached by all methods and singles out an interface mediated by helices H9, H10 and the C-terminal F domain as having characteristics of a biologically relevant assembly. Interestingly, a similar assembly was previously identified for GRα, MR closest homolog. Alternative architectures that were proposed for GRα were not observed for MR. These data call for further experimental investigations of oxo-steroid dimer architectures.
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Affiliation(s)
- Laurent Bianchetti
- Laboratoire de Chimie Biophysique de la Signalisation de la Transcription, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch, France
| | - Deniz Sinar
- Laboratoire de Chimie Biophysique de la Signalisation de la Transcription, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch, France
| | - Camille Depenveiller
- Laboratoire de Chimie Biophysique de la Signalisation de la Transcription, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch, France
| | - Annick Dejaegere
- Laboratoire de Chimie Biophysique de la Signalisation de la Transcription, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch, France
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12
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Belorusova AY, Chalhoub S, Rovito D, Rochel N. Structural Analysis of VDR Complex with ZK168281 Antagonist. J Med Chem 2020; 63:9457-9463. [PMID: 32787090 DOI: 10.1021/acs.jmedchem.0c00656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Vitamin D receptor (VDR) antagonists prevent the VDR activation function helix 12 from folding into its active conformation, thus affecting coactivator recruitment and antagonizing the transcriptional regulation induced by 1α,25-dihydroxyvitamin D3. Here, we report the crystal structure of the zebrafish VDR ligand-binding domain in complex with the ZK168281 antagonist, revealing that the ligand prevents optimal folding of the C-terminal region of VDR. This interference was confirmed by hydrogen-deuterium exchange mass spectrometry (HDX-MS) in solution.
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Affiliation(s)
- Anna Y Belorusova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France.,Medicinal Chemistry, Early Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Sandra Chalhoub
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Daniela Rovito
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM), U1258, 67400 Illkirch, France.,Centre National de Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
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13
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Ribone SR, Ferronato MJ, Vitale C, Fall Y, Curino AC, Facchinetti MM, Quevedo MA. Vitamin D receptor exhibits different pharmacodynamic features in tumoral and normal microenvironments: A molecular modeling study. J Steroid Biochem Mol Biol 2020; 200:105649. [PMID: 32142933 DOI: 10.1016/j.jsbmb.2020.105649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/20/2022]
Abstract
The vitamin D receptor (VDR) constitutes a promising therapeutic target for the treatment of cancer. Unfortunately, its natural agonist calcitriol does not have clinical utility due to its potential to induce hypercalcemic effects at the concentrations required to display antitumoral activity. For this reason, the search for new calcitriol analogues with adequate therapeutic profiles has been actively pursued by the scientific community. We have previously reported the obtaining and the biological activity evaluation of new calcitriol analogues by modification of its sidechain, which exhibited relevant antiproliferative and selectivity profiles against tumoral and normal cells. In this work we conducted molecular modeling studies (i.e. molecular docking, molecular dynamics, constant pH molecular dynamics (CpHMD) and free energy of binding analysis) to elucidate at an atomistic level the molecular basis related to the potential of the new calcitriol analogues to achieve selectivity between tumoral and normal cells. Two histidine residues (His305 and His397) were found to exhibit a particular tautomeric configuration that produces the observed bioactivity. Also, different acid-based properties were observed for His305 and His307 with His305 showing an increased acidity (pKa 5.2) compared to His397 (pKa 6.8) and to the typical histidine residue. This behavior favored the pharmacodynamic interaction of the calcitriol analogues exhibiting selectivity for tumoral cells when VDR was modeled at the more acidic tumoral environment (pH ≅ 6) compared to the case when VDR was modeled at pH 7.4 (normal cell environment). On the other hand, non-selective compounds, including calcitriol, exhibited a similar interaction pattern with VDR when the receptor was modeled at both pH conditions. The results presented constitute the first evidence on the properties of the VDR receptor in different physicochemical environments and thus represent a significant contribution to the in silico screening and design of new calcitriol analogues.
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Affiliation(s)
- Sergio R Ribone
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. X5000HUA, Córdoba, Argentina
| | - Maria J Ferronato
- Laboratorio de Biología del Cáncer, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), Universidad Nacional del Sur (UNS), CONICET, Departamento de Biología, Bioquímica y Farmacia (UNS), Bahía Blanca, Argentina
| | - Cristian Vitale
- Laboratorio de Química Orgánica, Instituto de Química del Sur (INQUISUR), Universidad Nacional del Sur (UNS), CONICET, Departamento de Química (UNS), Bahía Blanca, Argentina
| | - Yagamare Fall
- Departamento de Química Orgánica, Facultad de Química e Instituto de Investigación Biomédica (IBI), Universidad de Vigo, Campus Lagoas de Marcosende, 36310, Vigo, Spain
| | - Alejandro C Curino
- Laboratorio de Biología del Cáncer, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), Universidad Nacional del Sur (UNS), CONICET, Departamento de Biología, Bioquímica y Farmacia (UNS), Bahía Blanca, Argentina
| | - Maria M Facchinetti
- Laboratorio de Biología del Cáncer, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), Universidad Nacional del Sur (UNS), CONICET, Departamento de Biología, Bioquímica y Farmacia (UNS), Bahía Blanca, Argentina
| | - Mario A Quevedo
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba. X5000HUA, Córdoba, Argentina.
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14
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Shang J, Mosure SA, Zheng J, Brust R, Bass J, Nichols A, Solt LA, Griffin PR, Kojetin DJ. A molecular switch regulating transcriptional repression and activation of PPARγ. Nat Commun 2020; 11:956. [PMID: 32075969 PMCID: PMC7031403 DOI: 10.1038/s41467-020-14750-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Nuclear receptor (NR) transcription factors use a conserved activation function-2 (AF-2) helix 12 mechanism for agonist-induced coactivator interaction and NR transcriptional activation. In contrast, ligand-induced corepressor-dependent NR repression appears to occur through structurally diverse mechanisms. We report two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation. Helix 12 is displaced from the solvent-exposed active conformation and occupies the orthosteric ligand-binding pocket enabled by a conformational change that doubles the pocket volume. Paramagnetic relaxation enhancement (PRE) NMR and chemical crosslinking mass spectrometry confirm the repressive helix 12 conformation. PRE NMR also defines the mechanism of action of the corepressor-selective inverse agonist T0070907, and reveals that apo-helix 12 exchanges between transcriptionally active and repressive conformations—supporting a fundamental hypothesis in the NR field that helix 12 exchanges between transcriptionally active and repressive conformations. Structural studies of nuclear receptor transcription factors revealed that nearly all nuclear receptors share a conserved helix 12 dependent transcriptional activation mechanism. Here the authors present two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation, where helix 12 is located within the orthosteric ligand-binding pocket instead, and discuss mechanistic implications.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Sarah A Mosure
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Jie Zheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Richard Brust
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Jared Bass
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ashley Nichols
- Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Laura A Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, 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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15
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Espada A, Haro R, Castañon J, Sayago C, Perez-Cozar F, Cano L, Redero P, Molina-Martin M, Broughton H, Stites RE, Pascal BD, Griffin PR, Dodge JA, Chalmers MJ. A Decoupled Automation Platform for Hydrogen/Deuterium Exchange Mass Spectrometry Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2580-2583. [PMID: 31724102 DOI: 10.1007/s13361-019-02331-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a biophysical technique well suited to the characterization of protein dynamics and protein-ligand interactions. In order to accurately define the rate of exchange, HDX experiments require the repeated measure of deuterium incorporation into the target protein across a range of time points. Accordingly, the HDX-MS experiment is well suited to automation, and a number of automated systems for HDX-MS have been developed. The most widely utilized platforms all operate an integrated design, where robotic liquid handling is interfaced directly with a mass spectrometer. With integrated designs, the exchange samples are prepared and injected into the LC-MS following a "real-time" serial workflow. Here we describe a new HDX-MS platform that is comprised of two complementary pieces of automation that disconnect the sample preparation from the LC-MS analysis. For preparation, a plate-based automation system is used to prepare samples in parallel, followed by immediate freezing and storage. A second piece of automation has been constructed to perform the thawing and LC-MS analysis of frozen samples in a serial mode and has been optimized to maximize the duty cycle of the mass spectrometer. The decoupled configuration described here reduces experiment time, significantly improves capacity, and improves the flexibility of the platform when compared with a fully integrated system.
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Affiliation(s)
- Alfonso Espada
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Ruben Haro
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Jesus Castañon
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Cristina Sayago
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Francisco Perez-Cozar
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Leticia Cano
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Pablo Redero
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Manuel Molina-Martin
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Howard Broughton
- Centro de Investigación Lilly, SA, Avenida de la Industria 30, 28108, Alcobendas, Spain
| | - Ryan E Stites
- Eli Lilly and Company, Lilly Corporate Center, Lilly Research Laboratories, Indianapolis, IN, 46285, USA
| | - Bruce D Pascal
- Omics Informatics LLC, 1050 Bishop Street #517, Honolulu, HI, 96813, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Jeffrey A Dodge
- Eli Lilly and Company, Lilly Corporate Center, Lilly Research Laboratories, Indianapolis, IN, 46285, USA
| | - Michael J Chalmers
- Eli Lilly and Company, Lilly Corporate Center, Lilly Research Laboratories, Indianapolis, IN, 46285, USA.
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16
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Chai SC, Wright WC, Chen T. Strategies for developing pregnane X receptor antagonists: Implications from metabolism to cancer. Med Res Rev 2019; 40:1061-1083. [PMID: 31782213 DOI: 10.1002/med.21648] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/24/2019] [Accepted: 11/19/2019] [Indexed: 12/11/2022]
Abstract
Pregnane X receptor (PXR) is a ligand-activated nuclear receptor (NR) that was originally identified as a master regulator of xenobiotic detoxification. It regulates the expression of drug-metabolizing enzymes and transporters to control the degradation and excretion of endobiotics and xenobiotics, including therapeutic agents. The metabolism and disposition of drugs might compromise their efficacy and possibly cause drug toxicity and/or drug resistance. Because many drugs can promiscuously bind and activate PXR, PXR antagonists might have therapeutic value in preventing and overcoming drug-induced PXR-mediated drug toxicity and drug resistance. Furthermore, PXR is now known to have broader cellular functions, including the regulation of cell proliferation, and glucose and lipid metabolism. Thus, PXR might be involved in human diseases such as cancer and metabolic diseases. The importance of PXR antagonists is discussed in the context of the role of PXR in xenobiotic sensing and other disease-related pathways. This review focuses on the development of PXR antagonists, which has been hampered by the promiscuity of PXR ligand binding. However, substantial progress has been made in recent years, suggesting that it is feasible to develop selective PXR antagonists. We discuss the current status, challenges, and strategies in developing selective PXR antagonists. The strategies are based on the molecular mechanisms of antagonism in related NRs that can be applied to the design of PXR antagonists, primarily driven by structural information.
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Affiliation(s)
- Sergio C Chai
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - William C Wright
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee
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17
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Yamamoto K. Discovery of Nuclear Receptor Ligands and Elucidation of Their Mechanisms of Action. Chem Pharm Bull (Tokyo) 2019; 67:609-619. [DOI: 10.1248/cpb.c19-00131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
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18
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Mutchie TR, Yu OB, Di Milo ES, Arnold LA. Alternative binding sites at the vitamin D receptor and their ligands. Mol Cell Endocrinol 2019; 485:1-8. [PMID: 30654005 PMCID: PMC6444937 DOI: 10.1016/j.mce.2019.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/04/2019] [Accepted: 01/11/2019] [Indexed: 01/02/2023]
Abstract
In recent decades, the majority of ligands developed for the vitamin D receptor (VDR) bind at its deeply buried genomic ligand binding pocket. Theses ligands can be categorized into agonists and partial agonists/antagonists. A limited number of ligands, most of them peptides, bind the VDR‒coactivator binding site that is formed in the presence of an agonist and inhibit coactivator recruitment, and therefore transcription. Another solvent exposed VDR‒ligand binding pocket was identified for lithocholic acid, improving the overall stability of the VDR complex. Additional proposed interactions with VDR are discussed herein that include the alternative VDR‒ligand binding pocket that may mediate both non-genomic cellular responses and binding function 3 that was identified for the androgen receptor. Many VDR ligands increase blood calcium levels at therapeutic concentrations in vivo, thus the identification of alternative VDR‒ligand binding pockets might be crucial to develop non-calcemic and potent ligands for VDR to treat cancer and inflammatory disease.
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Affiliation(s)
- Tania R Mutchie
- Department of Chemistry and Biochemistry and Milwaukee Institute for Drug Discovery (MIDD), University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Olivia B Yu
- Department of Chemistry and Biochemistry and Milwaukee Institute for Drug Discovery (MIDD), University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Elliot S Di Milo
- Department of Chemistry and Biochemistry and Milwaukee Institute for Drug Discovery (MIDD), University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Leggy A Arnold
- Department of Chemistry and Biochemistry and Milwaukee Institute for Drug Discovery (MIDD), University of Wisconsin, Milwaukee, WI, 53211, USA.
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19
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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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20
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Devaurs D, Antunes DA, Kavraki LE. Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data. Int J Mol Sci 2018; 19:E3406. [PMID: 30384411 PMCID: PMC6280153 DOI: 10.3390/ijms19113406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 11/17/2022] Open
Abstract
Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein structure. However, experimentally observing and computationally modeling large proteins remain critical challenges for structural biology. Our work aims at addressing these challenges by combining computational and experimental techniques relying on each other to overcome their respective limitations. Indeed, despite its advantages, an experimental technique such as hydrogen-exchange monitoring cannot produce structural models because of its low resolution. Additionally, the computational methods that can generate such models suffer from the curse of dimensionality when applied to large proteins. Adopting a common solution to this issue, we have recently proposed a framework in which our computational method for protein conformational sampling is biased by experimental hydrogen-exchange data. In this paper, we present our latest application of this computational framework: generating an atomic-resolution structural model for an unknown protein state. For that, starting from an available protein structure, we explore the conformational space of this protein, using hydrogen-exchange data on this unknown state as a guide. We have successfully used our computational framework to generate models for three proteins of increasing size, the biggest one undergoing large-scale conformational changes.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA.
| | - Dinler A Antunes
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA.
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA.
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21
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Sicinska W, Gront D, Sicinski K. Mutation goals in the vitamin D receptor predicted by computational methods. J Steroid Biochem Mol Biol 2018; 183:210-220. [PMID: 29966696 DOI: 10.1016/j.jsbmb.2018.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/21/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
The mechanism through which nuclear receptors respond differentially to structurally distinct agonists is a poorly understood process. We present a computational method that identifies nuclear receptor amino acids that are likely involved in biological responses triggered by ligand binding. The method involves tracing how structural changes spread from the ligand binding pocket to the sites on the receptor surface, which makes it a good tool for studying allosteric effects. We employ the method to the vitamin D receptor and verify that the identified amino acids are biologically relevant using a broad range of experimental data and a genome browser. We infer that surface vitamin D receptor residues K141, R252, I260, T280, T287 and L417 are likely involved in cell differentiation and antiproliferation, whereas P122, D149, K321, E353 and Q385 are linked to carcinogenesis.
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Affiliation(s)
- Wanda Sicinska
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Dominik Gront
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Kamil Sicinski
- Center for Demography of Health and Aging, University of Wisconsin-Madison, 1180 Observatory Drive, Madison, WI 53706, United States
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22
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Zhang J, Woods C, He F, Han M, Treuheit MJ, Volkin DB. Structural Changes and Aggregation Mechanisms of Two Different Dimers of an IgG2 Monoclonal Antibody. Biochemistry 2018; 57:5466-5479. [DOI: 10.1021/acs.biochem.8b00575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun Zhang
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Christopher Woods
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66049, United States
| | - Feng He
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Mei Han
- Pharmacokinetics & Drug Metabolism, Amgen Inc., South San Francisco, California 94080, United States
| | - Michael J. Treuheit
- Process Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66049, United States
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23
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Yoshizawa M, Itoh T, Hori T, Kato A, Anami Y, Yoshimoto N, Yamamoto K. Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands. J Med Chem 2018; 61:6339-6349. [DOI: 10.1021/acs.jmedchem.8b00774] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mami Yoshizawa
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Tatsuya Hori
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Akira Kato
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yasuaki Anami
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Nobuko Yoshimoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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24
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Buchman CD, Chai SC, Chen T. A current structural perspective on PXR and CAR in drug metabolism. Expert Opin Drug Metab Toxicol 2018; 14:635-647. [PMID: 29757018 DOI: 10.1080/17425255.2018.1476488] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Pregnane X receptor (PXR) and the constitutive androstane receptor (CAR) are two members of the nuclear receptor superfamily that play major roles in the expression of various drug metabolism enzymes and are known for their ligand promiscuity. As with other nuclear receptors, PXR and CAR are each composed of a ligand-binding domain (LBD) and a DNA-binding domain (DBD) connected by a hinge region. Areas covered: This review focuses on the information obtained over the last 15+ years from X-ray crystallography studies of the structure of PXR and CAR. Areas of focus include the mobility of each structure, based on temperature factors (B factors); multimeric interactions; the binding of coregulators and ligands; and how the crystal structures were obtained. The first use of hydrogen-deuterium exchange coupled with mass spectroscopy (HDX-MS) to study compound-protein interactions in the PXR-LBD is also addressed. Expert opinion: X-ray crystallography studies have provided us with an excellent understanding of how the LBDs of each receptor function; however, many questions remain concerning the structure of these receptors. Future research should focus on determining the co-crystal structure of an antagonist bound to PXR and on studying the structural aspects of the full-length CAR and PXR proteins.
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Affiliation(s)
- Cameron D Buchman
- a Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Sergio C Chai
- a Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , Memphis , TN , USA
| | - Taosheng Chen
- a Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , Memphis , TN , USA
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25
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Rochel N, Molnár F. Structural aspects of Vitamin D endocrinology. Mol Cell Endocrinol 2017; 453:22-35. [PMID: 28257826 DOI: 10.1016/j.mce.2017.02.046] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/27/2017] [Accepted: 02/27/2017] [Indexed: 12/12/2022]
Abstract
1α,25-Dihydroxvitamin D3 (1,25(OH)2D3) is the hormonally active form of vitamin D3. Its synthesis and its metabolites, their transport and elimination as well as action on transcriptional regulation involves the harmonic cooperation of diverse proteins with vitamin D binding capacities such as vitamin D binding protein (DBP), cytochrome P450 enzymes or the nuclear vitamin receptor (VDR). The genomic mechanism of 1,25(OH)2D3 action involves its binding to VDR that functionally acts as a heterodimer with retinoid X receptor. The crystal structures of the most important proteins for vitamin D3, VDR, DBP, CYP2R1 and CYP24A1, have provided identification of mechanisms of actions of these proteins and those mediating VDR-regulated transcription. This review will present the structural information on recognition of the vitamin D3 and metabolites by CYP proteins and DBP as well as the structural basis of VDR activation by 1,25(OH)2D3 and metabolites. Additionally, we will describe, the implications of the VDR mutants associated with hereditary vitamin D-resistant rickets (HVDRR) that display impaired function.
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Affiliation(s)
- Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U964/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404 Illkirch, France.
| | - Ferdinand Molnár
- Institute of Biopharmacy, School of Pharmacy, Faculty of Heath Science, University of Eastern Finland, Yliopistonranta 1C, Canthia 2036, 70210 Kuopio, Finland.
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26
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Zhang J, Li J, Craig TA, Kumar R, Gross ML. Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM). Biochemistry 2017. [PMID: 28627884 DOI: 10.1021/acs.biochem.7b00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca2+-binding protein that also binds to a specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca2+ but detaches from DRE under Ca2+ stimulation, allowing gene expression. The Ca2+ binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca2+ binding properties and the subsequent conformational changes of full-length DREAM. We demonstrate that all EF-hands undergo large conformation changes upon calcium binding even though the EF-1 hand is not capable of binding to Ca2+. Moreover, EF-2 is a lower-affinity site compared to EF-3 and -4 hands. Comparison of HDX profiles between wild-type DREAM and two EF-1 mutated constructs illustrates that the conformational changes in the EF-1 hand are induced by long-range structural interactions. HDX analyses also reveal a conformational change in an N-terminal leucine-charged residue-rich domain (LCD) remote from Ca2+-binding EF-hands. This LCD domain is responsible for the direct interaction between DREAM and cAMP response element-binding protein (CREB) and regulates the recruitment of the co-activator, CREB-binding protein. These long-range interactions strongly suggest how conformational changes transmit the Ca2+ signal to CREB-mediated gene transcription.
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Affiliation(s)
- Jun Zhang
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Jing Li
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Theodore A Craig
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic , Rochester, Minnesota 55905, United States
| | - Rajiv Kumar
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic , Rochester, Minnesota 55905, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
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27
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Doebelin C, Patouret R, Garcia-Ordonez RD, Chang MR, Dharmarajan V, Kuruvilla DS, Novick SJ, Lin L, Cameron MD, Griffin PR, Kamenecka TM. N-Arylsulfonyl Indolines as Retinoic Acid Receptor-Related Orphan Receptor γ (RORγ) Agonists. ChemMedChem 2016; 11:2607-2620. [PMID: 27879053 PMCID: PMC5158182 DOI: 10.1002/cmdc.201600491] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/20/2016] [Indexed: 11/08/2022]
Abstract
The nuclear retinoic acid receptor-related orphan receptor γ (RORγ; NR1F3) is a key regulator of inflammatory gene programs involved in T helper 17 (TH 17) cell proliferation. As such, synthetic small-molecule repressors (inverse agonists) targeting RORγ have been extensively studied for their potential as therapeutic agents for various autoimmune diseases. Alternatively, enhancing TH 17 cell proliferation through activation (agonism) of RORγ may boost an immune response, thereby offering a potentially new approach in cancer immunotherapy. Herein we describe the development of N-arylsulfonyl indolines as RORγ agonists. Structure-activity studies reveal a critical linker region in these molecules as the major determinant for agonism. Hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) analysis of RORγ-ligand complexes help rationalize the observed results.
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Affiliation(s)
- Christelle Doebelin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Rémi Patouret
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Ruben D Garcia-Ordonez
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Mi Ra Chang
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | | | - Dana S Kuruvilla
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Scott J Novick
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Li Lin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Michael D Cameron
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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28
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Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions. J Phys Chem B 2016; 121:3493-3501. [PMID: 27807976 DOI: 10.1021/acs.jpcb.6b09358] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand. Residue-level analysis of these data, however, must account for experimental error, sparseness, and ambiguity due to overlapping peptides. Here, we propose a Bayesian method consisting of a forward model, noise model, prior probabilities, and a Monte Carlo sampling scheme. This method exploits a residue-resolved exponential rate model of HDX-MS data obtained from all peptides simultaneously, and explicitly models experimental error. The result is the best possible estimate of ΔHDX magnitude and significance for each residue given the data. We demonstrate the method by revealing richer structural interpretation of ΔHDX data on two nuclear receptors: vitamin D-receptor (VDR) and retinoic acid receptor gamma (RORγ). The method is implemented in HDX Workbench and as a standalone module of the open source Integrative Modeling Platform.
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Affiliation(s)
- Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California, United States
| | - Howard B Broughton
- Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California, United States.,Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528 , Paris, France
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana, United States
| | - Alfonso Espada
- Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Jeffrey A Dodge
- Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana, United States
| | - Bruce D Pascal
- Bioinformatics Core, The Scripps Research Institute-Scripps Florida , Jupiter, Florida, United States
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida , Jupiter, Florida, United States
| | - Christine Humblet
- Lilly Research Laboratories, Eli Lilly and Company , Indianapolis, Indiana, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California, United States
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29
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Tee WV, Ripen AM, Mohamad SB. The conformational dynamics of H2-H3n and S2-H6 in gating ligand entry into the buried binding cavity of vitamin D receptor. Sci Rep 2016; 6:35937. [PMID: 27786277 PMCID: PMC5081507 DOI: 10.1038/srep35937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022] Open
Abstract
Crystal structures of holo vitamin D receptor (VDR) revealed a canonical conformation in which the ligand is entrapped in a hydrophobic cavity buried in the ligand-binding domain (LBD). The mousetrap model postulates that helix 12 is positioned away from the domain to expose the interior cavity. However, the extended form of helix 12 is likely due to artifacts during crystallization. In this study, we set out to investigate conformational dynamics of apo VDR using molecular dynamics simulation on microsecond timescale. Here we show the neighboring backbones of helix 2-helix 3n and beta strand 2-helix 6 of LBD, instead of the helix 12, undergo large-scale motion, possibly gating the entrance of ligand to the ligand binding domain. Docking analysis to the simulated open structure of VDR with the estimated free energy of -37.0 kJ/mol, would emphasise the role of H2-H3n and S2-H6 in facilitating the entrance of calcitriol to the LBD of VDR.
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Affiliation(s)
- Wei-Ven Tee
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Adiratna Mat Ripen
- Allergy and Immunology Research Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, 50603 Kuala Lumpur, Malaysia
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30
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Conformational modulation of the farnesoid X receptor by prenylflavonoids: Insights from hydrogen deuterium exchange mass spectrometry (HDX-MS), fluorescence titration and molecular docking studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1667-1677. [PMID: 27596062 DOI: 10.1016/j.bbapap.2016.08.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 12/20/2022]
Abstract
We report on the molecular interactions of the farnesoid X receptor (FXR) with prenylflavonoids, an emerging class of FXR modulators. FXR is an attractive therapeutic target for mitigating metabolic syndromes (MetS) because FXR activates the inhibitory nuclear receptor, small heterodimer partner (SHP), thereby inhibiting both gluconeogenesis and de novo lipogenesis. We and others have shown that xanthohumol (XN), the principal prenylflavonoid of the hop plant (Humulus lupulus L.), is a FXR agonist based on its ability to affect lipid and glucose metabolism in vivo and to induces FXR target genes in biliary carcinoma cells and HEK293 cells. However, studies are currently lacking to rationalize the molecular mechanisms of FXR modulation by prenylflavonoids. We addressed this deficiency and report the first systematic study of FXR prenylflavonoid interactions. We combined hydrogen deuterium exchange mass spectrometry (HDX-MS) with computational studies for dissecting molecular recognition and conformational impact of prenylflavonoid interactions on the ligand binding domain (LBD) of human FXR. Four prenylflavonoids were tested: xanthohumol, a prenylated chalcone, two prenylated flavonones, namely isoxanthohumol (IX) and 8-prenylnaringenin (8PN), and a semisynthetic prenylflavonoid derivative, tetrahydroxanthohumol (TX). Enhancement of the HDX protection profile data by in silico predicted models of FXR prenylflavonoid complexes resulted in mapping of the prenylflavonoid interactions within the canonical ligand binding pocket. Our findings provide a foundation for the exploration of the chemical scaffolds of prenylated chalcones and flavanones as leads for future structure activity studies of this important nuclear receptor with potential relevance for ameliorating lipid metabolic disorders associated with obesity and MetS.
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31
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Anami Y, Shimizu N, Ekimoto T, Egawa D, Itoh T, Ikeguchi M, Yamamoto K. Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics. J Med Chem 2016; 59:7888-900. [DOI: 10.1021/acs.jmedchem.6b00682] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasuaki Anami
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Nobutaka Shimizu
- Photon
Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toru Ekimoto
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Daichi Egawa
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Mitsunori Ikeguchi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Keiko Yamamoto
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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32
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Asano L, Waku T, Abe R, Kuwabara N, Ito I, Yanagisawa J, Nagasawa K, Shimizu T. Regulation of the vitamin D receptor by vitamin D lactam derivatives. FEBS Lett 2016; 590:3270-9. [PMID: 27500498 DOI: 10.1002/1873-3468.12348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 11/06/2022]
Abstract
The active metabolite of vitamin D3 , 1α,25-dihydroxyvitamin D3 , acts as a ligand for the vitamin D receptor (VDR) and activates VDR-mediated gene expression. Recently, we characterized 1α,25-dihydroxyvitamin D3 -26,23-lactams (DLAMs), which mimic vitamin D3 metabolites, as noncalcemic VDR ligands that barely activate the receptor. In this study, we present structural insights onto the regulation of VDR function by DLAMs. X-ray crystallographic analysis revealed that DLAMs induced a large conformational change in the loop region between helices H6 and H7 in the VDR ligand-binding domain. Our structural analysis suggests that targeting of the loop region may be a new mode of VDR regulation.
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Affiliation(s)
- Lisa Asano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Tsuyoshi Waku
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Rumi Abe
- Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Naoyuki Kuwabara
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
| | - Ichiaki Ito
- Graduate School of Life and Environmental Sciences/Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Junn Yanagisawa
- Graduate School of Life and Environmental Sciences/Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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33
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Quanico J, Franck J, Salzet M, Fournier I. On-tissue Direct Monitoring of Global Hydrogen/Deuterium Exchange by MALDI Mass Spectrometry: Tissue Deuterium Exchange Mass Spectrometry (TDXMS). Mol Cell Proteomics 2016; 15:3321-3330. [PMID: 27512083 DOI: 10.1074/mcp.o116.059832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022] Open
Abstract
Hydrogen/deuterium exchange mass spectrometric (H/DXMS) methods for protein structural analysis are conventionally performed in solution. We present Tissue Deuterium Exchange Mass Spectrometry (TDXMS), a method to directly monitor deuterium uptake on tissue, as a means to better approximate the deuterium exchange behavior of proteins in their native microenvironment. Using this method, a difference in deuterium uptake behavior was observed when the same proteins were monitored in solution and on tissue. The higher maximum deuterium uptake at equilibrium for all proteins analyzed in solution suggests a more open conformation in the absence of interacting partners normally observed on tissue. We also demonstrate a difference in the deuterium uptake behavior of a few proteins across different morphological regions of the same tissue section. Modifications of the total number of hydrogens exchanged, as well as the kinetics of exchange, were both observed. These results provide information on the implication of protein interactions with partners as well as on the conformational changes related to these interactions, and illustrate the importance of examining protein deuterium exchange behavior in the presence of its specific microenvironment directly at the level of tissues.
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Affiliation(s)
- Jusal Quanico
- From the ‡Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Julien Franck
- From the ‡Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Michel Salzet
- From the ‡Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
| | - Isabelle Fournier
- From the ‡Univ. Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, France
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34
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Ishii K, Noda M, Uchiyama S. Mass spectrometric analysis of protein-ligand interactions. Biophys Physicobiol 2016; 13:87-95. [PMID: 27924262 PMCID: PMC5042164 DOI: 10.2142/biophysico.13.0_87] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 12/01/2022] Open
Abstract
The interactions of small molecules with proteins (protein–ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein–ligand interactions. These interactions typically accompany association–dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development. Mass spectrometry (MS) has been used to determine the precise molecular masses of molecules. Recent advancements in MS enable us to determine the molecular masses of protein–ligand complexes without disrupting the non-covalent interactions through the gentle desolvation of the complexes by increasing the vacuum pressure of a chamber in a mass spectrometer. This method is called MS under non-denaturing conditions or native MS and allows the unambiguous determination of protein–ligand interactions. Under a few assumptions, MS has also been applied to determine the dissociation constants for protein–ligand interactions. The structural information of a protein–ligand interaction, such as the location of the interaction and conformational change in a protein, can also be analyzed using hydrogen/deuterium exchange MS. In this paper, we briefly describe the history, principle, and recent applications of MS for the study of protein–ligand interactions.
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Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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35
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Kato A, Itoh T, Anami Y, Egawa D, Yamamoto K. Helix12-Stabilization Antagonist of Vitamin D Receptor. Bioconjug Chem 2016; 27:1750-61. [PMID: 27294600 DOI: 10.1021/acs.bioconjchem.6b00246] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
To develop strong vitamin D receptor (VDR) antagonists and reveal their antagonistic mechanism, we designed and synthesized vitamin D analogues with bulky side chains based on the "active antagonist" concept in which antagonist prevents helix 12 (H12) folding. Of the synthesized analogues, compounds 3a and 3b showed strong antagonistic activity. Dynamic hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) and static X-ray crystal structure analyses indicated that compound 3a stabilizes H11-H12 but displaces H6-H7 so that 3a is a novel rather than "active" or "passive" type of antagonist. We classified 3a as a third type of antagonist and called it "H11-H12 stabilization antagonist". HDX-MS analysis indicated that antagonist 3b is an "active" antagonist. To date there are no reports relating to nuclear receptor antagonist that strongly stabilizes H12. In this study, we found first VDR antagonist that stabilizes H12 and we showed that antagonistic mechanism is diverse depending on each antagonist structure. Additionally, HDX-MS was proven to be very useful for investigations of protein structure alterations resulting from ligand binding.
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Affiliation(s)
- Akira Kato
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yasuaki Anami
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Daichi Egawa
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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Cummins DJ, Espada A, Novick SJ, Molina-Martin M, Stites RE, Espinosa JF, Broughton H, Goswami D, Pascal BD, Dodge JA, Chalmers MJ, Griffin PR. Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform. Anal Chem 2016; 88:6607-14. [PMID: 27224086 DOI: 10.1021/acs.analchem.6b01650] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) is an information-rich biophysical method for the characterization of protein dynamics. Successful applications of differential HDX-MS include the characterization of protein-ligand binding. A single differential HDX-MS data set (protein ± ligand) is often comprised of more than 40 individual HDX-MS experiments. To eliminate laborious manual processing of samples, and to minimize random and gross errors, automated systems for HDX-MS analysis have become routine in many laboratories. However, an automated system, while less prone to random errors introduced by human operators, may have systematic errors that go unnoticed without proper detection. Although the application of automated (and manual) HDX-MS has become common, there are only a handful of studies reporting the systematic evaluation of the performance of HDX-MS experiments, and no reports have been published describing a cross-site comparison of HDX-MS experiments. Here, we describe an automated HDX-MS platform that operates with a parallel, two-trap, two-column configuration that has been installed in two remote laboratories. To understand the performance of the system both within and between laboratories, we have designed and completed a test-retest repeatability study for differential HDX-MS experiments implemented at each of two laboratories, one in Florida and the other in Spain. This study provided sufficient data to do both within and between laboratory variability assessments. Initial results revealed a systematic run-order effect within one of the two systems. Therefore, the study was repeated, and this time the conclusion was that the experimental conditions were successfully replicated with minimal systematic error.
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Affiliation(s)
- David J Cummins
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Alfonso Espada
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Scott J Novick
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Manuel Molina-Martin
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Juan Felix Espinosa
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Howard Broughton
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Devrishi Goswami
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruce D Pascal
- The Scripps Research institute, Informatics Core, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jeffrey A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Patrick R Griffin
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
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Chang MR, Dharmarajan V, Doebelin C, Garcia-Ordonez RD, Novick SJ, Kuruvilla DS, Kamenecka TM, Griffin PR. Synthetic RORγt Agonists Enhance Protective Immunity. ACS Chem Biol 2016; 11:1012-8. [PMID: 26785144 DOI: 10.1021/acschembio.5b00899] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The T cell specific RORγ isoform RORγt has been shown to be the key lineage-defining transcription factor to initiate the differentiation program of TH17 and TC17 cells, cells that have demonstrated antitumor efficacy. RORγt controls gene networks that enhance immunity including increased IL17 production and decreased immune suppression. Both synthetic and putative endogenous agonists of RORγt have been shown to increase the basal activity of RORγt enhancing TH17 cell proliferation. Here, we show that activation of RORγt using synthetic agonists drives proliferation of TH17 cells while decreasing levels of the immune checkpoint protein PD-1, a mechanism that should enhance antitumor immunity while blunting tumor associated adaptive immune resistance. Interestingly, putative endogenous agonists drive proliferation of TH17 cells but do not repress PD-1. These findings suggest that synthetic agonists of RORγt should activate TC17/TH17 cells (with concomitant reduction in the Tregs population), repress PD-1, and produce IL17 in situ (a factor associated with good prognosis in cancer). Enhanced immunity and blockage of immune checkpoints has transformed cancer treatment; thus such a molecule would provide a unique approach for the treatment of cancer.
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Affiliation(s)
- Mi Ra Chang
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Venkatasubramanian Dharmarajan
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christelle Doebelin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Ruben D. Garcia-Ordonez
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Scott J. Novick
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Dana S. Kuruvilla
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Theodore M. Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Patrick R. Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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38
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Deredge D, Li J, Johnson KA, Wintrode PL. Hydrogen/Deuterium Exchange Kinetics Demonstrate Long Range Allosteric Effects of Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase. J Biol Chem 2016; 291:10078-88. [PMID: 27006396 DOI: 10.1074/jbc.m115.708370] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Indexed: 01/08/2023] Open
Abstract
New nonnucleoside analogs are being developed as part of a multi-drug regimen to treat hepatitis C viral infections. Particularly promising are inhibitors that bind to the surface of the thumb domain of the viral RNA-dependent RNA polymerase (NS5B). Numerous crystal structures have been solved showing small molecule non-nucleoside inhibitors bound to the hepatitis C viral polymerase, but these structures alone do not define the mechanism of inhibition. Our prior kinetic analysis showed that nonnucleoside inhibitors binding to thumb site-2 (NNI2) do not block initiation or elongation of RNA synthesis; rather, they block the transition from the initiation to elongation, which is thought to proceed with significant structural rearrangement of the enzyme-RNA complex. Here we have mapped the effect of three NNI2 inhibitors on the conformational dynamics of the enzyme using hydrogen/deuterium exchange kinetics. All three inhibitors rigidify an extensive allosteric network extending >40 Å from the binding site, thus providing a structural rationale for the observed disruption of the transition from distributive initiation to processive elongation. The two more potent inhibitors also suppress slow cooperative unfolding in the fingers extension-thumb interface and primer grip, which may contribute their stronger inhibition. These results establish that NNI2 inhibitors act through long range allosteric effects, reveal important conformational changes underlying normal polymerase function, and point the way to the design of more effective allosteric inhibitors that exploit this new information.
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Affiliation(s)
- Daniel Deredge
- From the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201 and
| | - Jiawen Li
- Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Kenneth A Johnson
- Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712
| | - Patrick L Wintrode
- From the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201 and
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Zhi X, Zhou XE, Melcher K, Xu HE. Structures and regulation of non-X orphan nuclear receptors: A retinoid hypothesis. J Steroid Biochem Mol Biol 2016; 157:27-40. [PMID: 26159912 DOI: 10.1016/j.jsbmb.2015.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 12/28/2022]
Abstract
Nuclear receptors are defined as a family of ligand regulated transcription factors [1-6]. While this definition reflects that ligand binding is a key property of nuclear receptors, it is still a heated subject of debate if all the nuclear receptors (48 human members) can bind ligands (ligands referred here to both physiological and synthetic ligands). Recent studies in nuclear receptor structure biology and pharmacology have undoubtedly increased our knowledge of nuclear receptor functions and their regulation. As a result, they point to new avenues for the discovery and development of nuclear receptor regulators, including nuclear receptor ligands. Here we review the recent literature on orphan nuclear receptor structural analysis and ligand identification, particularly on the orphan nuclear receptors that do not heterodimerize with retinoid X receptors, which we term as non-X orphan receptors. We also propose a speculative "retinoid hypothesis" for a subset of non-X orphan nuclear receptors, which we hope to help shed light on orphan nuclear receptor biology and drug discovery. This article is part of a Special Issue entitled 'Orphan Nuclear Receptors'.
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Affiliation(s)
- Xiaoyong Zhi
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA; Autophagy Research Center, University of Texas Southwestern Medical Center, 6000Harry Hines Blvd., Dallas, TX 75390, USA.
| | - X Edward Zhou
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA
| | - H Eric Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA; VARI-SIMM Center, Key Laboratory of Receptor Research, Shanghai Institute of MateriaMedica, Chinese Academy of Sciences, Shanghai 201203, China.
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40
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Zhang J, Kitova EN, Li J, Eugenio L, Ng K, Klassen JS. Localizing Carbohydrate Binding Sites in Proteins Using Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:83-90. [PMID: 26423923 DOI: 10.1007/s13361-015-1263-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/24/2015] [Accepted: 08/31/2015] [Indexed: 06/05/2023]
Abstract
The application of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to localize ligand binding sites in carbohydrate-binding proteins is described. Proteins from three bacterial toxins, the B subunit homopentamers of Cholera toxin and Shiga toxin type 1 and a fragment of Clostridium difficile toxin A, and their interactions with native carbohydrate receptors, GM1 pentasaccharides (β-Gal-(1→3)-β-GalNAc-(1→4)[α-Neu5Ac-(2→3)]-β-Gal-(1→4)-Glc), Pk trisaccharide (α-Gal-(1→4)-β-Gal-(1→4)-Glc) and CD-grease (α-Gal-(1→3)-β-Gal-(1→4)-β-GlcNAcO(CH2)8CO2CH3), respectively, served as model systems for this study. Comparison of the differences in deuterium uptake for peptic peptides produced in the absence and presence of ligand revealed regions of the proteins that are protected against deuterium exchange upon ligand binding. Notably, protected regions generally coincide with the carbohydrate binding sites identified by X-ray crystallography. However, ligand binding can also result in increased deuterium exchange in other parts of the protein, presumably through allosteric effects. Overall, the results of this study suggest that HDX-MS can serve as a useful tool for localizing the ligand binding sites in carbohydrate-binding proteins. However, a detailed interpretation of the changes in deuterium exchange upon ligand binding can be challenging because of the presence of ligand-induced changes in protein structure and dynamics.
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Affiliation(s)
- Jingjing Zhang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Alberta Glycomics Centre, Edmonton, Alberta, Canada
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Alberta Glycomics Centre, Edmonton, Alberta, Canada
| | - Jun Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Alberta Glycomics Centre, Edmonton, Alberta, Canada
| | - Luiz Eugenio
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Alberta Glycomics Centre, Edmonton, Alberta, Canada
| | - Kenneth Ng
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Alberta Glycomics Centre, Edmonton, Alberta, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
- Alberta Glycomics Centre, Edmonton, Alberta, Canada.
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41
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Belorusova AY, Rochel N. Structural Studies of Vitamin D Nuclear Receptor Ligand-Binding Properties. VITAMINS AND HORMONES 2015; 100:83-116. [PMID: 26827949 DOI: 10.1016/bs.vh.2015.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The vitamin D nuclear receptor (VDR) and its natural ligand, 1α,25-dihydroxyvitamin D3 hormone (1,25(OH)2D3, or calcitriol), classically regulate mineral homeostasis and metabolism but also much broader range of biological functions, such as cell growth, differentiation, antiproliferation, apoptosis, adaptive/innate immune responses. Being widely expressed in various tissues, VDR represents an important therapeutic target in the treatment of diverse disorders. Since ligand binding is a key step in VDR-mediated signaling, numerous 1,25(OH)2D3 analogs have been synthesized in order to selectively modulate the receptor activity. Most of the synthetic analogs have been developed by modification of a parental compound and some of them mimic 1,25(OH)2D3 scaffold without being structurally related to it. The ability of ligands that have different size and conformation to bind to VDR and to demonstrate biological effects is intriguing, and therefore, ligand-binding properties of the receptor have been extensively investigated using a variety of biochemical, biophysical, and computational methods. In this chapter, we describe different aspects of the structure-function relationship of VDR in complex with natural and synthetic ligands coming from structural analysis. With the emphasis on the binding modes of the most promising compounds, such as secosteroidal agonists and 1,25(OH)2D3 mimics, we also highlight the action of VDR antagonists and the evidence for the existence of an alternative ligand-binding site within the receptor. Additionally, we describe the crystal structures of VDR mutants associated with hereditary vitamin D-resistant rickets that display impaired ligand-binding function.
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Affiliation(s)
- Anna Y Belorusova
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, Illkirch, France.
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42
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Relationship between Structure and Conformational Change of the Vitamin D Receptor Ligand Binding Domain in 1α,25-Dihydroxyvitamin D3 Signaling. Molecules 2015; 20:20473-86. [PMID: 26593892 PMCID: PMC6332228 DOI: 10.3390/molecules201119713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/02/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Vitamin D Receptor (VDR) belongs to the nuclear receptor (NR) superfamily. Whereas the structure of the ligand binding domain (LBD) of VDR has been determined in great detail, the role of its amino acid residues in stabilizing the structure and ligand triggering conformational change is still under debate. There are 13 α-helices and one β-sheet in the VDR LBD and they form a three-layer sandwich structure stabilized by 10 residues. Thirty-six amino acid residues line the ligand binding pocket (LBP) and six of these residues have hydrogen-bonds linking with the ligand. In 1α,25-dihydroxyvitamin D3 signaling, H3 and H12 play an important role in the course of conformational change resulting in the provision of interfaces for dimerization, coactivator (CoA), corepressor (CoR), and hTAFII 28. In this paper we provide a detailed description of the amino acid residues stabilizing the structure and taking part in conformational change of VDR LBD according to functional domains.
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43
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Kojetin DJ, Matta-Camacho E, Hughes TS, Srinivasan S, Nwachukwu JC, Cavett V, Nowak J, Chalmers MJ, Marciano DP, Kamenecka TM, Shulman AI, Rance M, Griffin PR, Bruning JB, Nettles KW. Structural mechanism for signal transduction in RXR nuclear receptor heterodimers. Nat Commun 2015; 6:8013. [PMID: 26289479 PMCID: PMC4547401 DOI: 10.1038/ncomms9013] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/06/2015] [Indexed: 12/14/2022] Open
Abstract
A subset of nuclear receptors (NRs) function as obligate heterodimers with retinoid X receptor (RXR), allowing integration of ligand-dependent signals across the dimer interface via an unknown structural mechanism. Using nuclear magnetic resonance (NMR) spectroscopy, x-ray crystallography and hydrogen/deuterium exchange (HDX) mass spectrometry, here we show an allosteric mechanism through which RXR co-operates with a permissive dimer partner, peroxisome proliferator-activated receptor (PPAR)-γ, while rendered generally unresponsive by a non-permissive dimer partner, thyroid hormone (TR) receptor. Amino acid residues that mediate this allosteric mechanism comprise an evolutionarily conserved network discovered by statistical coupling analysis (SCA). This SCA network acts as a signalling rheostat to integrate signals between dimer partners, ligands and coregulator-binding sites, thereby affecting signal transmission in RXR heterodimers. These findings define rules guiding how NRs integrate two ligand-dependent signalling pathways into RXR heterodimer-specific responses. Some nuclear receptors dimerize with retinoid X receptor to allow ligand-dependent signalling. Here, Kojetin et al. use structural and biophysical techniques to identify structural changes that guide these complex signalling networks.
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Affiliation(s)
- Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Edna Matta-Camacho
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Travis S Hughes
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Valerie Cavett
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Jason Nowak
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Michael J Chalmers
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - David P Marciano
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - Andrew I Shulman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mark Rance
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45267, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
| | - John B Bruning
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA
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Zheng J, Yong HY, Panutdaporn N, Liu C, Tang K, Luo D. High-resolution HDX-MS reveals distinct mechanisms of RNA recognition and activation by RIG-I and MDA5. Nucleic Acids Res 2015; 43:1216-30. [PMID: 25539915 PMCID: PMC4333383 DOI: 10.1093/nar/gku1329] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 12/07/2014] [Accepted: 12/09/2014] [Indexed: 12/25/2022] Open
Abstract
RIG-I and MDA5 are the major intracellular immune receptors that recognize viral RNA species and undergo a series of conformational transitions leading to the activation of the interferon-mediated antiviral response. However, to date, full-length RLRs have resisted crystallographic efforts and a molecular description of their activation pathways remains hypothetical. Here we employ hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) to probe the apo states of RIG-I and MDA5 and to dissect the molecular details with respect to distinct RNA species recognition, ATP binding and hydrolysis and CARDs activation. We show that human RIG-I maintains an auto-inhibited resting state owing to the intra-molecular HEL2i-CARD2 interactions while apo MDA5 lacks the analogous intra-molecular interactions and therefore adopts an extended conformation. Our work demonstrates that RIG-I binds and responds differently to short triphosphorylated RNA and long duplex RNA and that sequential addition of RNA and ATP triggers specific allosteric effects leading to RIG-I CARDs activation. We also present a high-resolution protein surface mapping technique that refines the cooperative oligomerization model of neighboring MDA5 molecules on long duplex RNA. Taken together, our data provide a high-resolution view of RLR activation in solution and offer new evidence for the molecular mechanism of RLR activation.
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Affiliation(s)
- Jie Zheng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Hui Yee Yong
- Lee Kong Chian School of Medicine, Nanyang Technological University, 61 Biopolis Drive, Proteos Building, #07-03, 138673, Singapore
| | - Nantika Panutdaporn
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Chuanfa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Kai Tang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 61 Biopolis Drive, Proteos Building, #07-03, 138673, Singapore
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45
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Li J, Rodnin MV, Ladokhin AS, Gross ML. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain. Biochemistry 2014; 53:6849-56. [PMID: 25290210 PMCID: PMC4222528 DOI: 10.1021/bi500893y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.
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Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University , St. Louis, Missouri 63130, United States
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46
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Marciano DP, Dharmarajan V, Griffin PR. HDX-MS guided drug discovery: small molecules and biopharmaceuticals. Curr Opin Struct Biol 2014; 28:105-11. [PMID: 25179005 DOI: 10.1016/j.sbi.2014.08.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/24/2014] [Accepted: 08/13/2014] [Indexed: 12/24/2022]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS or DXMS) has emerged as an important tool for the development of small molecule therapeutics and biopharmaceuticals. Central to these advances have been improvements to automated HDX-MS platforms and software that allow for the rapid acquisition and processing of experimental data. Correlating the HDX-MS profile of large numbers of ligands with their functional outputs has enabled the development of structure activity relationships (SAR) and delineation of ligand classes based on functional selectivity. HDX-MS has also been applied to address many of the unique challenges posed by the continued emergence of biopharmaceuticals. Here we review the latest applications of HDX-MS to drug discovery, recent advances in technology and software, and provide perspective on future outlook.
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Affiliation(s)
- David P Marciano
- Molecular Therapeutics Department, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | | | - Patrick R Griffin
- Molecular Therapeutics Department, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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47
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Banks DD, Zhang J, Siska CC. Relationship between Native-State Solubility and Non-Native Aggregation of Recombinant Human Granulocyte Colony Stimulating Factor: Practical Implications for Protein Therapeutic Development. Mol Pharm 2014; 11:3431-42. [PMID: 25144791 DOI: 10.1021/mp500165j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Douglas D. Banks
- Department of Process and
Product Development, Amgen, Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, United States
| | - Jun Zhang
- Department of Process and
Product Development, Amgen, Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, United States
| | - Christine C. Siska
- Department of Process and
Product Development, Amgen, Inc., 1201 Amgen Court West, Seattle, Washington 98119-3105, United States
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48
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Janero DR. The future of drug discovery: enabling technologies for enhancing lead characterization and profiling therapeutic potential. Expert Opin Drug Discov 2014; 9:847-58. [PMID: 24965547 DOI: 10.1517/17460441.2014.925876] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Technology often serves as a handmaiden and catalyst of invention. The discovery of safe, effective medications depends critically upon experimental approaches capable of providing high-impact information on the biological effects of drug candidates early in the discovery pipeline. This information can enable reliable lead identification, pharmacological compound differentiation and successful translation of research output into clinically useful therapeutics. The shallow preclinical profiling of candidate compounds promulgates a minimalistic understanding of their biological effects and undermines the level of value creation necessary for finding quality leads worth moving forward within the development pipeline with efficiency and prognostic reliability sufficient to help remediate the current pharma-industry productivity drought. Three specific technologies discussed herein, in addition to experimental areas intimately associated with contemporary drug discovery, appear to hold particular promise for strengthening the preclinical valuation of drug candidates by deepening lead characterization. These are: i) hydrogen-deuterium exchange mass spectrometry for characterizing structural and ligand-interaction dynamics of disease-relevant proteins; ii) activity-based chemoproteomics for profiling the functional diversity of mammalian proteomes; and iii) nuclease-mediated precision gene editing for developing more translatable cellular and in vivo models of human diseases. When applied in an informed manner congruent with the clinical understanding of disease processes, technologies such as these that span levels of biological organization can serve as valuable enablers of drug discovery and potentially contribute to reducing the current, unacceptably high rates of compound clinical failure.
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Affiliation(s)
- David R Janero
- Northeastern University, Bouvé College of Health Sciences, Center for Drug Discovery, Department of Pharmaceutical Sciences, Health Sciences Entrepreneurs , 360 Huntington Avenue, 116 Mugar Life Sciences Hall, Boston, MA 02115-5000 , USA +1 617 373 2208 ; +1 617 373 7493 ;
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Yang L, Broderick D, Jiang Y, Hsu V, Maier CS. Conformational dynamics of human FXR-LBD ligand interactions studied by hydrogen/deuterium exchange mass spectrometry: insights into the antagonism of the hypolipidemic agent Z-guggulsterone. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1684-93. [PMID: 24953769 DOI: 10.1016/j.bbapap.2014.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/22/2014] [Accepted: 06/10/2014] [Indexed: 02/06/2023]
Abstract
Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of transcription factors that plays a key role in the regulation of bile acids, lipid and glucose metabolisms. The regulative function of FXR is governed by conformational changes of the ligand binding domain (LBD) upon ligand binding. Although FXR is a highly researched potential therapeutic target, only a limited number of FXR-agonist complexes have been successfully crystallized and subsequently yielded high resolution structures. There is currently no structural information of any FXR-antagonist complexes publically available. We therefore explored the use of amide hydrogen/deuterium exchange (HDX) coupled with mass spectrometry for characterizing conformational changes in the FXR-LBD upon ligand binding. Ligand-specific deuterium incorporation profiles were obtained for three FXR ligand chemotypes: GW4064, a synthetic non-steroidal high affinity agonist; the bile acid chenodeoxycholic acid (CDCA), the endogenous low affinity agonist of FXR; and Z-guggulsterone (GG), an in vitro antagonist of the steroid chemotype. A comparison of the HDX profiles of their ligand-bound FXR-LBD complexes revealed a unique mode of interaction for GG. The conformational features of the FXR-LBD-antagonist interaction are discussed.
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Affiliation(s)
- Liping Yang
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - David Broderick
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
| | - Victor Hsu
- Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
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50
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Carson MW, Zhang J, Chalmers MJ, Bocchinfuso WP, Holifield KD, Masquelin T, Stites RE, Stayrook KR, Griffin PR, Dodge JA. HDX reveals unique fragment ligands for the vitamin D receptor. Bioorg Med Chem Lett 2014; 24:3459-63. [PMID: 24974344 DOI: 10.1016/j.bmcl.2014.05.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/16/2014] [Accepted: 05/20/2014] [Indexed: 11/30/2022]
Abstract
Modulation of the vitamin D receptor (VDR) with a ligand has the potential to be useful for the oral treatment of osteoporosis. One component of our lead generation strategy to identify synthetic ligands for VDR included a fragment based drug design approach. Screening of ligands in a VDR fluorescence polarization assay and a RXR/VDR conformation sensing assay resulted in the identification of multiple fragment hits (lean >0.30). These fragment scaffolds were subsequently evaluated for interaction with the VDR ligand binding domain using hydrogen-deuterium exchange (HDX) mass spectrometry. Significant protection of H/D exchange was observed for some fragments in helixes 3, 7, and 8 of the ligand binding domain, regions which are similar to those seen for the natural hormone VD3. The fragments appear to mimic the A-ring of VD3 thereby providing viable starting points for synthetic expansion.
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Affiliation(s)
- Matthew W Carson
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States.
| | - Jun Zhang
- Department of Molecular Therapeutics, United States
| | - Michael J Chalmers
- Department of Molecular Therapeutics, United States; The Scripps Research Molecular Screening Center (SRMSC), United States
| | - Wayne P Bocchinfuso
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Karol D Holifield
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Keith R Stayrook
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Patrick R Griffin
- Department of Molecular Therapeutics, United States; The Scripps Research Molecular Screening Center (SRMSC), United States
| | - Jeffery A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, United States
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