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Hazarika S, Yu T, Biswas A, Dube N, Villalona P, Okafor CD. Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579785. [PMID: 38405809 PMCID: PMC10888817 DOI: 10.1101/2024.02.10.579785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (> 10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein-protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full length nuclear receptors.
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Affiliation(s)
- Saurov Hazarika
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tracy Yu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Arumay Biswas
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Namita Dube
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Priscilla Villalona
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - C. Denise Okafor
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
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Allosteric Antagonism of the Pregnane X Receptor (PXR): Current-State-of-the-Art and Prediction of Novel Allosteric Sites. Cells 2022; 11:cells11192974. [PMID: 36230936 PMCID: PMC9563780 DOI: 10.3390/cells11192974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
The pregnane X receptor (PXR, NR1I2) is a xenobiotic-activated transcription factor with high levels of expression in the liver. It not only plays a key role in drug metabolism and elimination, but also promotes tumor growth, drug resistance, and metabolic diseases. It has been proposed as a therapeutic target for type II diabetes, metabolic syndrome, and inflammatory bowel disease, and PXR antagonists have recently been considered as a therapy for colon cancer. There are currently no PXR antagonists that can be used in a clinical setting. Nevertheless, due to the large and complex ligand-binding pocket (LBP) of the PXR, it is challenging to discover PXR antagonists at the orthosteric site. Alternative ligand binding sites of the PXR have also been proposed and are currently being studied. Recently, the AF-2 allosteric binding site of the PXR has been identified, with several compounds modulating the site discovered. Herein, we aimed to summarize our current knowledge of allosteric modulation of the PXR as well as our attempt to unlock novel allosteric sites. We describe the novel binding function 3 (BF-3) site of PXR, which is also common for other nuclear receptors. In addition, we also mention a novel allosteric site III based on in silico prediction. The identified allosteric sites of the PXR provide new insights into the development of safe and efficient allosteric modulators of the PXR receptor. We therefore propose that novel PXR allosteric sites might be promising targets for treating chronic metabolic diseases and some cancers.
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Zhang C, Wu J, Chen Q, Tan H, Huang F, Guo J, Zhang X, Yu H, Shi W. Allosteric binding on nuclear receptors: Insights on screening of non-competitive endocrine-disrupting chemicals. ENVIRONMENT INTERNATIONAL 2022; 159:107009. [PMID: 34883459 DOI: 10.1016/j.envint.2021.107009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) can compete with endogenous hormones and bind to the orthosteric site of nuclear receptors (NRs), affecting normal endocrine system function and causing severe symptoms. Recently, a series of pharmaceuticals and personal care products (PPCPs) have been discovered to bind to the allosteric sites of NRs and induce similar effects. However, it remains unclear how diverse EDCs work in this new way. Therefore, we have systematically summarized the allosteric sites and underlying mechanisms based on existing studies, mainly regarding drugs belonging to the PPCP class. Advanced methods, classified as structural biology, biochemistry and computational simulation, together with their advantages and hurdles for allosteric site recognition and mechanism insight have also been described. Furthermore, we have highlighted two available strategies for virtual screening of numerous EDCs, relying on the structural features of allosteric sites and lead compounds, respectively. We aim to provide reliable theoretical and technical support for a broader view of various allosteric interactions between EDCs and NRs, and to drive high-throughput and accurate screening of potential EDCs with non-competitive effects.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Jinqiu Wu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Qinchang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Haoyue Tan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Fuyan Huang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Jing Guo
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China.
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Secondary (iso)BAs cooperate with endogenous ligands to activate FXR under physiological and pathological conditions. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166153. [PMID: 33895309 PMCID: PMC8177068 DOI: 10.1016/j.bbadis.2021.166153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 12/30/2022]
Abstract
IsoBAs, stereoisomers of primary and secondary BAs, are found in feces and plasma of human individuals. BA signaling via the nuclear receptor FXR is crucial for regulation of hepatic and intestinal physiology/pathophysiology. AIM Investigate the ability of BA-stereoisomers to bind and modulate FXR under physiological/pathological conditions. METHODS Expression-profiling, luciferase-assays, fluorescence-based coactivator-association assays, administration of (iso)-BAs to WT and cholestatic mice. RESULTS Compared to CDCA/isoCDCA, administration of DCA/isoDCA, UDCA/isoUDCA only slightly increased mRNA expression of FXR target genes; the induction was more evident looking at pre-mRNAs. Notably, almost 50% of isoBAs were metabolized to 3-oxo-BAs within 4 h in cell-based assays, making it difficult to study their actions. FRET-based real-time monitoring of FXR activity revealed that isoCDCA>CDCA stimulated FXR, and isoDCA and isoUDCA allowed fully activated FXR to be re-stimulated by a second dose of GW4064. In vivo co-administration of a single dose of isoBAs followed by GW4064 cooperatively activated FXR, as did feeding of UDCA in a background of endogenous FXR ligands. However, in animals with biliary obstruction and concomitant loss of intestinal BAs, UDCA was unable to increase intestinal Fgf15. In contrast, mice with an impaired enterohepatic circulation of BAs (Asbt-/-, Ostα-/-), administration of UDCA was still able to induce ileal Fgf15 and repress hepatic BA-synthesis, arguing that UDCA is only effective in the presence of endogenous FXR ligands. CONCLUSION Secondary (iso)BAs cooperatively activate FXR in the presence of endogenous BAs, which is important to consider in diseases linked to disturbances in BA enterohepatic cycling.
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Silvestris N, Argentiero A, Beretta GD, Di Bartolo P, Montagnani M, Danesi R, Ferrari P, D'Oronzo S, Gori S, Russo A, Acquati S, Gallo M. Management of metabolic adverse events of targeted therapies and immune checkpoint inhibitors in cancer patients: an Associazione Italiana Oncologia Medica (AIOM)/Associazione Medici Diabetologi (AMD)/Società Italiana Farmacologia (SIF) multidisciplinary consensus position paper. Crit Rev Oncol Hematol 2020; 154:103066. [PMID: 32853883 DOI: 10.1016/j.critrevonc.2020.103066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022] Open
Abstract
The growing insights in the next-generation immunotherapy and the state-of-the-art advancement in targeted-agents significantly improved clinical outcome of cancer patients by pointing towards a unexplored Achilles' heel. Novel toxicity profiles have been uncovered, representing unmet medical needs. Thus, a panel of expert provide comprehensive pharmacological and clinical evidence, to provide a patient-tailored approach to metabolic adverse events associated with novel anti-cancer treatments. Prompted by the need of a multidisciplinary cooperation, a working group of Associazione Italiana Oncologia Medica (AIOM), Associazione Medici Diabetologi (AMD) and Società Italiana Farmacologia (SIF) examined the available literature data. The identification of patient risk profile and the characterization of metabolic effects of novel anti-tumour drugs is clearly a clinical challenge that can be addressed by a multidisciplinary clinical approach. Therefore, this review pinpoints the relevance of the challenging profiling of the patient suffering from dysmetabolic conditions induced by the novel therapeutics in medical oncology.
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Affiliation(s)
- Nicola Silvestris
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Italy; Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy.
| | | | | | - Paolo Di Bartolo
- Diabetology Unit, Rete Clinica di Diabetologia Aziendale - Dipartimento, Internistico di Ravenna - AUSL Romagna, Ravenna, Italy
| | - Monica Montagnani
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Pietro Ferrari
- Palliative Care Unit, Istituti Clinici Scientifici Maugeri SPA SB, IRCCS (PV), Italy
| | - Stella D'Oronzo
- IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Italy; Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Stefania Gori
- Oncologia Medica, IRCCS Ospedale Don Calabria-Sacro Cuore di Negrar, Verona, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Italy
| | - Silvia Acquati
- Endocrinology Unit, Ospedale Pierantoni-Morgagni, Forlì, Italy
| | - Marco Gallo
- Oncological Endocrinology Unit, Department of Medical Sciences, University of Torino, AOU Città della Salute e della Scienza di Torino, Torino, Italy
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Matsuzaka Y, Uesawa Y. Molecular Image-Based Prediction Models of Nuclear Receptor Agonists and Antagonists Using the DeepSnap-Deep Learning Approach with the Tox21 10K Library. Molecules 2020; 25:molecules25122764. [PMID: 32549344 PMCID: PMC7356846 DOI: 10.3390/molecules25122764] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
The interaction of nuclear receptors (NRs) with chemical compounds can cause dysregulation of endocrine signaling pathways, leading to adverse health outcomes due to the disruption of natural hormones. Thus, identifying possible ligands of NRs is a crucial task for understanding the adverse outcome pathway (AOP) for human toxicity as well as the development of novel drugs. However, the experimental assessment of novel ligands remains expensive and time-consuming. Therefore, an in silico approach with a wide range of applications instead of experimental examination is highly desirable. The recently developed novel molecular image-based deep learning (DL) method, DeepSnap-DL, can produce multiple snapshots from three-dimensional (3D) chemical structures and has achieved high performance in the prediction of chemicals for toxicological evaluation. In this study, we used DeepSnap-DL to construct prediction models of 35 agonist and antagonist allosteric modulators of NRs for chemicals derived from the Tox21 10K library. We demonstrate the high performance of DeepSnap-DL in constructing prediction models. These findings may aid in interpreting the key molecular events of toxicity and support the development of new fields of machine learning to identify environmental chemicals with the potential to interact with NR signaling pathways.
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7
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Chen Y, Li J, Wu Z, Liu G, Li H, Tang Y, Li W. Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor. J Chem Inf Model 2020; 60:1540-1550. [PMID: 32097559 DOI: 10.1021/acs.jcim.9b00914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The farnesoid X receptor (FXR) is a bile acid-sensing transcription factor with indispensable roles in regulating metabolic processes. Nowadays, FXR has become a highly promising drug target for severe liver disorders, especially nonalcoholic steatohepatitis (NASH). A recent study showed that imatinib and its analogues were able to allosterically enhance agonist-induced FXR activation and its target gene expression. However, the allosteric modulation mechanism of FXR by these compounds remains unclear. In this work, the most effective imatinib analogue, P16, was used as a probe to explore this issue by computational approaches. Our results identified one potential allosteric site surrounded by residues Ile335, Phe336, Lys338, Glu339, Leu340, and Leu348, which could efficiently accommodate P16. In addition, the long-time molecular dynamics simulations indicated that the binding of P16 could significantly decrease the fluctuation of the co-activator and enhance the communications between the endogenous ligand chenodeoxycholic acid (CDCA) and FXR. By analyzing the residue interaction network, we observed two unique communication pathways connecting P16 and CDCA through three key residues, Arg331, Ser332, and Phe336. The communications of network organization in the P16-bound complex may allow the synergistic effect of the two compounds via robust signal transmission between the binding sites and global network bridges, which coordinate allosteric transitions and modulate the receptor activity. Our study offers insights into the allosteric modulation occurring in FXR and would be helpful for discovery of new allosteric modulators targeting FXR for further clinical research.
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Affiliation(s)
- Yue Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Junhao Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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8
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Lamers C, Merk D. Discovery, Structural Refinement and Therapeutic Potential of Farnesoid X Receptor Activators. ANTI-FIBROTIC DRUG DISCOVERY 2020. [DOI: 10.1039/9781788015783-00076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Farnesoid X receptor acts as bile acid sensing transcription factor and has been identified as valuable molecular drug target to treat severe liver disorders, such as non-alcoholic steatohepatitis (NASH). Preclinical and clinical data indicate anti-fibrotic effects obtained with FXR activation that also appear promising for other fibrotic diseases beyond NASH. Strong efforts in FXR ligand discovery have yielded potent steroidal and non-steroidal FXR activators, some of which have been studied in clinical trials. While the structure–activity relationship of some FXR agonist frameworks have been studied extensively, the structural diversity of potent FXR activator chemotypes is still limited to a handful of well-studied compound classes. Together with safety concerns related to full therapeutic activation of FXR, this indicates the need for novel innovative FXR ligands with selective modulatory properties. This chapter evaluates FXR's value as drug target with emphasis on fibrotic diseases, analyses FXR ligand recognition and requirements and focuses on the discovery and structural refinement of leading FXR activator chemotypes.
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Affiliation(s)
- Christina Lamers
- University Basel, Molecular Pharmacy Klingelberstr. 50 CH-4056 Basel Switzerland
| | - Daniel Merk
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry Max-von-Laue-Str. 9 D-60438 Frankfurt Germany
- Swiss Federal Institute of Technology (ETH) Zurich, Institute of Pharmaceutical Sciences Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
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9
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Schierle S, Helmstädter M, Schmidt J, Hartmann M, Horz M, Kaiser A, Weizel L, Heitel P, Proschak A, Hernandez‐Olmos V, Proschak E, Merk D. Dual Farnesoid X Receptor/Soluble Epoxide Hydrolase Modulators Derived from Zafirlukast. ChemMedChem 2020; 15:50-67. [PMID: 31670489 PMCID: PMC7004070 DOI: 10.1002/cmdc.201900576] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/21/2019] [Indexed: 12/28/2022]
Abstract
The nuclear farnesoid X receptor (FXR) and the enzyme soluble epoxide hydrolase (sEH) are validated molecular targets to treat metabolic disorders such as non-alcoholic steatohepatitis (NASH). Their simultaneous modulation in vivo has demonstrated a triad of anti-NASH effects and thus may generate synergistic efficacy. Here we report dual FXR activators/sEH inhibitors derived from the anti-asthma drug Zafirlukast. Systematic structural optimization of the scaffold has produced favorable dual potency on FXR and sEH while depleting the original cysteinyl leukotriene receptor antagonism of the lead drug. The resulting polypharmacological activity profile holds promise in the treatment of liver-related metabolic diseases.
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Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Moritz Helmstädter
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Jurema Schmidt
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Markus Hartmann
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Maximiliane Horz
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Astrid Kaiser
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Lilia Weizel
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Pascal Heitel
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Anna Proschak
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Victor Hernandez‐Olmos
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEBranch for Translational Medicine and Pharmacology TMPTheodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Ewgenij Proschak
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
| | - Daniel Merk
- Institute of Pharmaceutical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 960438FrankfurtGermany
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Merk D, Sreeramulu S, Kudlinzki D, Saxena K, Linhard V, Gande SL, Hiller F, Lamers C, Nilsson E, Aagaard A, Wissler L, Dekker N, Bamberg K, Schubert-Zsilavecz M, Schwalbe H. Molecular tuning of farnesoid X receptor partial agonism. Nat Commun 2019; 10:2915. [PMID: 31266946 PMCID: PMC6606567 DOI: 10.1038/s41467-019-10853-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/31/2019] [Indexed: 12/18/2022] Open
Abstract
The bile acid-sensing transcription factor farnesoid X receptor (FXR) regulates multiple metabolic processes. Modulation of FXR is desired to overcome several metabolic pathologies but pharmacological administration of full FXR agonists has been plagued by mechanism-based side effects. We have developed a modulator that partially activates FXR in vitro and in mice. Here we report the elucidation of the molecular mechanism that drives partial FXR activation by crystallography- and NMR-based structural biology. Natural and synthetic FXR agonists stabilize formation of an extended helix α11 and the α11-α12 loop upon binding. This strengthens a network of hydrogen bonds, repositions helix α12 and enables co-activator recruitment. Partial agonism in contrast is conferred by a kink in helix α11 that destabilizes the α11-α12 loop, a critical determinant for helix α12 orientation. Thereby, the synthetic partial agonist induces conformational states, capable of recruiting both co-repressors and co-activators leading to an equilibrium of co-activator and co-repressor binding.
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Affiliation(s)
- Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, 60348, Germany.
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany
| | - Denis Kudlinzki
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany.,German Cancer Consortium (DKTK), Heidelberg, 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany.,German Cancer Consortium (DKTK), Heidelberg, 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany
| | - Santosh L Gande
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany.,German Cancer Consortium (DKTK), Heidelberg, 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Fabian Hiller
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany
| | - Christina Lamers
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, 60348, Germany
| | - Ewa Nilsson
- Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, 43183, Sweden
| | - Anna Aagaard
- Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, 43183, Sweden
| | - Lisa Wissler
- Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, 43183, Sweden
| | - Niek Dekker
- Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, 43183, Sweden
| | - Krister Bamberg
- Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, 43183, Sweden
| | | | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, 60438, Germany. .,German Cancer Consortium (DKTK), Heidelberg, 69120, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
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11
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Di Ciaula A, Wang DQH, Portincasa P. Cholesterol cholelithiasis: part of a systemic metabolic disease, prone to primary prevention. Expert Rev Gastroenterol Hepatol 2019; 13:157-171. [PMID: 30791781 DOI: 10.1080/17474124.2019.1549988] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cholesterol gallstone disease have relationships with various conditions linked with insulin resistance, but also with heart disease, atherosclerosis, and cancer. These associations derive from mechanisms active at a local (i.e. gallbladder, bile) and a systemic level and are involved in inflammation, hormones, nuclear receptors, signaling molecules, epigenetic modulation of gene expression, and gut microbiota. Despite advanced knowledge of these pathways, the available therapeutic options for symptomatic gallstone patients remain limited. Therapy includes oral litholysis by the bile acid ursodeoxycholic acid (UDCA) in a small subgroup of patients at high risk of postdissolution recurrence, or laparoscopic cholecystectomy, which is the therapeutic radical gold standard treatment. Cholecystectomy, however, may not be a neutral event, and potentially generates health problems, including the metabolic syndrome. Areas covered: Several studies on risk factors and pathogenesis of cholesterol gallstone disease, acting at a systemic level have been reviewed through a PubMed search. Authors have focused on primary prevention and novel potential therapeutic strategies. Expert commentary: The ultimate goal appears to target the manageable systemic mechanisms responsible for gallstone occurrence, pointing to primary prevention measures. Changes must target lifestyles, as well as experimenting innovative pharmacological tools in subgroups of patients at high risk of developing gallstones.
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Affiliation(s)
- Agostino Di Ciaula
- a Division of Internal Medicine , Hospital of Bisceglie , Bisceglie , Italy
| | - David Q-H Wang
- b Department of Medicine, Division of Gastroenterology and Liver Diseases , Marion Bessin Liver Research Center, Albert Einstein College of Medicine , Bronx , NY , USA
| | - Piero Portincasa
- c Department of Biomedical Sciences and Human Oncology, Clinica Medica "A. Murri" , University of Bari Medical School , Bari , Italy
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Merk D, Grisoni F, Schaller K, Friedrich L, Schneider G. Discovery of Novel Molecular Frameworks of Farnesoid X Receptor Modulators by Ensemble Machine Learning. ChemistryOpen 2019; 8:7-14. [PMID: 30622878 PMCID: PMC6317935 DOI: 10.1002/open.201800156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Indexed: 11/23/2022] Open
Abstract
The bile acid activated transcription factor farnesoid X receptor (FXR) has revealed therapeutic potential as a molecular drug target for the treatment of hepatic and metabolic disorders. Despite strong efforts in FXR ligand development, the structural diversity among the known FXR modulators is limited. Only four molecular frameworks account for more than 50 % of the FXR modulators annotated in ChEMBL. Here, we leverage machine learning methods to expand the chemical space of FXR-targeting small molecules by employing an ensemble of three complementary machine learning approaches. A counter-propagation artificial neural network, a k-nearest neighbor learner, and a three-dimensional pharmacophore descriptor were combined to retrieve novel FXR ligands from a collection of more than 3 million compounds. The ensemble machine learning model identified six new FXR modulators among ten top-ranked candidates. These active hits comprise both FXR activators and antagonists with micromolar potencies. With four novel FXR ligand scaffolds, these computationally identified bioactive compounds appreciably expand the chemical space of known FXR modulators and may serve as starting points for hit-to-lead expansion.
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Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
- Department of Earth and Environmental SciencesUniversity of Milano-BicoccaPiazza della Scienza 120126MilanoItaly
| | - Kay Schaller
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Lukas Friedrich
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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Heering J, Merk D. Hybrid Reporter Gene Assays: Versatile In Vitro Tools to Characterize Nuclear Receptor Modulators. Methods Mol Biol 2019; 1966:175-192. [PMID: 31041747 DOI: 10.1007/978-1-4939-9195-2_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nuclear receptors act as ligand-activated transcription factors translating ligand signals into changes in gene expression. The 48 members of the superfamily of nuclear receptors identified so far are involved amongst others in maintenance of metabolic balance, inflammation, and cancer. Thus, they hold enormous potential for drug discovery and some nuclear receptors are experiencing considerable academic and industrial interest. Nuclear receptor modulator discovery requires reliable, robust, and economic test systems that allow for high throughput. In this chapter, we discuss the principle, strengths, and advantages of hybrid reporter gene assays for nuclear receptor focused drug discovery and describe how they can be developed, established, and validated.
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Affiliation(s)
- Jan Heering
- Branch for Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt, Germany
| | - Daniel Merk
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland.
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.
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Wang N, Zou Q, Xu J, Zhang J, Liu J. Ligand binding and heterodimerization with retinoid X receptor α (RXRα) induce farnesoid X receptor (FXR) conformational changes affecting coactivator binding. J Biol Chem 2018; 293:18180-18191. [PMID: 30275017 DOI: 10.1074/jbc.ra118.004652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
Nuclear receptor farnesoid X receptor (FXR) functions as the major bile acid sensor coordinating cholesterol metabolism, lipid homeostasis, and absorption of dietary fats and vitamins. Because of its central role in metabolism, FXR represents an important drug target to manage metabolic and other diseases, such as primary biliary cirrhosis and nonalcoholic steatohepatitis. FXR and nuclear receptor retinoid X receptor α (RXRα) form a heterodimer that controls the expression of numerous downstream genes. To date, the structural basis and functional consequences of the FXR/RXR heterodimer interaction have remained unclear. Herein, we present the crystal structures of the heterodimeric complex formed between the ligand-binding domains of human FXR and RXRα. We show that both FXR and RXR bind to the transcriptional coregulator steroid receptor coactivator 1 with higher affinity when they are part of the heterodimer complex than when they are in their respective monomeric states. Furthermore, structural comparisons of the FXR/RXRα heterodimers and the FXR monomers bound with different ligands indicated that both heterodimerization and ligand binding induce conformational changes in the C terminus of helix 11 in FXR that affect the stability of the coactivator binding surface and the coactivator binding in FXR. In summary, our findings shed light on the allosteric signal transduction in the FXR/RXR heterodimer, which may be utilized for future drug development targeting FXR.
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Affiliation(s)
- Na Wang
- From the School of Life Sciences, University of Science and Technology of China, Hefei 230026, China,; the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and
| | - Qingan Zou
- Guangzhou Henovcom Biosciences Inc., Guangzhou 510530, China
| | - Jinxin Xu
- the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and
| | - Jiancun Zhang
- the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and; Guangzhou Henovcom Biosciences Inc., Guangzhou 510530, China
| | - Jinsong Liu
- the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and.
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