1
|
Heering J, Jores N, Kilu W, Schallmayer E, Peelen E, Muehler A, Kohlhof H, Vitt D, Linhard V, Gande SL, Chaikuad A, Sreeramulu S, Schwalbe H, Merk D. Mechanistic Impact of Different Ligand Scaffolds on FXR Modulation Suggests Avenues to Selective Modulators. ACS Chem Biol 2022; 17:3159-3168. [PMID: 36318238 DOI: 10.1021/acschembio.2c00599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The bile-acid sensing nuclear farnesoid X receptor (FXR) is an attractive target for the treatment of hepatic and metabolic diseases, but application of this chemotherapeutic concept remains limited due to adverse effects of FXR activation observed in clinical trials. To elucidate the mechanistic basis of FXR activation at the molecular level, we have systematically studied FXR co-regulator interactions and dimerization in response to seven chemically diverse FXR ligands. Different molecular effects on FXR activation mediated by different scaffolds were evident and aligned with characteristic structural changes within the ligand binding domain of FXR. A partial FXR agonist acted mainly through co-repressor displacement from FXR and caused an FXR-regulated gene expression pattern markedly differing from FXR agonist effects. These results suggest selective modulation of FXR dimerization and co-regulator interactions for different ligands, offering a potential avenue for the design of gene- or tissue-selective FXR modulators.
Collapse
Affiliation(s)
- Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, 60596Frankfurt, Germany
| | - Nathalie Jores
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Whitney Kilu
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Espen Schallmayer
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438Frankfurt, Germany
| | | | | | | | | | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Santosh L Gande
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438Frankfurt, Germany.,Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377Munich, Germany
| |
Collapse
|
2
|
Yang Y, Zhao Y, Li W, Wu Y, Wang X, Wang Y, Liu T, Ye T, Xie Y, Cheng Z, He J, Bai P, Zhang Y, Ouyang L. Emerging targets and potential therapeutic agents in non-alcoholic fatty liver disease treatment. Eur J Med Chem 2020; 197:112311. [PMID: 32339855 DOI: 10.1016/j.ejmech.2020.112311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/29/2020] [Accepted: 04/04/2020] [Indexed: 02/08/2023]
Abstract
Nonalcoholic Fatty Liver Disease (NAFLD) is the most common chronic liver disease in the world, which is characterized by liver fat accumulation unrelated to excessive drinking. Indeed, it attracts growing attention and becomes a global health problem. Due to the complexity of the NAFLD pathogenic mechanism, no related drugs were approved by Food and Drug Administration (FDA) till now. However, it is encouraging that a series of candidate drugs have entered the clinical trial stage with expectation to treat NAFLD. In this review, we summarized the main pathways and pathogenic mechanisms of NAFLD, as well as introduced the main potential therapeutic targets and the corresponding compounds involved in metabolism, inflammation and fibrosis. Furthermore, we also discuss the progress of these compounds, such as drug design and optimization, the choice of pharmacological properties and druglikeness, and the analysis of structure-activity relationship. This review offers a medium on future drug design and development, to be beneficial to relevant studies.
Collapse
Affiliation(s)
- Yu Yang
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yu Zhao
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenzhen Li
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yuyao Wu
- West China School of Public Health/No.4 West China Teaching Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Wang
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yijie Wang
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Tingmei Liu
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Tinghong Ye
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yongmei Xie
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Zhiqiang Cheng
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jun He
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Yiwen Zhang
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy & Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| |
Collapse
|
3
|
Jin LH, Fang ZP, Fan MJ, Huang WD. Bile-ology: from bench to bedside. J Zhejiang Univ Sci B 2019; 20:414-427. [PMID: 31090267 PMCID: PMC6568232 DOI: 10.1631/jzus.b1900158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022]
Abstract
Bile acids (BAs) are originally known as detergents essential for the digestion and absorption of lipids. In recent years, extensive research has unveiled new functions of BAs as gut hormones that modulate physiological and pathological processes, including glucose and lipid metabolism, energy expenditure, inflammation, tumorigenesis, cardiovascular disease, and even the central nervous system in addition to cholesterol homeostasis, enterohepatic protection and liver regeneration. BAs are closely linked with gut microbiota which might explain some of their crucial roles in organs. The signaling actions of BAs can also be mediated through specific nuclear receptors and membrane-bound G protein-coupled receptors. Several pharmacological agents or bariatric surgeries have demonstrated efficacious therapeutic effects on metabolic diseases through targeting BA signaling. In this mini-review, we summarize recent advances in bile-ology, focusing on its translational studies.
Collapse
Affiliation(s)
- Li-hua Jin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- State Key Laboratory of Cellular Stress Biology; Innovation Center for Cell Signaling Network; School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Zhi-peng Fang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Min-jie Fan
- College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Wen-dong Huang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Schierle S, Schmidt J, Kaiser A, Merk D. Selective Optimization of Pranlukast to Farnesoid X Receptor Modulators. ChemMedChem 2018; 13:2530-2545. [DOI: 10.1002/cmdc.201800549] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/05/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Jurema Schmidt
- Institute of Pharmaceutical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Daniel Merk
- Institute of Pharmaceutical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt Germany
| |
Collapse
|
6
|
Qiu R, Luo G, Li X, Zheng F, Li H, Zhang J, You Q, Xiang H. Lipid accumulation inhibitory activities of novel isoxazole-based chenodeoxycholic acids: Design, synthesis and preliminary mechanism study. Bioorg Med Chem Lett 2018; 28:2879-2884. [DOI: 10.1016/j.bmcl.2018.07.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/29/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
|
7
|
Rifai EA, van Dijk M, Vermeulen NPE, Geerke DP. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2. J Comput Aided Mol Des 2018; 32:239-249. [PMID: 28889350 PMCID: PMC5767202 DOI: 10.1007/s10822-017-0055-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 01/21/2023]
Abstract
Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.
Collapse
Affiliation(s)
- Eko Aditya Rifai
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Marc van Dijk
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Nico P E Vermeulen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| |
Collapse
|
8
|
Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters P, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des 2018; 32:1-20. [PMID: 29204945 PMCID: PMC5767524 DOI: 10.1007/s10822-017-0088-4] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/20/2017] [Indexed: 01/07/2023]
Abstract
The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank ( http://www.pdb.org ), and in affinity ranking and scoring of bound ligands.
Collapse
Affiliation(s)
- Zied Gaieb
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093
| | - Shuai Liu
- Silicon Therapeutics, Boston MA 02210
| | | | - Michael Chiu
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093
| | - Huanwang Yang
- RCSB Protein Data Bank Rutgers University, New Brunswick, NJ 08901
| | - Chenghua Shao
- RCSB Protein Data Bank Rutgers University, New Brunswick, NJ 08901
| | - Victoria A. Feher
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093
| | | | - Bernd Kuhn
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G. Rudolph
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | | | - Michael K. Gilson
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093,Correspondence to:
| | - Rommie E. Amaro
- Drug Design Data Resource, University of California, San Diego, La Jolla, CA 92093,Correspondence to:
| |
Collapse
|
9
|
Mey ASJS, Jiménez JJ, Michel J. Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations. J Comput Aided Mol Des 2018; 32:199-210. [PMID: 29134431 PMCID: PMC5767197 DOI: 10.1007/s10822-017-0083-9] [Citation(s) in RCA: 15] [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: 06/15/2017] [Accepted: 11/03/2017] [Indexed: 11/28/2022]
Abstract
The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.
Collapse
Affiliation(s)
- Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Jordi Juárez Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| |
Collapse
|
10
|
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. J Comput Aided Mol Des 2017; 32:299-311. [PMID: 29134430 PMCID: PMC5767208 DOI: 10.1007/s10822-017-0085-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/08/2017] [Indexed: 01/31/2023]
Abstract
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org/ ). The challenge was focused on the ligands of the farnesoid X receptor (FXR), a highly flexible nuclear receptor of the cholesterol derivative chenodeoxycholic acid. FXR is considered an important therapeutic target for metabolic, inflammatory, bowel and obesity related diseases (Expert Opin Drug Metab Toxicol 4:523-532, 2015), but in the context of this competition it is also interesting due to the significant ligand-induced conformational changes displayed by the protein. To deal with these conformational changes we employed multiple simulations of molecular dynamics (MD). Our MD-based protocols were top-ranked in estimating the free energy of binding of the ligands and FXR protein. Our approach was ranked second in the prediction of the binding poses where we also combined MD with molecular docking and artificial neural networks. Our approach showed mediocre results for high-throughput scoring of interactions.
Collapse
|
11
|
Athanasiou C, Vasilakaki S, Dellis D, Cournia Z. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2. J Comput Aided Mol Des 2017; 32:21-44. [DOI: 10.1007/s10822-017-0075-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023]
|
12
|
Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort. J Comput Aided Mol Des 2017; 32:129-142. [PMID: 28986733 DOI: 10.1007/s10822-017-0072-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/23/2017] [Indexed: 12/21/2022]
Abstract
The 2016 D3R Grand Challenge 2 includes both pose and affinity or ranking predictions. This article is focused exclusively on affinity predictions submitted to the D3R challenge from a collaborative effort of the modeling and informatics group. Our submissions include ranking of 102 ligands covering 4 different chemotypes against the FXR ligand binding domain structure, and the relative binding affinity predictions of the two designated free energy subsets of 15 and 18 compounds. Using all the complex structures prepared in the same way allowed us to cover many types of workflows and compare their performances effectively. We evaluated typical workflows used in our daily structure-based design modeling support, which include docking scores, force field-based scores, QM/MM, MMGBSA, MD-MMGBSA, and MacroModel interaction energy estimations. The best performing methods for the two free energy subsets are discussed. Our results suggest that affinity ranking still remains very challenging; that the knowledge of more structural information does not necessarily yield more accurate predictions; and that visual inspection and human intervention are considerably important for ranking. Knowledge of the mode of action and protein flexibility along with visualization tools that depict polar and hydrophobic maps are very useful for visual inspection. QM/MM-based workflows were found to be powerful in affinity ranking and are encouraged to be applied more often. The standardized input and output enable systematic analysis and support methodology development and improvement for high level blinded predictions.
Collapse
|
13
|
Fradera X, Verras A, Hu Y, Wang D, Wang H, Fells JI, Armacost KA, Crespo A, Sherborne B, Wang H, Peng Z, Gao YD. Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016. J Comput Aided Mol Des 2017; 32:113-127. [PMID: 28913710 DOI: 10.1007/s10822-017-0053-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 10/18/2022]
Abstract
We describe the performance of multiple pose prediction methods for the D3R 2016 Grand Challenge. The pose prediction challenge includes 36 ligands, which represent 4 chemotypes and some miscellaneous structures against the FXR ligand binding domain. In this study we use a mix of fully automated methods as well as human-guided methods with considerations of both the challenge data and publicly available data. The methods include ensemble docking, colony entropy pose prediction, target selection by molecular similarity, molecular dynamics guided pose refinement, and pose selection by visual inspection. We evaluated the success of our predictions by method, chemotype, and relevance of publicly available data. For the overall data set, ensemble docking, visual inspection, and molecular dynamics guided pose prediction performed the best with overall mean RMSDs of 2.4, 2.2, and 2.2 Å respectively. For several individual challenge molecules, the best performing method is evaluated in light of that particular ligand. We also describe the protein, ligand, and public information data preparations that are typical of our binding mode prediction workflow.
Collapse
Affiliation(s)
- Xavier Fradera
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA, 02215, USA.
| | - Andreas Verras
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA.
| | - Yuan Hu
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Deping Wang
- Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Hongwu Wang
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - James I Fells
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Kira A Armacost
- Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Alejandro Crespo
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Brad Sherborne
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Huijun Wang
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Zhengwei Peng
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Ying-Duo Gao
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| |
Collapse
|
14
|
CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2. J Comput Aided Mol Des 2017; 32:89-102. [PMID: 28884249 DOI: 10.1007/s10822-017-0050-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/19/2017] [Indexed: 01/09/2023]
Abstract
The opportunity to prospectively predict ligand bound poses and free energies of binding to the Farnesoid X Receptor in the D3R Grand Challenge 2 provided a useful exercise to evaluate CHARMM based docking (CDOCKER) and [Formula: see text]-dynamics methodologies for use in "real-world" applications in computer aided drug design. In addition to measuring their current performance, several recent methodological developments have been analyzed retrospectively to highlight best procedural practices in future applications. For pose prediction with CDOCKER, when the protein structure used for rigid receptor docking was close to the crystallographic holo structure, reliable poses were obtained. Benzimidazoles, with a known holo receptor structure, were successfully docked with an average RMSD of 0.97 [Formula: see text]. Other non-benzimidazole ligands displayed less accuracy largely because the receptor structures we chose for docking were too different from the experimental holo structures. However, retrospective analysis has shown that when these ligands were re-docked into their holo structures, the average RMSD dropped to 1.18 [Formula: see text] for all ligands. When sulfonamides and spiros were docked with the apo structure, which agrees more with their holo structure than the structures we chose, five out of six ligands were correctly docked. These docking results emphasize the need for flexible receptor docking approaches. For [Formula: see text]-dynamics techniques, including multisite [Formula: see text]-dynamics (MS[Formula: see text]D), reasonable agreement with experiment was observed for the 33 ligands investigated; root mean square errors of 2.08 and 1.67 kcal/mol were obtained for free energy sets 1 and 2, respectively. Retrospectively, soft-core potentials, adaptive landscape flattening, and biasing potential replica exchange (BP-REX) algorithms were critical to model large substituent perturbations with sufficient precision and within restrictive timeframes, such as was required with participation in Grand Challenge 2. These developments, their associated benefits, and proposed procedures for their use in future applications are discussed.
Collapse
|
15
|
Selwa E, Elisée E, Zavala A, Iorga BI. Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations. J Comput Aided Mol Des 2017; 32:273-286. [DOI: 10.1007/s10822-017-0054-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 12/14/2022]
|
16
|
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2. J Comput Aided Mol Des 2017; 32:251-264. [DOI: 10.1007/s10822-017-0051-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/21/2017] [Indexed: 10/19/2022]
|
17
|
Novel substituted isoxazole FXR agonists with cyclopropyl, hydroxycyclobutyl and hydroxyazetidinyl linkers: Understanding and improving key determinants of pharmacological properties. Bioorg Med Chem Lett 2016; 26:3746-53. [DOI: 10.1016/j.bmcl.2016.05.070] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/19/2016] [Accepted: 05/21/2016] [Indexed: 11/23/2022]
|
18
|
Yuan ZQ, Li KW. Role of farnesoid X receptor in cholestasis. J Dig Dis 2016; 17:501-509. [PMID: 27383832 DOI: 10.1111/1751-2980.12378] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/23/2016] [Accepted: 07/03/2016] [Indexed: 12/11/2022]
Abstract
The nuclear receptor farnesoid X receptor (FXR) plays an important role in physiological bile acid synthesis, secretion and transport. Defects of FXR regulation in these processes can cause cholestasis and subsequent pathological changes. FXR regulates the synthesis and uptake of bile acid via enzymes. It also increases bile acid solubility and elimination by promoting conjugation reactions and exports pump expression in cholestasis. The changes in bile acid transporters are involved in cholestasis, which can result from the mutations of transporter genes or acquired dysfunction of transport systems, such as inflammation-induced intrahepatic cholestasis. The modulation function of FXR in extrahepatic cholestasis is not identical to that in intrahepatic cholestasis, but the discrepancy may be reduced over time. In extrahepatic cholestasis, increasing biliary pressure can induce bile duct proliferation and bile infarcts, but the absence of FXR may ameliorate them. This review provides an update on the function of FXR in the regulation of bile acid metabolism, its role in the pathophysiological process of cholestasis and the therapeutic use of FXR agonists.
Collapse
Affiliation(s)
- Zhi Qing Yuan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ke Wei Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
| |
Collapse
|
19
|
Xu Y. Recent Progress on Bile Acid Receptor Modulators for Treatment of Metabolic Diseases. J Med Chem 2016; 59:6553-79. [DOI: 10.1021/acs.jmedchem.5b00342] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yanping Xu
- Lilly Research
Laboratories, Eli Lilly and Company, Lilly Corporate Center, DC 1910, Indianapolis, Indiana 46285, United States
| |
Collapse
|
20
|
NSAIDs Ibuprofen, Indometacin, and Diclofenac do not interact with Farnesoid X Receptor. Sci Rep 2015; 5:14782. [PMID: 26424593 PMCID: PMC4589779 DOI: 10.1038/srep14782] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 02/01/2023] Open
Abstract
The nuclear farnesoid X receptor (FXR) is a ligand activated transcription factor and acts as cellular sensor for bile acids. In this role, FXR is a highly important liver protector and FXR inhibition by antagonists or knockout has shown several deleterious effects. A recent report characterized non-steroidal anti-rheumatic drugs (NSAIDs) such as ibuprofen or diclofenac as FXR antagonists and linked hepatotoxic effects of these drugs with antagonistic activity on FXR. Since this would guide a way to develop safer anti-inflammatory agents by sparing FXR, we intended to further characterize the reported antagonistic activity and intensively investigated ibuprofen, indometacin and diclofenac. However, we conclude that these agents do not interact with FXR and that the reported reduced FXR signaling induced by CDCA in presence of NSAIDs is merely a consequence than a cause of hepatotoxicity.
Collapse
|
21
|
Design, Synthesis, and Biological Evaluation of Novel Nonsteroidal Farnesoid X Receptor (FXR) Antagonists: Molecular Basis of FXR Antagonism. ChemMedChem 2015; 10:1184-99. [DOI: 10.1002/cmdc.201500136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Indexed: 01/24/2023]
|
22
|
Flesch D, Gabler M, Lill A, Gomez RC, Steri R, Schneider G, Stark H, Schubert-Zsilavecz M, Merk D. Fragmentation of GW4064 led to a highly potent partial farnesoid X receptor agonist with improved drug-like properties. Bioorg Med Chem 2015; 23:3490-8. [PMID: 25934227 DOI: 10.1016/j.bmc.2015.04.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/24/2015] [Accepted: 04/10/2015] [Indexed: 12/12/2022]
Abstract
The ligand activated transcription factor farnesoid X receptor (FXR) is a crucial regulator of several metabolic and inflammatory pathways and its activation by agonistic ligands seems a valuable therapeutic approach for many disorders. Most known non-steroidal FXR agonists however, have limitations that hinder their clinical development and novel FXR ligands are required. Evaluation of the co-crystal structures of the widely used FXR agonist GW4064 and related compounds in complex with the FXR ligand binding domain indicated that their disubstituted isoxazole moiety is especially relevant for FXR activation. By investigation of GW4064-fragments missing the aromatic tail, we discovered a highly potent and soluble partial FXR agonist (14, ST-1892) as well as a fluorescent FXR ligand (15) as potential pharmacological tool.
Collapse
Affiliation(s)
- Daniel Flesch
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Matthias Gabler
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Andreas Lill
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Roberto Carrasco Gomez
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Ramona Steri
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog Weg 1-5/10, 8093 Zürich, Switzerland
| | - Holger Stark
- Institute for Pharmaceutical und Medicinal Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
| |
Collapse
|
23
|
Liu P, Xu X, Chen L, Ma L, Shen X, Hu L. Discovery and SAR study of hydroxyacetophenone derivatives as potent, non-steroidal farnesoid X receptor (FXR) antagonists. Bioorg Med Chem 2014; 22:1596-607. [PMID: 24513188 DOI: 10.1016/j.bmc.2014.01.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 11/26/2022]
Abstract
Compound 1 (IC50=35.2 ± 7.2 μM), a moderate FXR antagonist was discovered via high-throughput screening. Structure-activity relationship studies indicated that the shape and the lipophilicity of the substituents of the aromatic ring affect the activity dramatically, increasing the shape and the lipophilicity of the substituents of the aromatic ring enhances the potency of FXR antagonists. Especially, when the OH at C2 position of the aromatic ring was replaced by the OBn substituent (analog 2b), its activity could be improved to IC50=1.1 ± 0.1μM. Besides, the length of the linker and the tetrazole structure are essential for retaining the activity.
Collapse
Affiliation(s)
- Peng Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Xing Xu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Lili Chen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Lei Ma
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
| | - Xu Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
| | - Lihong Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
| |
Collapse
|
24
|
Merk D, Steinhilber D, Schubert-Zsilavecz M. Characterizing ligands for farnesoid X receptor – availablein vitrotest systems for farnesoid X receptor modulator development. Expert Opin Drug Discov 2013; 9:27-37. [DOI: 10.1517/17460441.2014.860129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
25
|
Asymmetric synthesis of the four diastereoisomers of a novel non-steroidal farnesoid X receptor (FXR) agonist: Role of the chirality on the biological activity. Bioorg Med Chem 2013; 21:3780-9. [DOI: 10.1016/j.bmc.2013.04.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 12/21/2022]
|
26
|
Matsubara T, Li F, Gonzalez FJ. FXR signaling in the enterohepatic system. Mol Cell Endocrinol 2013; 368:17-29. [PMID: 22609541 PMCID: PMC3491147 DOI: 10.1016/j.mce.2012.05.004] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 04/18/2012] [Accepted: 05/08/2012] [Indexed: 02/07/2023]
Abstract
Enterohepatic circulation serves to capture bile acids and other steroid metabolites produced in the liver and secreted to the intestine, for reabsorption back into the circulation and reuptake to the liver. This process is under tight regulation by nuclear receptor signaling. Bile acids, produced from cholesterol, can alter gene expression in the liver and small intestine via activating the nuclear receptors farnesoid X receptor (FXR; NR1H4), pregnane X receptor (PXR; NR1I2), vitamin D receptor (VDR; NR1I1), G protein coupled receptor TGR5, and other cell signaling pathways (JNK1/2, AKT and ERK1/2). Among these controls, FXR is known to be a major bile acid-responsive ligand-activated transcription factor and a crucial control element for maintaining bile acid homeostasis. FXR has a high affinity for several major endogenous bile acids, notably cholic acid, deoxycholic acid, chenodeoxycholic acid, and lithocholic acid. By responding to excess bile acids, FXR is a bridge between the liver and small intestine to control bile acid levels and regulate bile acid synthesis and enterohepatic flow. FXR is highly expressed in the liver and gut, relative to other tissues, and contributes to the maintenance of cholesterol/bile acid homeostasis by regulating a variety of metabolic enzymes and transporters. FXR activation also affects lipid and glucose metabolism, and can influence drug metabolism.
Collapse
Affiliation(s)
- Tsutomu Matsubara
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Fei Li
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- Correspondence: Frank J. Gonzalez, Laboratory of Metabolism, National Cancer Institute, Building 37, Room 3106, Bethesda, MD 20892, Tel: 301-496-9067, Fax: 301-496-8419,
| |
Collapse
|
27
|
Identification of liver X receptor and farnesoid X receptor dual agonists from Tithonia diversifolia. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0359-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
28
|
Sardella R, Marinozzi M, Ianni F, Lisanti A, Natalini B. Simultaneous diastereo- and enantioseparation of farnesoid X receptor (FXR) agonists with a quinine carbamate-based chiral stationary phase. Anal Bioanal Chem 2012; 405:847-62. [DOI: 10.1007/s00216-012-6348-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/24/2012] [Accepted: 08/09/2012] [Indexed: 10/27/2022]
|
29
|
Marinozzi M, Carotti A, Sansone E, Macchiarulo A, Rosatelli E, Sardella R, Natalini B, Rizzo G, Adorini L, Passeri D, De Franco F, Pruzanski M, Pellicciari R. Pyrazole[3,4-e][1,4]thiazepin-7-one derivatives as a novel class of Farnesoid X Receptor (FXR) agonists. Bioorg Med Chem 2012; 20:3429-45. [DOI: 10.1016/j.bmc.2012.04.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/02/2012] [Accepted: 04/07/2012] [Indexed: 02/01/2023]
|
30
|
Medicinal chemistry of farnesoid X receptor ligands: from agonists and antagonists to modulators. Future Med Chem 2012; 4:1015-36. [DOI: 10.4155/fmc.12.47] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The nuclear receptor farnesoid X receptor (FXR) has emerged as a highly promising target in preclinical development in recent years. A significant amount of research has been conducted and, although none has reached clinical use, many synthetic ligands of FXR have been described. This review outlines the available knowledge regarding the medicinal chemistry and SAR of these FXR ligands, and discusses the molecular interactions of the compounds with the FXR ligand-binding domain by interpreting the existing co-crystal structures.
Collapse
|
31
|
Sepe V, Ummarino R, D'Auria MV, Chini MG, Bifulco G, Renga B, D'Amore C, Debitus C, Fiorucci S, Zampella A. Conicasterol E, a small heterodimer partner sparing farnesoid X receptor modulator endowed with a pregnane X receptor agonistic activity, from the marine sponge Theonella swinhoei. J Med Chem 2011; 55:84-93. [PMID: 22126372 DOI: 10.1021/jm201004p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the isolation and pharmacological characterization of conicasterol E isolated from the marine sponge Theonella swinhoei. Pharmacological characterization of this steroid in comparison to CDCA, a natural FXR ligand, and 6-ECDCA, a synthetic FXR agonist generated by an improved synthetic strategy, and rifaximin, a potent PXR agonist, demonstrated that conicasterol E is an FXR modulator endowed with PXR agonistic activity. Conicasterol E induces the expression of genes involved in bile acids detoxification without effect on the expression of small heterodimer partner (SHP), thus sparing the expression of genes involved in bile acids biosynthesis. The relative positioning in the ligand binding domain of FXR, explored through docking calculations, demonstrated a different spatial arrangement for conicasterol E and pointed to the presence of simultaneous and efficient interactions with the receptor. In summary, conicasterol E represents a FXR modulator and PXR agonist that might hold utility in treatment of liver disorders.
Collapse
Affiliation(s)
- Valentina Sepe
- Dipartimento di Chimica delle Sostanze Naturali, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Schuster D, Markt P, Grienke U, Mihaly-Bison J, Binder M, Noha SM, Rollinger JM, Stuppner H, Bochkov VN, Wolber G. Pharmacophore-based discovery of FXR agonists. Part I: Model development and experimental validation. Bioorg Med Chem 2011; 19:7168-80. [PMID: 22018919 PMCID: PMC3254253 DOI: 10.1016/j.bmc.2011.09.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 02/05/2023]
Abstract
The farnesoid X receptor (FXR) is involved in glucose and lipid metabolism regulation, which makes it an attractive target for the metabolic syndrome, dyslipidemia, atherosclerosis, and type 2 diabetes. In order to find novel FXR agonists, a structure-based pharmacophore model collection was developed and theoretically evaluated against virtual databases including the ChEMBL database. The most suitable models were used to screen the National Cancer Institute (NCI) database. Biological evaluation of virtual hits led to the discovery of a novel FXR agonist with a piperazine scaffold (compound 19) that shows comparable activity as the endogenous FXR agonist chenodeoxycholic acid (CDCA, compound 2).
Collapse
Key Words
- 6-ecdca, 6-ethylchenodeoxycholic acid
- af, activation function
- bsep, bile salt export pump
- ca, cholic acid
- cdca, chenodeoxycholic acid
- dca, deoxycholic acid
- dmem, dulbecco’s modified eagle’s medium
- ef, enrichment factor
- fbs, fetal bovine serum
- fxr, farnesoid x receptor
- h-bond, hydrogen bond
- hek-293, human embryonic kidney-293
- ibabp, intestinal bile acid-binding protein
- lca, lithocholic acid
- lrh-1, liver receptor homolog 1
- lxr, liver x receptor
- nci, national cancer institute
- pdb, protein data bank
- rxr, 9-cis-retionic acid receptor
- sd file, structure-data file
- shp-1, small heterodimer partner 1
- wdi, world drug index
- farnesoid x receptor
- molecular modeling
- virtual screening
- lead identification
- fxr agonist
Collapse
Affiliation(s)
- Daniela Schuster
- Computer-Aided Molecular Design Group, Institute of Pharmacy, Department of Pharmaceutical Chemistry, Center for Molecular Biosciences Innsbruck - CMBI, University of Innsbruck, Innrain 52c, A-6020 Innsbruck, Austria.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Grienke U, Mihály-Bison J, Schuster D, Afonyushkin T, Binder M, Guan SH, Cheng CR, Wolber G, Stuppner H, Guo DA, Bochkov VN, Rollinger JM. Pharmacophore-based discovery of FXR-agonists. Part II: identification of bioactive triterpenes from Ganoderma lucidum. Bioorg Med Chem 2011; 19:6779-91. [PMID: 22014750 PMCID: PMC3254236 DOI: 10.1016/j.bmc.2011.09.039] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/15/2011] [Accepted: 09/21/2011] [Indexed: 01/06/2023]
Abstract
The farnesoid X receptor (FXR) belonging to the metabolic subfamily of nuclear receptors is a ligand-induced transcriptional activator. Its central function is the physiological maintenance of bile acid homeostasis including the regulation of glucose and lipid metabolism. Accessible structural information about its ligand-binding domain renders FXR an attractive target for in silico approaches. Integrated to natural product research these computational tools assist to find novel bioactive compounds showing beneficial effects in prevention and treatment of, for example, the metabolic syndrome, dyslipidemia, atherosclerosis, and type 2 diabetes. Virtual screening experiments of our in-house Chinese Herbal Medicine database with structure-based pharmacophore models, previously generated and validated, revealed mainly lanostane-type triterpenes of the TCM fungus Ganoderma lucidum Karst. as putative FXR ligands. To verify the prediction of the in silico approach, two Ganoderma fruit body extracts and compounds isolated thereof were pharmacologically investigated. Pronounced FXR-inducing effects were observed for the extracts at a concentration of 100 μg/mL. Intriguingly, five lanostanes out of 25 secondary metabolites from G. lucidum, that is, ergosterol peroxide (2), lucidumol A (11), ganoderic acid TR (12), ganodermanontriol (13), and ganoderiol F (14), dose-dependently induced FXR in the low micromolar range in a reporter gene assay. To rationalize the binding interactions, additional pharmacophore profiling and molecular docking studies were performed, which allowed establishing a first structure-activity relationship of the investigated triterpenes.
Collapse
Key Words
- cdca, chenodeoxycholic acid
- chm, 3d structural database of chinese herbal medicine
- dmem, dulbecco’s modified eagle’s medium
- fbs, fetal bovine serum
- fxr, farnesoid x receptor
- hek-293, human embryonic kidney-293
- pdb, protein data bank
- rxr, 9-cis-retionic acid receptor
- shp-1, small heterodimer partner 1
- vh, virtual hit
- farnesoid x receptor
- ganoderma lucidum
- lanostane triterpenes
- ganoderic acids
- molecular modeling
- virtual screening
- natural products
Collapse
Affiliation(s)
- Ulrike Grienke
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Judit Mihály-Bison
- Center of Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Daniela Schuster
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Taras Afonyushkin
- Center of Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Markus Binder
- Center of Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Shu-hong Guan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, 201203 Shanghai, China
| | - Chun-ru Cheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, 201203 Shanghai, China
| | - Gerhard Wolber
- Institute of Pharmacy/Pharmaceutical Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
| | - Hermann Stuppner
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - De-an Guo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, 201203 Shanghai, China
| | - Valery N. Bochkov
- Center of Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria
| | - Judith M. Rollinger
- Institute of Pharmacy/Pharmacognosy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| |
Collapse
|
34
|
Conformationally constrained farnesoid X receptor (FXR) agonists: Alternative replacements of the stilbene. Bioorg Med Chem Lett 2011; 21:6154-60. [DOI: 10.1016/j.bmcl.2011.08.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 08/01/2011] [Accepted: 08/02/2011] [Indexed: 12/20/2022]
|
35
|
Gioiello A, Macchiarulo A, Carotti A, Filipponi P, Costantino G, Rizzo G, Adorini L, Pellicciari R. Extending SAR of bile acids as FXR ligands: Discovery of 23-N-(carbocinnamyloxy)-3α,7α-dihydroxy-6α-ethyl-24-nor-5β-cholan-23-amine. Bioorg Med Chem 2011; 19:2650-8. [DOI: 10.1016/j.bmc.2011.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 02/28/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
|
36
|
Conformationally constrained farnesoid X receptor (FXR) agonists: Heteroaryl replacements of the naphthalene. Bioorg Med Chem Lett 2011; 21:1206-13. [DOI: 10.1016/j.bmcl.2010.12.089] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/15/2010] [Accepted: 12/16/2010] [Indexed: 12/20/2022]
|
37
|
Bile Acid Receptor Modulators in Metabolic Diseases. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-386009-5.00022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
38
|
Abstract
IMPORTANCE OF THE FIELD The farnesoid X receptor (FXR) is a key regulator of cholesterol homeostasis, triglyceride synthesis and lipogenesis. Given some patients' inability to tolerate existing medications, such as the statins, for cholesterol reduction, there is a pressing need for additional medicines to treat dyslipidemia. FXR agonists have emerged in discovery and preclinical efforts to show great potential for the treatment of these and other life-impairing and life-threatening conditions. AREAS COVERED IN THIS REVIEW Recent advances in the search for novel FXR modulators are reviewed, with a particular focus on patent applications and peer-reviewed publications disclosed in the past 5 years. WHAT THE READER WILL GAIN A total of 72 patent applications and peer-reviewed articles, containing 16 generic structure classes with nearly 5000 novel synthesized structures are reviewed. Where possible, the structure-activity relationship of these structure classes is surveyed, new insights into in vitro and in vivo efficacy of FXR agonists are disclosed, and potential new and promising therapeutic applications are revealed. TAKE HOME MESSAGE FXR agonists have proven their efficacy and safety in primates and have significant potential as therapeutic agents for the treatment of dyslipidemia and potentially an array of other disease areas.
Collapse
|
39
|
Synthesis and pharmacological validation of a novel series of non-steroidal FXR agonists. Bioorg Med Chem Lett 2010; 20:4911-7. [PMID: 20638278 DOI: 10.1016/j.bmcl.2010.06.084] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 06/10/2010] [Accepted: 06/11/2010] [Indexed: 01/12/2023]
Abstract
To overcome the known liabilities of GW4064 a series of analogs were synthesized where the stilbene double bond is replaced by an oxymethylene or amino-methylene linker connecting a terminal benzoic acid with a substituted heteroaryl in the middle ring position. As a result we discovered compounds with increased potency in vitro that cause dose-dependent reduction of plasma triglycerides and cholesterol in db/db mice down to 2 x 1 mg/kg/day upon oral administration.
Collapse
|
40
|
Antidiabetic sulfonylureas modulate farnesoid X receptor activation and target gene transcription. Future Med Chem 2010; 2:575-86. [DOI: 10.4155/fmc.10.10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: The sulfonylureas glibenclamide and glimepiride are oral antidiabetic drugs that stimulate insulin secretion by closing pancreatic ATP-dependent potassium channels. The farnesoid X receptor (FXR) is a ligand-activated transcription factor that regulates the expression of several target genes involved in bile acid metabolism and lipid and glucose homeostasis. Methods: In this study we investigated the potential effects of sulfonylureas on the signaling of FXR using a reporter-gene assay, real-time qPCR and computational methods such as molecular docking and molecular dynamic simulations. Results: We demonstrate that glibenclamide and glimepiride modulate FXR activation in a reporter-gene assay and induce FXR target genes in HepG2 cells. Within the docking experiments and molecular dynamics simulation, we found glibenclamide interacting with the ligand-binding domain of FXR and with helix 12. Conclusion: Glibenclamide and glimepiride are potential ligands of FXR and modulate activation and signaling.
Collapse
|