51
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Novel hepatoprotective role of Leonurine hydrochloride against experimental non-alcoholic steatohepatitis mediated via AMPK/SREBP1 signaling pathway. Biomed Pharmacother 2019; 110:571-581. [DOI: 10.1016/j.biopha.2018.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/19/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
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52
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Hiesinger K, Wagner KM, Hammock BD, Proschak E, Hwang SH. Development of multitarget agents possessing soluble epoxide hydrolase inhibitory activity. Prostaglandins Other Lipid Mediat 2019; 140:31-39. [PMID: 30593866 PMCID: PMC6345559 DOI: 10.1016/j.prostaglandins.2018.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/27/2018] [Accepted: 12/24/2018] [Indexed: 02/08/2023]
Abstract
Over the last two decades polypharmacology has emerged as a new paradigm in drug discovery, even though developing drugs with high potency and selectivity toward a single biological target is still a major strategy. Often, targeting only a single enzyme or receptor shows lack of efficacy. High levels of inhibitor of a single target also can lead to adverse side effects. A second target may offer additive or synergistic effects to affecting the first target thereby reducing on- and off-target side effects. Therefore, drugs that inhibit multiple targets may offer a great potential for increased efficacy and reduced the adverse effects. In this review we summarize recent findings of rationally designed multitarget compounds that are aimed to improve efficacy and safety profiles compared to those that target a single enzyme or receptor. We focus on dual inhibitors/modulators that target the soluble epoxide hydrolase (sEH) as a common part of their design to take advantage of the beneficial effects of sEH inhibition.
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Affiliation(s)
- Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60439, Frankfurt am Main, Germany
| | - Karen M Wagner
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60439, Frankfurt am Main, Germany
| | - Sung Hee Hwang
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
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53
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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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54
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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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55
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Abstract
Therapeutics for arachidonic acid pathways began with the development of non-steroidal anti-inflammatory drugs that inhibit cyclooxygenase (COX). The enzymatic pathways and arachidonic acid metabolites and respective receptors have been successfully targeted and therapeutics developed for pain, inflammation, pulmonary and cardiovascular diseases. These drugs target the COX and lipoxygenase pathways but not the third branch for arachidonic acid metabolism, the cytochrome P450 (CYP) pathway. Small molecule compounds targeting enzymes and CYP epoxy-fatty acid metabolites have evolved rapidly over the last two decades. These therapeutics have primarily focused on inhibiting soluble epoxide hydrolase (sEH) or agonist mimetics for epoxyeicosatrienoic acids (EET). Based on preclinical animal model studies and human studies, major therapeutic indications for these sEH inhibitors and EET mimics/analogs are renal and cardiovascular diseases. Novel small molecules that inhibit sEH have advanced to human clinical trials and demonstrate promise for cardiovascular diseases. Challenges remain for sEH inhibitor and EET analog drug development; however, there is a high likelihood that a drug that acts on this third branch of arachidonic acid metabolism will be utilized to treat a cardiovascular or kidney disease in the next decade.
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Affiliation(s)
- John D Imig
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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56
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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
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57
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Grisoni F, Merk D, Byrne R, Schneider G. Scaffold-Hopping from Synthetic Drugs by Holistic Molecular Representation. Sci Rep 2018; 8:16469. [PMID: 30405170 PMCID: PMC6220272 DOI: 10.1038/s41598-018-34677-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022] Open
Abstract
The discovery of novel ligand chemotypes allows to explore uncharted regions in chemical space, thereby potentially improving synthetic accessibility, potency, and the drug-likeness of molecules. Here, we demonstrate the scaffold-hopping ability of the new Weighted Holistic Atom Localization and Entity Shape (WHALES) molecular descriptors compared to seven state-of-the-art molecular representations on 30,000 compounds and 182 biological targets. In a prospective application, we apply WHALES to the discovery of novel retinoid X receptor (RXR) modulators. WHALES descriptors identified four agonists with innovative molecular scaffolds, populating uncharted regions of the chemical space. One of the agonists, possessing a rare non-acidic chemotype, revealed high selectivity on 12 nuclear receptors and comparable efficacy as bexarotene on induction of ATP-binding cassette transporter A1, angiopoietin like protein 4 and apolipoprotein E. The outcome of this research supports WHALES as an innovative tool to explore novel regions of the chemical space and to detect novel bioactive chemotypes by straightforward similarity searching.
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Affiliation(s)
- Francesca Grisoni
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland. .,Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, IT-20126, Milano, Italy.
| | - Daniel Merk
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Ryan Byrne
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland.
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58
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Merk D, Grisoni F, Friedrich L, Schneider G. Tuning artificial intelligence on the de novo design of natural-product-inspired retinoid X receptor modulators. Commun Chem 2018. [DOI: 10.1038/s42004-018-0068-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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59
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Heitel P, Gellrich L, Heering J, Goebel T, Kahnt A, Proschak E, Schubert-Zsilavecz M, Merk D. Urate transporter inhibitor lesinurad is a selective peroxisome proliferator-activated receptor gamma modulator (sPPARγM) in vitro. Sci Rep 2018; 8:13554. [PMID: 30202096 PMCID: PMC6131501 DOI: 10.1038/s41598-018-31833-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Gout is the most common arthritic disease in human but was long neglected and therapeutic options are not satisfying. However, with the recent approval of the urate transporter inhibitor lesinurad, gout treatment has experienced a major innovation. Here we show that lesinurad possesses considerable modulatory potency on peroxisome proliferator-activated receptor γ (PPARγ). Since gout has a strong association with metabolic diseases such as type 2 diabetes, this side-activity appears as very valuable contributing factor to the clinical efficacy profile of lesinurad. Importantly, despite robustly activating PPARγ in vitro, lesinurad lacked adipogenic activity, which seems due to differential coactivator recruitment and is characterized as selective PPARγ modulator (sPPARγM).
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Affiliation(s)
- Pascal Heitel
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Leonie Gellrich
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Jan Heering
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, D-60596, Frankfurt, Germany
| | - Tamara Goebel
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Astrid Kahnt
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Ewgenij Proschak
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Manfred Schubert-Zsilavecz
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Daniel Merk
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.
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60
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Proschak E, Stark H, Merk D. Polypharmacology by Design: A Medicinal Chemist's Perspective on Multitargeting Compounds. J Med Chem 2018; 62:420-444. [PMID: 30035545 DOI: 10.1021/acs.jmedchem.8b00760] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multitargeting compounds comprising activity on more than a single biological target have gained remarkable relevance in drug discovery owing to the complexity of multifactorial diseases such as cancer, inflammation, or the metabolic syndrome. Polypharmacological drug profiles can produce additive or synergistic effects while reducing side effects and significantly contribute to the high therapeutic success of indispensable drugs such as aspirin. While their identification has long been the result of serendipity, medicinal chemistry now tends to design polypharmacology. Modern in vitro pharmacological methods and chemical probes allow a systematic search for rational target combinations and recent innovations in computational technologies, crystallography, or fragment-based design equip multitarget compound development with valuable tools. In this Perspective, we analyze the relevance of multiple ligands in drug discovery and the versatile toolbox to design polypharmacology. We conclude that despite some characteristic challenges remaining unresolved, designed polypharmacology holds enormous potential to secure future therapeutic innovation.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , Universitaetsstrasse 1 , D-40225 , Duesseldorf , Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany.,Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences , Swiss Federal Institute of Technology (ETH) Zürich , Vladimir-Prelog-Weg 4 , CH-8093 Zürich , Switzerland
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61
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Merk D, Grisoni F, Friedrich L, Gelzinyte E, Schneider G. Scaffold hopping from synthetic RXR modulators by virtual screening and de novo design. MEDCHEMCOMM 2018; 9:1289-1292. [PMID: 30151082 PMCID: PMC6096356 DOI: 10.1039/c8md00134k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 04/15/2018] [Indexed: 01/03/2023]
Abstract
The lack of potent subtype-selective modulators of retinoid X receptors (RXRs) has hindered their full exploitation as promising drug targets. Using computational similarity searching, target prediction and automated de novo design, we identified novel RXR ligands exhibiting innovative molecular frameworks, pronounced receptor-subtype preference and suitable properties for hit-to-lead expansion.
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Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , P.za della Scienza, 1 , IT-20126 Milan , Italy
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Elena Gelzinyte
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
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62
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Boeckmans J, Natale A, Buyl K, Rogiers V, De Kock J, Vanhaecke T, Rodrigues RM. Human-based systems: Mechanistic NASH modelling just around the corner? Pharmacol Res 2018; 134:257-267. [PMID: 29964161 DOI: 10.1016/j.phrs.2018.06.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023]
Abstract
Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by excessive triglyceride accumulation in the liver accompanied by inflammation, cell stress and apoptosis. It is the tipping point to the life-threatening stages of non-alcoholic fatty liver disease (NAFLD). Despite the high prevalence of NASH, up to five percent of the global population, there are currently no approved drugs to treat this disease. Animal models, mostly based on specific diets and genetic modifications, are often employed in anti-NASH drug development. However, due to interspecies differences and artificial pathogenic conditions, they do not represent the human situation accurately and are inadequate for testing the efficacy and safety of potential new drugs. Human-based in vitro models provide a more legitimate representation of the human NASH pathophysiology and can be used to investigate the dysregulation of cellular functions associated with the disease. Also in silico methodologies and pathway-based approaches using human datasets, may contribute to a more accurate representation of NASH, thereby facilitating the quest for new anti-NASH drugs. In this review, we describe the molecular components of NASH and how human-based tools can contribute to unraveling the pathogenesis of this disease and be used in anti-NASH drug development. We also propose a roadmap for the development and application of human-based approaches for future investigation of NASH.
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Affiliation(s)
- Joost Boeckmans
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Alessandra Natale
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Karolien Buyl
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Vera Rogiers
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Joery De Kock
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Tamara Vanhaecke
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
| | - Robim M Rodrigues
- Department of In VitroToxicology & Dermato-Cosmetology (IVTD) Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
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63
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Merk D, Grisoni F, Friedrich L, Gelzinyte E, Schneider G. Computer-Assisted Discovery of Retinoid X Receptor Modulating Natural Products and Isofunctional Mimetics. J Med Chem 2018; 61:5442-5447. [DOI: 10.1021/acs.jmedchem.8b00494] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza, 1, IT-20126 Milan, Italy
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Elena Gelzinyte
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
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64
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Schierle S, Flauaus C, Heitel P, Willems S, Schmidt J, Kaiser A, Weizel L, Goebel T, Kahnt AS, Geisslinger G, Steinhilber D, Wurglics M, Rovati GE, Schmidtko A, Proschak E, Merk D. Boosting Anti-Inflammatory Potency of Zafirlukast by Designed Polypharmacology. J Med Chem 2018; 61:5758-5764. [DOI: 10.1021/acs.jmedchem.8b00458] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Cathrin Flauaus
- Institute of Pharmacology, College of Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Jurema Schmidt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Tamara Goebel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Astrid S. Kahnt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Mario Wurglics
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - G. Enrico Rovati
- Institute of Pharmacological Sciences, University of Milan, Via Balzaretti 9, I-20133 Milan, Italy
| | - Achim Schmidtko
- Institute of Pharmacology, College of Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
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65
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Allosteric modulation of the farnesoid X receptor by a small molecule. Sci Rep 2018; 8:6846. [PMID: 29717168 PMCID: PMC5931576 DOI: 10.1038/s41598-018-25158-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/17/2018] [Indexed: 11/25/2022] Open
Abstract
The bile acid activated transcription factor farnesoid X receptor (FXR) regulates numerous metabolic processes and is a rising target for the treatment of hepatic and metabolic disorders. FXR agonists have revealed efficacy in treating non-alcoholic steatohepatitis (NASH), diabetes and dyslipidemia. Here we characterize imatinib as first-in-class allosteric FXR modulator and report the development of an optimized descendant that markedly promotes agonist induced FXR activation in a reporter gene assay and FXR target gene expression in HepG2 cells. Differential effects of imatinib on agonist-induced bile salt export protein and small heterodimer partner expression suggest that allosteric FXR modulation could open a new avenue to gene-selective FXR modulators.
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66
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Bachon AK, Steinkamp AD, Bolm C. N-Arylated Sulfoximines as Cross-Coupling Building Blocks. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201701394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Anne-Katrin Bachon
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| | | | - Carsten Bolm
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
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67
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Merk D, Friedrich L, Grisoni F, Schneider G. De Novo Design of Bioactive Small Molecules by Artificial Intelligence. Mol Inform 2018; 37:1700153. [PMID: 29319225 PMCID: PMC5838524 DOI: 10.1002/minf.201700153] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 11/12/2022]
Abstract
Generative artificial intelligence offers a fresh view on molecular design. We present the first-time prospective application of a deep learning model for designing new druglike compounds with desired activities. For this purpose, we trained a recurrent neural network to capture the constitution of a large set of known bioactive compounds represented as SMILES strings. By transfer learning, this general model was fine-tuned on recognizing retinoid X and peroxisome proliferator-activated receptor agonists. We synthesized five top-ranking compounds designed by the generative model. Four of the compounds revealed nanomolar to low-micromolar receptor modulatory activity in cell-based assays. Apparently, the computational model intrinsically captured relevant chemical and biological knowledge without the need for explicit rules. The results of this study advocate generative artificial intelligence for prospective de novo molecular design, and demonstrate the potential of these methods for future medicinal chemistry.
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Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
| | - Lukas Friedrich
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
- Department of Earth and Environmental SciencesUniversity of Milano-BicoccaP.za della Scienza, 1, IT-20126MilanItaly
| | - Gisbert Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 4, CH-8093ZurichSwitzerland
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