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Sai M, Hank EC, Tai HM, Kasch T, Lewandowski M, Vincendeau M, Marschner JA, Merk D. Development of Nurr1 agonists from amodiaquine by scaffold hopping and fragment growing. Commun Chem 2024; 7:149. [PMID: 38951694 PMCID: PMC11217349 DOI: 10.1038/s42004-024-01224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
The neuroprotective transcription factor nuclear receptor-related 1 (Nurr1) has shown great promise as a therapeutic target in Parkinson's and Alzheimer's disease as well as multiple sclerosis but high-quality chemical tools for pharmacological target validation of Nurr1 are rare. We have employed the weak Nurr1 modulator amodiaquine (AQ) and AQ-derived fragments as templates to design a new Nurr1 agonist chemotype by scaffold hopping and fragment growing strategies. Systematic structural optimization of this scaffold yielded Nurr1 agonists with nanomolar potency and binding affinity. Comprehensive in vitro profiling revealed efficient cellular target engagement and compliance with the highest probe criteria. In human midbrain organoids bearing a Parkinson-driving LRRK2 mutation, a novel Nurr1 agonist rescued tyrosine hydroxylase expression highlighting the potential of the new Nurr1 modulator chemotype as lead and as a chemical tool for biological studies.
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Affiliation(s)
- Minh Sai
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Emily C Hank
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Hin-Man Tai
- Helmholtz Munich, Institute of Virology, 85764, Munich, Germany
| | - Till Kasch
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Max Lewandowski
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Michelle Vincendeau
- Helmholtz Munich, Institute of Virology, 85764, Munich, Germany
- Technical University of Munich, Institute of Virology, School of Medicine, 81675, Munich, Germany
| | - Julian A Marschner
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Daniel Merk
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany.
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Masaryk L, Zoufalý P, Słoczyńska K, Zahradniková E, Milde D, Koczurkiewicz-Adamczyk P, Štarha P. New Pt(II) diiodido complexes containing bidentate 1,3,4-thiadiazole-based ligands: synthesis, characterization, cytotoxicity. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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3
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Reis M, Willis GR, Fernandez-Gonzalez A, Yeung V, Taglauer E, Magaletta M, Parsons T, Derr A, Liu X, Maehr R, Kourembanas S, Mitsialis SA. Mesenchymal Stromal Cell-Derived Extracellular Vesicles Restore Thymic Architecture and T Cell Function Disrupted by Neonatal Hyperoxia. Front Immunol 2021; 12:640595. [PMID: 33936055 PMCID: PMC8082426 DOI: 10.3389/fimmu.2021.640595] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/24/2021] [Indexed: 11/28/2022] Open
Abstract
Treating premature infants with high oxygen is a routine intervention in the context of neonatal intensive care. Unfortunately, the increase in survival rates is associated with various detrimental sequalae of hyperoxia exposure, most notably bronchopulmonary dysplasia (BPD), a disease of disrupted lung development. The effects of high oxygen exposure on other developing organs of the infant, as well as the possible impact such disrupted development may have on later life remain poorly understood. Using a neonatal mouse model to investigate the effects of hyperoxia on the immature immune system we observed a dramatic involution of the thymic medulla, and this lesion was associated with disrupted FoxP3+ regulatory T cell generation and T cell autoreactivity. Significantly, administration of mesenchymal stromal cell-derived extracellular vesicles (MEx) restored thymic medullary architecture and physiological thymocyte profiles. Using single cell transcriptomics, we further demonstrated preferential impact of MEx treatment on the thymic medullary antigen presentation axis, as evidenced by enrichment of antigen presentation and antioxidative-stress related genes in dendritic cells (DCs) and medullary epithelial cells (mTECs). Our study demonstrates that MEx treatment represents a promising restorative therapeutic approach for oxygen-induced thymic injury, thus promoting normal development of both central tolerance and adaptive immunity.
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Affiliation(s)
- Monica Reis
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Gareth R Willis
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Angeles Fernandez-Gonzalez
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Vincent Yeung
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Elizabeth Taglauer
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Margaret Magaletta
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, United States
| | - Teagan Parsons
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, United States
| | - Alan Derr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, United States
| | - Xianlan Liu
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Rene Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, United States
| | - Stella Kourembanas
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - S Alex Mitsialis
- Division of Newborn Medicine & Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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de Bruyn Kops C, Šícho M, Mazzolari A, Kirchmair J. GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. Chem Res Toxicol 2020; 34:286-299. [PMID: 32786543 PMCID: PMC7887798 DOI: 10.1021/acs.chemrestox.0c00224] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Predicting
the structures of metabolites formed in humans can provide
advantageous insights for the development of drugs and other compounds.
Here we present GLORYx, which integrates machine learning-based site
of metabolism (SoM) prediction with reaction rule sets to predict
and rank the structures of metabolites that could potentially be formed
by phase 1 and/or phase 2 metabolism. GLORYx extends the approach
from our previously developed tool GLORY, which predicted metabolite
structures for cytochrome P450-mediated metabolism only. A robust
approach to ranking the predicted metabolites is attained by using
the SoM probabilities predicted by the FAME 3 machine learning models
to score the predicted metabolites. On a manually curated test data
set containing both phase 1 and phase 2 metabolites, GLORYx achieves
a recall of 77% and an area under the receiver operating characteristic
curve (AUC) of 0.79. Separate analysis of performance on a large amount
of freely available phase 1 and phase 2 metabolite data indicates
that achieving a meaningful ranking of predicted metabolites is more
difficult for phase 2 than for phase 1 metabolites. GLORYx is freely
available as a web server at https://nerdd.zbh.uni-hamburg.de/ and is also provided as a software package upon request. The data
sets as well as all the reaction rules from this work are also made
freely available.
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Affiliation(s)
- Christina de Bruyn Kops
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany
| | - Martin Šícho
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, 166 28 Prague 6, Czech Republic
| | - Angelica Mazzolari
- Facoltà di Scienze del Farmaco, Dipartimento di Scienze Farmaceutiche "Pietro Pratesi", Università degli Studi di Milano, I-20133 Milan, Italy
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.,Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
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The antimalarial drug amodiaquine stabilizes p53 through ribosome biogenesis stress, independently of its autophagy-inhibitory activity. Cell Death Differ 2019; 27:773-789. [PMID: 31285544 PMCID: PMC7205879 DOI: 10.1038/s41418-019-0387-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/09/2019] [Accepted: 06/21/2019] [Indexed: 12/11/2022] Open
Abstract
Pharmacological inhibition of ribosome biogenesis is a promising avenue for cancer therapy. Herein, we report a novel activity of the FDA-approved antimalarial drug amodiaquine which inhibits rRNA transcription, a rate-limiting step for ribosome biogenesis, in a dose-dependent manner. Amodiaquine triggers degradation of the catalytic subunit of RNA polymerase I (Pol I), with ensuing RPL5/RPL11-dependent stabilization of p53. Pol I shutdown occurs in the absence of DNA damage and without the subsequent ATM-dependent inhibition of rRNA transcription. RNAseq analysis revealed mechanistic similarities of amodiaquine with BMH-21, the first-in-class Pol I inhibitor, and with chloroquine, the antimalarial analog of amodiaquine, with well-established autophagy-inhibitory activity. Interestingly, autophagy inhibition caused by amodiaquine is not involved in the inhibition of rRNA transcription, suggesting two independent anticancer mechanisms. In vitro, amodiaquine is more efficient than chloroquine in restraining the proliferation of human cell lines derived from colorectal carcinomas, a cancer type with predicted susceptibility to ribosome biogenesis stress. Taken together, our data reveal an unsuspected activity of a drug approved and used in the clinics for over 30 years, and provide rationale for repurposing amodiaquine in cancer therapy.
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Feng Q, Zhao N, Xia W, Liang C, Dai G, Yang J, Sun J, Liu L, Luo L, Yang J. Integrative proteomics and immunochemistry analysis of the factors in the necrosis and repair in acetaminophen-induced acute liver injury in mice. J Cell Physiol 2018; 234:6561-6581. [PMID: 30417486 DOI: 10.1002/jcp.27397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/17/2018] [Indexed: 12/16/2022]
Abstract
Acetaminophen (APAP) overdose-induced acute liver injury (AILI) is a significant clinical problem worldwide, the hepatotoxicity mechanisms are well elucidated, but the factors involved in the necrosis and repair still remain to be investigated. APAP was injected intraperitoneally in male Institute of Cancer Research (ICR) mice. Quantitative proteome analysis of liver tissues was performed by 2-nitrobenzenesulfenyl tagging, two-dimensional-nano high-performance liquid chromatography separation, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis. Diffrenetial proteins were verified by the immunochemistry method. 36 and 44 differentially expressed proteins were identified, respectively, at 24 hr after APAP (200 or 300 mg·kg -1 ) administration. The decrease in the mitochondrial protective proteins Prdx6, Prdx3, and Aldh2 accounted for the accumulation of excessive reactive oxygen species (ROS) and aldehydes, impairing mitochondria structure and function. The Gzmf combined with Bax and Apaf-1 jointly contributed to the necrosis. The blockage of Stat3 activation led to the overexpression of unphosphorylated Stat3 and the overproduction of Bax. The overexpression of unphosphorylated Stat3 represented necrosis; the alternation from Stat3 to p-Stat3 in necrotic regions represented hepatocytes from death to renewal. The high expressions of P4hα1, Ncam, α-SMA, and Cygb were involved in the liver repair, they were not only the markers of activated HSC but also represented an intermediate stage of hepatocytes from damage or necrosis to renewal. Our data provided a comprehensive report on the profile and dynamic changes of the liver proteins in AILI; the involvement of Gzmf and the role of Stat3 in necrosis were revealed; and the role of hepatocyte in liver self-repair was well clarified.
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Affiliation(s)
- Qin Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Ningwei Zhao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Shimadzu Biomedical Research Laboratory, Shanghai, China
| | - Wenkai Xia
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - ChengJie Liang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guoxin Dai
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Jian Yang
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Jingxia Sun
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Lanying Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lan Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jie Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
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