1
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Wang F, Ma J, Yang L, Hu P, Tang S, Wang J, Li Z. Discovery of novel CXCR4 inhibitors for the treatment of inflammation by virtual screening and biological evaluation. Eur J Med Chem 2024; 275:116605. [PMID: 38885550 DOI: 10.1016/j.ejmech.2024.116605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
C-X-C chemokine receptor type 4 (CXCR4) exerts considerable influence on the pathogenesis of inflammatory disorders and offers a potent avenue for drug intervention. This research utilizes a hybrid virtual screening methodology constructed using computer-aided drug design to discover novel CXCR4 inhibitors for the treatment of inflammation. First, a compound library was screened by Lipinski's five rules and adsorption, distribution, metabolism, excretion and toxicity properties. Second, the HypoGen algorithm was used in constructing a 3D-QSAR pharmacophore model and verify it layer by layer, and the obtained optimal pharmacophore 1 (Hypo 1) was used as a 3D query for compound screening. Then, hit compounds were obtained through molecular docking (Libdock and CDOCKER). The toxicity of the compounds to MDA-MB-231 cells was evaluated in vitro, and their binding affinity to the target was evaluated according to how they compete with 12G5 antibody for CXCR4 on the surfaces of the MDA-MB-231 cells. Compound Hit14 showed the strongest binding affinity among the hit compounds and inhibited cell migration and invasion in Matrigel invasion and wound healing assay at a concentration of 100 nM, demonstrating a better effect than AMD3100. Western Blot experiments further showed that Hit14 blocked the CXCR4/CXCL12-mediated phosphorylation of Akt. Meanwhile, cellular thermal displacement assay analysis showed that CXCR4 protein bound to Hit14 had high thermal stability. Finally, through in vivo experiments, we found that Hit14 inhibited mouse ear inflammation and reduced ear swelling and damage. Therefore, Hit14 is a promising drug for the further development of CXCR4 inhibitors for inflammation treatment.
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Affiliation(s)
- Fang Wang
- The Key Laboratory for Joint Construction of Synthetic Bioprotein of Anhui Province, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jie Ma
- The Central Hospital of Wuhan, Tongji Medical College of HUST, Wuhan, China
| | - Lili Yang
- The Key Laboratory for Joint Construction of Synthetic Bioprotein of Anhui Province, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Ping Hu
- The Key Laboratory for Joint Construction of Synthetic Bioprotein of Anhui Province, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Siming Tang
- The Key Laboratory for Joint Construction of Synthetic Bioprotein of Anhui Province, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jing Wang
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| | - Zeng Li
- The Key Laboratory for Joint Construction of Synthetic Bioprotein of Anhui Province, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.
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2
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Mackinnon SR, Zarganes-Tzitzikas T, Adams CJ, Brennan PE, Yue WW. Luminescence-based complementation assay to assess target engagement and cell permeability of glycolate oxidase (HAO1) inhibitors. Biochimie 2024:S0300-9084(24)00199-8. [PMID: 39151880 DOI: 10.1016/j.biochi.2024.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Glycolate oxidase (HAO1) catalyses the synthesis of glyoxylate, a common metabolic intermediate that causes renal failure if accumulated. HAO1 inhibition is an emerging treatment for primary hyperoxaluria, a rare disorder of glyoxylate metabolism. Here we report the first cell-based measurement of inhibitor uptake and engagement with HAO1, by adapting the cellular thermal shift assay (CETSA) based on Nano luciferase complementation and luminescence readout. By profiling the interaction between HAO1 and four well-characterised inhibitors in intact and lysed HEK293T cells, we showed that our CETSA method differentiates between low-permeability/high-engagement and high-permeability/low-engagement ligands and is able to rank HAO1 inhibitors in line with both recombinant protein methods and previously reported indirect cellular assays. Our methodology addresses the unmet need for a robust, sensitive, and scalable cellular assay to guide HAO1 inhibitor development and, in broader terms, can be rapidly adapted for other targets to simultaneously monitor compound affinity and cellular permeability.
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Affiliation(s)
- Sabrina R Mackinnon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Cassandra J Adams
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building (NDMRB), University of Oxford, Oxford, UK
| | - Paul E Brennan
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building (NDMRB), University of Oxford, Oxford, UK.
| | - Wyatt W Yue
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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3
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Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024; 19:2317-2357. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
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Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
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4
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Addis P, Bali U, Baron F, Campbell A, Harborne S, Jagger L, Milne G, Pearce M, Rosethorne EM, Satchell R, Swift D, Young B, Unitt JF. Key aspects of modern GPCR drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:1-22. [PMID: 37625784 DOI: 10.1016/j.slasd.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most versatile cell surface receptor family with a broad repertoire of ligands and functions. We've learned an enormous amount about discovering drugs of this receptor class since the first GPCR was cloned and expressed in 1986, such that it's now well-recognized that GPCRs are the most successful target class for approved drugs. Here we take the reader through a GPCR drug discovery journey from target to the clinic, highlighting the key learnings, best practices, challenges, trends and insights on discovering drugs that ultimately modulate GPCR function therapeutically in patients. The future of GPCR drug discovery is inspiring, with more desirable drug mechanisms and new technologies enabling the delivery of better and more successful drugs.
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Affiliation(s)
- Phil Addis
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Utsav Bali
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Frank Baron
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Adrian Campbell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Steven Harborne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Liz Jagger
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Gavin Milne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Martin Pearce
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Elizabeth M Rosethorne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Rupert Satchell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Denise Swift
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Barbara Young
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - John F Unitt
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK.
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5
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Hansel CS, Lanne A, Rowlands H, Shaw J, Collier MJ, Plant H. High-throughput differential scanning fluorimetry (DSF) and cellular thermal shift assays (CETSA): Shifting from manual to automated screening. SLAS Technol 2023; 28:411-415. [PMID: 37598756 DOI: 10.1016/j.slast.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
Biophysical affinity screening is increasingly being adopted as a high-throughput hit finding technique in drug discovery. Automation is highly beneficial to high-throughput screening (HTS) since a large number of compounds need to be reproducibly tested against a biological target. Herein, we describe how we have automated two biophysical affinity screening methods that rely on a thermal shift in protein melting temperature upon small molecule binding: differential scanning fluorimetry (DSF) and the cellular thermal shift assay (CETSA).
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Affiliation(s)
- Catherine S Hansel
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK.
| | - Alice Lanne
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Hannah Rowlands
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Joseph Shaw
- Assay Development, Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Matthew J Collier
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Helen Plant
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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6
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Bingham M, Pesnot T, Scott AD. Biophysical screening and characterisation in medicinal chemistry. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:61-104. [PMID: 37981351 DOI: 10.1016/bs.pmch.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In the last two decades the use of biophysical assays and methods in medicinal chemistry has increased significantly, to meet the demands of the novel targets and modalities that drug discoverers are looking to tackle. The desire to obtain accurate affinities, kinetics, thermodynamics and structural data as early as possible in the drug discovery process has fuelled this innovation. This review introduces the principles underlying the techniques in common use and provides a perspective on the weaknesses and strengths of different methods. Case studies are used to further illustrate some of the applications in medicinal chemistry and a discussion of the emerging biophysical methods on the horizon is presented.
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7
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Miao Q, Kadam VD, Mukherjee A, Tan Z, Teng M. Unlocking DCAFs To Catalyze Degrader Development: An Arena for Innovative Approaches. J Med Chem 2023; 66:13369-13383. [PMID: 37738232 DOI: 10.1021/acs.jmedchem.3c01209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Chemically induced proximity-based targeted protein degradation (TPD) has become a prominent paradigm in drug discovery. With the clinical benefit demonstrated by certain small-molecule protein degraders that target the cullin-RING E3 ubiquitin ligases (CRLs), the field has proactively strategized to tackle anticipated drug resistance by harnessing additional E3 ubiquitin ligases to enrich the arsenal of this therapeutic approach. Here, we endeavor to explore the collaborative efforts involved in unlocking a broad range of CRL4DCAF for degrader drug development. Throughout the discussion, we also highlight how both conventional and innovative approaches in drug discovery can be taken to realize this objective. Moving ahead, we expect a greater allocation of resources in TPD to pursue these high-hanging fruits.
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Affiliation(s)
- Qi Miao
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Vilas D Kadam
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ayan Mukherjee
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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8
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Yin TC, Van Vranken JG, Srivastava D, Mittal A, Buscaglia P, Moore AE, Verdinez JA, Graham AE, Walsh SA, Acevedo MA, Kerns RJ, Artemyev NO, Gygi SP, Sebag JA. Insulin sensitization by small molecules enhancing GLUT4 translocation. Cell Chem Biol 2023; 30:933-942.e6. [PMID: 37453421 PMCID: PMC11191318 DOI: 10.1016/j.chembiol.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Insulin resistance (IR) is the root cause of type II diabetes, yet no safe treatment is available to address it. Using a high throughput compatible assay that measures real-time translocation of the glucose transporter glucose transporter 4 (GLUT4), we identified small molecules that potentiate insulin action. In vivo, these insulin sensitizers improve insulin-stimulated GLUT4 translocation, glucose tolerance, and glucose uptake in a model of IR. Using proteomic and CRISPR-based approaches, we identified the targets of those compounds as Unc119 proteins and solved the structure of Unc119 bound to the insulin sensitizer. This study identifies compounds that have the potential to be developed into diabetes treatment and establishes Unc119 proteins as targets for improving insulin sensitivity.
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Affiliation(s)
- Terry C Yin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242, USA
| | | | - Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Ayushi Mittal
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Paul Buscaglia
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Autumn E Moore
- Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA
| | - Jissele A Verdinez
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242, USA
| | - Aschleigh E Graham
- Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA
| | - Susan A Walsh
- Small Animal Imaging Core, University of Iowa, Iowa City, IA 52242, USA
| | - Michael A Acevedo
- Small Animal Imaging Core, University of Iowa, Iowa City, IA 52242, USA
| | - Robert J Kerns
- Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; College of Pharmacy, University of Iowa, Iowa City, IA 52242, USA
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Julien A Sebag
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA; Fraternal Order of Eagle Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242, USA.
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9
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Schwalm MP, Krämer A, Dölle A, Weckesser J, Yu X, Jin J, Saxena K, Knapp S. Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization. Cell Chem Biol 2023:S2451-9456(23)00157-5. [PMID: 37354907 DOI: 10.1016/j.chembiol.2023.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/03/2023] [Accepted: 06/01/2023] [Indexed: 06/26/2023]
Abstract
The multi-step degradation process of PROteolysis TArgeting Chimeras (PROTACs) poses a challenge for their rational development, as the rate-limiting steps that determine PROTACs efficiency remain largely unknown. Moreover, the slow throughput of currently used endpoint assays does not allow the comprehensive analysis of larger series of PROTACs. Here, we developed cell-based assays using the NanoLuciferase and HaloTag that allow measuring PROTAC-induced degradation and ternary complex formation kinetics and stability in cells. Using PROTACs developed for the degradation of WD40 repeat domain protein 5 (WDR5), the characterization of the mode of action of these PROTACs in the early degradation cascade revealed a key role of ternary complex formation and stability. Comparing a series of ternary complex crystal structures highlighted the importance of an efficient E3-target interface for ternary complex stability. The developed assays outline a strategy for the rational optimization of PROTACs using a series of live cell assays monitoring key steps of the early PROTAC-induced degradation pathway.
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Affiliation(s)
- Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Anja Dölle
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Janik Weckesser
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Krishna Saxena
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany.
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10
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Llowarch P, Usselmann L, Ivanov D, Holdgate GA. Thermal unfolding methods in drug discovery. BIOPHYSICS REVIEWS 2023; 4:021305. [PMID: 38510342 PMCID: PMC10903397 DOI: 10.1063/5.0144141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 03/22/2024]
Abstract
Thermal unfolding methods, applied in both isolated protein and cell-based settings, are increasingly used to identify and characterize hits during early drug discovery. Technical developments over recent years have facilitated their application in high-throughput approaches, and they now are used more frequently for primary screening. Widespread access to instrumentation and automation, the ability to miniaturize, as well as the capability and capacity to generate the appropriate scale and quality of protein and cell reagents have all played a part in these advances. As the nature of drug targets and approaches to their modulation have evolved, these methods have broadened our ability to provide useful chemical start points. Target proteins without catalytic function, or those that may be difficult to express and purify, are amenable to these methods. Here, we provide a review of the applications of thermal unfolding methods applied in hit finding during early drug discovery.
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Affiliation(s)
- Poppy Llowarch
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Laura Usselmann
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A. Holdgate
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
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11
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Tu Y, Tan L, Tao H, Li Y, Liu H. CETSA and thermal proteome profiling strategies for target identification and drug discovery of natural products. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154862. [PMID: 37216761 DOI: 10.1016/j.phymed.2023.154862] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Monitoring target engagement at various stages of drug development is essential for natural product (NP)-based drug discovery and development. The cellular thermal shift assay (CETSA) developed in 2013 is a novel, broadly applicable, label-free biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins, which enables direct assessment of drug-target engagement in physiologically relevant contexts, including intact cells, cell lysates and tissues. This review aims to provide an overview of the work principles of CETSA and its derivative strategies and their recent progress in protein target validation, target identification and drug lead discovery of NPs. METHODS A literature-based survey was conducted using the Web of Science and PubMed databases. The required information was reviewed and discussed to highlight the important role of CETSA-derived strategies in NP studies. RESULTS After nearly ten years of upgrading and evolution, CETSA has been mainly developed into three formats: classic Western blotting (WB)-CETSA for target validation, thermal proteome profiling (TPP, also known as MS-CETSA) for unbiased proteome-wide target identification, and high-throughput (HT)-CETSA for drug hit discovery and lead optimization. Importantly, the application possibilities of a variety of TPP approaches for the target discovery of bioactive NPs are highlighted and discussed, including TPP-temperature range (TPP-TR), TPP-compound concentration range (TPP-CCR), two-dimensional TPP (2D-TPP), cell surface-TPP (CS-TPP), simplified TPP (STPP), thermal stability shift-based fluorescence difference in 2D gel electrophoresis (TS-FITGE) and precipitate supported TPP (PSTPP). In addition, the key advantages, limitations and future outlook of CETSA strategies for NP studies are discussed. CONCLUSION The accumulation of CETSA-based data can significantly accelerate the elucidation of the mechanism of action and drug lead discovery of NPs, and provide strong evidence for NP treatment against certain diseases. The CETSA strategy will certainly bring a great return far beyond the initial investment and open up more possibilities for future NP-based drug research and development.
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Affiliation(s)
- Yanbei Tu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hongxun Tao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Caballero I, Lundgren S. A Shift in Thinking: Cellular Thermal Shift Assay-Enabled Drug Discovery. ACS Med Chem Lett 2023; 14:369-375. [PMID: 37077396 PMCID: PMC10108388 DOI: 10.1021/acsmedchemlett.2c00545] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
A decade has passed since the cellular thermal shift assay (CETSA) was introduced to the drug discovery community. Over the years, the method has guided numerous projects by providing insights about, for example, target engagement, lead generation, target identification, lead optimization, and preclinical profiling. With this Microperspective, we intend to highlight recently published applications of CETSA and how the data generated can enable efficient decision-making and prioritization throughout the drug discovery and development value chain.
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Göricke F, Vu V, Smith L, Scheib U, Böhm R, Akkilic N, Wohlfahrt G, Weiske J, Bömer U, Brzezinka K, Lindner N, Lienau P, Gradl S, Beck H, Brown PJ, Santhakumar V, Vedadi M, Barsyte-Lovejoy D, Arrowsmith CH, Schmees N, Petersen K. Discovery and Characterization of BAY-805, a Potent and Selective Inhibitor of Ubiquitin-Specific Protease USP21. J Med Chem 2023; 66:3431-3447. [PMID: 36802665 PMCID: PMC10009755 DOI: 10.1021/acs.jmedchem.2c01933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
USP21 belongs to the ubiquitin-specific protease (USP) subfamily of deubiquitinating enzymes (DUBs). Due to its relevance in tumor development and growth, USP21 has been reported as a promising novel therapeutic target for cancer treatment. Herein, we present the discovery of the first highly potent and selective USP21 inhibitor. Following high-throughput screening and subsequent structure-based optimization, we identified BAY-805 to be a non-covalent inhibitor with low nanomolar affinity for USP21 and high selectivity over other DUB targets as well as kinases, proteases, and other common off-targets. Furthermore, surface plasmon resonance (SPR) and cellular thermal shift assays (CETSA) demonstrated high-affinity target engagement of BAY-805, resulting in strong NF-κB activation in a cell-based reporter assay. To the best of our knowledge, BAY-805 is the first potent and selective USP21 inhibitor and represents a valuable high-quality in vitro chemical probe to further explore the complex biology of USP21.
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Affiliation(s)
- Fabian Göricke
- Research & Development, Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany
| | - Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Leanna Smith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ulrike Scheib
- Nuvisan Innovation Campus Berlin, 13353 Berlin, Germany
| | - Raphael Böhm
- Nuvisan Innovation Campus Berlin, 13353 Berlin, Germany
| | - Namik Akkilic
- Nuvisan Innovation Campus Berlin, 13353 Berlin, Germany
| | - Gerd Wohlfahrt
- Research & Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany
| | - Jörg Weiske
- Nuvisan Innovation Campus Berlin, 13353 Berlin, Germany
| | - Ulf Bömer
- Nuvisan Innovation Campus Berlin, 13353 Berlin, Germany
| | | | - Niels Lindner
- Research & Development, Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany
| | - Philip Lienau
- Research & Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany
| | - Stefan Gradl
- Research & Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany
| | - Hartmut Beck
- Research & Development, Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | | | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | | | - Kirstin Petersen
- Research & Development, Pharmaceuticals, Bayer AG, 13353 Berlin, Germany
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Rowlands H, Tschapalda K, Blackett C, Ivanov D, Plant D, Shaw J, Thomas A, Packer M, Arnold L, Holdgate GA. High throughput screening of 0.5 Million compounds against CRAF using Alpha CETSA Ⓡ. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:102-110. [PMID: 36736830 DOI: 10.1016/j.slasd.2023.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
The cellular thermal shift assay (CETSA®) has increasingly been used in early drug discovery to provide a measure of cellular target engagement. Traditionally, CETSA has been employed for bespoke questions with small to medium throughput and has predominantly been applied during hit validation rather than in hit identification. Using a CETSA screen versus the kinase CRAF, we assessed 3 key questions: (1) technical feasibility - could the CETSA methodology technically be applied at truly high throughput scale? (2) relevance - could hits suitable for further optimisation be identified? (3) reliability - would the approach identify known chemical equity. Here, we describe the first large scale AlphaLISA SureFire based CETSA (Alpha CETSA) approach allowing us to screen a large library of almost 0.5 million compounds. We discuss the issues overcome in automating and executing the screen and describe the resulting screen output.
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Affiliation(s)
- Hannah Rowlands
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Kirsten Tschapalda
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Carolyn Blackett
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Delyan Ivanov
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Darren Plant
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Joseph Shaw
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | - Geoffrey A Holdgate
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK.
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Baljinnyam B, Ronzetti M, Simeonov A. Advances in luminescence-based technologies for drug discovery. Expert Opin Drug Discov 2023; 18:25-35. [PMID: 36562206 PMCID: PMC9892298 DOI: 10.1080/17460441.2023.2160441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Luminescence-based technologies, specifically bioluminescence and chemiluminescence, are powerful tools with extensive use in drug discovery. Production of light during chemiluminescence and bioluminescence, unlike fluorescence, doesn't require an excitation light source, resulting in high signal-to-noise ratio, less background interference, and no issues from phototoxicity and photobleaching. These characteristics of luminescence technologies offer unique advantages for experimental designs, allowing for greater flexibility to target a wide range of proteins and biological processes for drug discovery at different stages. AREAS COVERED This review provides a basic overview of luciferase-based technologies and details recent advances and use cases of luciferase and luciferin variations and their applicability in the drug discovery toolset. The authors expand upon specific applications of luciferase technologies, including chemiluminescent and bioluminescent-based microscopy. Finally, the authors lay out forward-looking statements on the field of luminescence and how it may shape the translational scientists' work moving forward. EXPERT OPINION The demand for improved luciferase and luciferin pairs correlates strongly with efforts to improve the sensitivity and robustness of high-throughput assays. As luminescent reporter systems improve, so will the expansion of use cases for luminescence-based technologies in early-stage drug discovery. With the synthesis of novel, non-enzymatic chemiluminescence-based probes, which previously were restrained to only basic research applications, they may now be readily implemented in drug discovery campaigns.
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Affiliation(s)
- Bolormaa Baljinnyam
- Staff Scientist, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Michael Ronzetti
- Predoctoral IRTA Fellow, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anton Simeonov
- Group Leader, Scientific Director, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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Abstract
Knowing that the drug candidate binds to its intended target is a vital part of drug discovery. Thus, several labeled and label-free methods have been developed to study target engagement. In recent years, the cellular thermal shift assay (CETSA) with its variations has been widely adapted to drug discovery workflows. Western blot–based CETSA is used primarily to validate the target binding of a molecule to its target protein whereas CETSA based on bead chemistry detection methods (CETSA HT) has been used to screen molecular libraries to find novel molecules binding to a pre-determined target. Mass spectrometry–based CETSA also known as thermal proteome profiling (TPP) has emerged as a powerful tool for target deconvolution and finding novel binding partners for old and novel molecules. With this technology, it is possible to probe thermal shifts among over 7,000 proteins from one sample and to identify the wanted target binding but also binding to unwanted off-targets known to cause adverse effects. In addition, this proteome-wide method can provide information on the biological process initiated by the ligand binding. The continued development of mass spectrometry labeling reagents, such as isobaric tandem mass tag technology (TMT) continues to increase the throughput of CETSA MS, allowing its use for structure–activity relationship (SAR) studies with a limited number of molecules. In this review, we discussed the differences between different label-free methods to study target engagement, but our focus was on CETSA and recent advances in the CETSA method.
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Affiliation(s)
- Tuomas Aleksi Tolvanen
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden.,Pelago Bioscience AB, Solna, Sweden
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Novel quinoline-based derivatives: A new class of PDE4B inhibitors for adjuvant-induced arthritis. Eur J Med Chem 2022; 238:114497. [PMID: 35660249 DOI: 10.1016/j.ejmech.2022.114497] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
Abstract
A total of 31 quinoline-based derivatives were designed and synthesized to develop novel anti-inflammatory drugs. After the toxicity of synthetic compounds to RAW264.7 cells were evaluated in vitro, their anti-inflammatory activity was assessed by inhibiting lipopolysaccharide (LPS)-induced NO production levels in the RAW264.7 cells. Among the derivatives, compound f4 had the best anti-inflammatory activity, which could reduce the production of pro-inflammatory cytokines NO, IL-1β, and TNF-α with corresponding IC50 values of 20.40 ± 0.94, 18.98 ± 0.21 and 23.48 ± 0.46 μM. Western blot showed that f4 could inhibit the expression of LPS-induced inflammatory mediators iNOS and COX-2. Molecular docking showed that f4 could also enter the PDE4B receptor binding pocket, and the cellular thermal shift assay method indicated that the PDE4B protein bound to f4 had increased stability. Meanwhile, the inhibitory effect of this compound on the PDE4B enzyme (IC50 = 0.94 ± 0.36 μM) was comparable to that of the positive drug rolipram (IC50 = 1.04 ± 0.28 μM). Finally, in vivo studies showed that f4 could improve the degree of foot swelling and knee joint pathology in adjuvant-induced arthritic rats and decrease the levels of serum inflammatory factors TNF-α and IL-1β in a dose-dependent manner. Therefore, the development and design of quinoline-based derivatives for anti-inflammatory applications could be considered opportunities and challenges.
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