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Howes JM, Harper MT. Application of the Cellular Thermal Shift Assay (CETSA) to validate drug target engagement in platelets. Platelets 2024; 35:2354833. [PMID: 38767506 DOI: 10.1080/09537104.2024.2354833] [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: 03/08/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Small molecule drugs play a major role in the study of human platelets. Effective action of a drug requires it to bind to one or more targets within the platelet (target engagement). However, although in vitro assays with isolated proteins can be used to determine drug affinity to these targets, additional factors affect target engagement and its consequences in an intact platelet, including plasma membrane permeability, intracellular metabolism or compartmentalization, and level of target expression. Mechanistic interpretation of the effect of drugs on platelet activity requires comprehensive investigation of drug binding in the proper cellular context, i.e. in intact platelets. The Cellular Thermal Shift Assay (CETSA) is a valuable method to investigate target engagement within complex cellular environments. The assay is based on the principle that drug binding to a target protein increases that protein's thermal stability. In this technical report, we describe the application of CETSA to platelets. We highlight CETSA as a quick and informative technique for confirming the direct binding of drugs to platelet protein targets, providing a platform for understanding the mechanism of action of drugs in platelets, and which will be a valuable tool for investigating platelet signaling and function.
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Affiliation(s)
| | - Matthew T Harper
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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2
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Forelli N, Eaton D, Patel J, Bowman CE, Kawakami R, Kuznetsov IA, Li K, Brady C, Bedi K, Yang Y, Koya K, Megill E, Kanter DS, Smith LG, Bowman GR, Snyder N, Edwards J, Margulies K, Arany Z. SGLT2 inhibitors activate pantothenate kinase in the human heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605401. [PMID: 39091820 PMCID: PMC11291109 DOI: 10.1101/2024.07.26.605401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Inhibitors of sodium glucose cotransporter-2 (SGLT2i) demonstrate strong symptomatic and mortality benefits in the treatment of heart failure but appear to do so independently of SGLT2. The relevant pharmacologic target of SGLT2i remains unclear. We show here that SGLT2i directly activate pantothenate kinase 1 (PANK1), the rate-limiting enzyme that initiates the conversion of pantothenate (vitamin B5) to coenzyme-A (CoA), an obligate co-factor for all major pathways of fuel use in the heart. Using stable-isotope infusion studies, we show that SGLT2i promote pantothenate consumption, activate CoA synthesis, rescue decreased levels of CoA in human failing hearts, and broadly stimulate fuel use in ex vivo perfused human cardiac blocks from patients with heart failure. Furthermore, we show that SGLT2i bind to PANK1 directly at physiological concentrations and promote PANK1 enzymatic activity in assays with purified components. Novel in silico dynamic modeling identified the site of SGLT2i binding on PANK1 and indicated a mechanism of activation involving prevention of allosteric inhibition of PANK1 by acyl-CoA species. Finally, we show that inhibition of PANK1 prevents SGLT2i-mediated increased contractility of isolated adult human cardiomyocytes. In summary, we demonstrate robust and specific off-target activation of PANK1 by SGLT2i, promoting CoA synthesis and efficient fuel use in human hearts, providing a likely explanation for the remarkable clinical benefits of SGLT2i.
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Affiliation(s)
- Nicholas Forelli
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deborah Eaton
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jiten Patel
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Caitlyn E. Bowman
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ryo Kawakami
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ivan A. Kuznetsov
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kristina Li
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Claire Brady
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kenneth Bedi
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Yijun Yang
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kaustubh Koya
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Emily Megill
- Aging & Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Daniel S. Kanter
- Aging & Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Louis G. Smith
- Departments of Biochemistry & Biophysics, and Bioengineering, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gregory R. Bowman
- Departments of Biochemistry & Biophysics, and Bioengineering, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nathaniel Snyder
- Aging & Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Jonathan Edwards
- Division of Cardiology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Kenneth Margulies
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Zoltan Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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3
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Zheng X, Zhu H, Zhao X, Wang J, Li Q, Zhao X. Emerging affinity methods for protein-drug interaction analysis. J Pharm Biomed Anal 2024; 249:116371. [PMID: 39047466 DOI: 10.1016/j.jpba.2024.116371] [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: 05/30/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
The study of protein-drug interaction plays a crucial role in understanding drug mechanisms, identifying new drug targets and biomarkers, and facilitating drug development and disease treatment. In recent years, significant progress has been made in various protein-drug interaction research methods due to the rapid development and in-depth application of mass spectrometry, nuclear magnetic resonance, Raman spectroscopy, and other technologies. The progress has enhanced the sensitivity, precision, accuracy, and applicability of analytical methods, enabling the establishment of drug-protein interaction networks. This review discusses various emerging research methods, such as native mass spectrometry, infrared spectroscopy, nuclear magnetic resonance and spectrum, biosensor technologies employing surface enhanced Raman, electrochemistry, and magneto resistive signals, as well as affinity magnetic levitation and affinity chromatography. The article also delves into the principles, applications, advantages, and limitations of these technologies.
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Affiliation(s)
- Xinxin Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huiting Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xue Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China.
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Kim G, Zhu R, Zhang Y, Jeon H, Shirinichi F, Wang Y. Fluorescent Chiral Quantum Dots to Unveil Origin-Dependent Exosome Uptake and Cargo Release. ACS APPLIED BIO MATERIALS 2024; 7:3358-3374. [PMID: 38717870 DOI: 10.1021/acsabm.4c00296] [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] [Indexed: 05/21/2024]
Abstract
Exosomes are promising nanocarriers for drug delivery. Yet, it is challenging to apply exosomes in clinical use due to the limited understanding of their physiological functions. While cellular uptake of exosomes is generally known through endocytosis and/or membrane fusion, the mechanisms of origin-dependent cellular uptake and subsequent cargo release of exosomes into recipient cells are still unclear. Herein, we investigated the intricate mechanisms of exosome entry into recipient cells and intracellular cargo release. In this study, we utilized chiral graphene quantum dots (GQDs) as representatives of exosomal cargo, taking advantage of the superior permeability of chiral GQDs into lipid membranes as well as their excellent optical properties for tracking analysis. We observed that the preferential cellular uptake of exosomes derived from the same cell-of-origin (intraspecies exosomes) is higher than that of exosomes derived from different cell-of-origin (cross-species exosomes). This uptake enhancement was attributed to receptor-ligand interaction-mediated endocytosis, as we identified the expression of specific ligands on exosomes that favorably interact with their parental cells and confirmed the higher lysosomal entrapment of intraspecies exosomes (intraspecies endocytic uptake). On the other hand, we found that the uptake of cross-species exosomes primarily occurred through membrane fusion, followed by direct cargo release into the cytosol (cross-species direct fusion uptake). We revealed the underlying mechanisms involved in the cellular uptake and subsequent cargo release of exosomes depending on their cell-of-origin and recipient cell types. Overall, this study envisions valuable insights into further advancements in effective drug delivery using exosomes, as well as a comprehensive understanding of cellular communication, including disease pathogenesis.
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Affiliation(s)
- Gaeun Kim
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Runyao Zhu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Youwen Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemistry, Rutgers University─Camden, Camden, New Jersey 08102, United States
| | - Hyunsu Jeon
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Farbod Shirinichi
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Kim G, Zhu R, Zhang Y, Jeon H, Wang Y. Fluorescent Chiral Quantum Dots to Unveil Origin-Dependent Exosome Uptake and Cargo Release. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572689. [PMID: 38187632 PMCID: PMC10769435 DOI: 10.1101/2023.12.20.572689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Exosomes are promising nanocarriers for drug delivery. Yet, it is challenging to apply exosomes in clinical use due to the limited understanding of their physiological functions. While cellular uptake of exosomes is generally known through endocytosis and/or membrane fusion, the mechanisms of origin-dependent cellular uptake and subsequent cargo release of exosomes into recipient cells are still unclear. Herein, we investigated the intricate mechanisms of exosome entry into recipient cells and the intracellular cargo release. In this study, we utilized chiral graphene quantum dots (GQDs) as representatives of exosomal cargo, taking advantage of the superior permeability of chiral GQDs into lipid membranes, as well as their excellent optical properties for tracking analysis. We observed a higher uptake rate of exosomes in their parental recipient cells. However, these exosomes were predominantly entrapped in lysosomes through endocytosis (intraspecies endocytic uptake). On the other hand, in non-parental recipient cells, exosomes exhibited a greater inclination for cellular uptake through membrane fusion, followed by direct cargo release into the cytosol (cross-species direct fusion uptake). We revealed the underlying mechanisms involved in the cellular uptake and the subsequent cargo release of exosomes depending on their cell-of-origin and recipient cell types. This study envisions valuable insights into further advancements in the effective drug delivery using exosomes, as well as a comprehensive understanding of cellular communication, including disease pathogenesis.
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Li J, Zhou Y, Eelen G, Zhou QT, Feng WB, Labroska V, Ma FF, Lu HP, Dewerchin M, Carmeliet P, Wang MW, Yang DH. A high-throughput screening campaign against PFKFB3 identified potential inhibitors with novel scaffolds. Acta Pharmacol Sin 2023; 44:680-692. [PMID: 36114272 PMCID: PMC9958033 DOI: 10.1038/s41401-022-00989-1] [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: 04/02/2022] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
The growth of solid tumors depends on tumor vascularization and the endothelial cells (ECs) that line the lumen of blood vessels. ECs generate a large fraction of ATP through glycolysis, and elevation of their glycolytic activity is associated with angiogenic behavior in solid tumors. 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) positively regulates glycolysis via fructose-2/6-bisphosphate, the product of its kinase activity. Partial inhibition of glycolysis in tumor ECs by targeting PFKFB3 normalizes the otherwise abnormal tumor vessels, thereby reducing metastasis and improving the outcome of chemotherapy. Although a limited number of tool compounds exist, orally available PFKFB3 inhibitors are unavailable. In this study we conducted a high-throughput screening campaign against the kinase activity of PFKFB3, involving 250,240 chemical compounds. A total of 507 initial hits showing >50% inhibition at 20 µM were identified, 66 of them plus 1 analog from a similarity search consistently displayed low IC50 values (<10 µM). In vitro experiments yielded 22 nontoxic hits that suppressed the tube formation of primary human umbilical vein ECs at 10 µM. Of them, 15 exhibited binding affinity to PFKFB3 in surface plasmon resonance assays, including 3 (WNN0403-E003, WNN1352-H007 and WNN1542-F004) that passed the pan-assay interference compounds screening without warning flags. This study provides potential leads to the development of new PFKFB3 inhibitors.
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Affiliation(s)
- Jie Li
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Zhou
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB-KU Leuven, Leuven, 3000, Belgium
| | - Qing-Tong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wen-Bo Feng
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fen-Fen Ma
- Department of Pharmacy, Pudong Hospital, Fudan University, Shanghai, 201300, China
| | - Hui-Ping Lu
- Department of Pharmacy, Pudong Hospital, Fudan University, Shanghai, 201300, China
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB-KU Leuven, Leuven, 3000, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven and Center for Cancer Biology, VIB-KU Leuven, Leuven, 3000, Belgium
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Research Center for Deepsea Bioresources, Sanya, 572025, China.
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - De-Hua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Research Center for Deepsea Bioresources, Sanya, 572025, China.
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7
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de Araujo ED, Orlova A, Ashraf QF, Moriggl R, Gunning PT. Inhibitor Library Screening of SH2 Domains Through Denaturation-Based Assays. Methods Mol Biol 2023; 2705:213-223. [PMID: 37668976 DOI: 10.1007/978-1-0716-3393-9_11] [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] [Indexed: 09/06/2023]
Abstract
Screening of inhibitor libraries for candidate ligands is an important step in the drug discovery process. Thermal denaturation-based screening strategies are built on the premise that a protein-ligand complex has an altered stability profile compared to the protein alone. As such, these assays provide an accessible and rapid methodology for stratifying ligands that directly engage with the protein target of interest. Here, we describe three denaturation-based strategies for examining protein-inhibitor binding, in the context of SH2 domains. This includes conventional dye-based Thermal Shift Assays (TSA), nonconventional labeled ligand-based TSA, and Cellular Thermal Shift Assays (CETSA). Conventional dye-based TSA reports on the fluorescence of an external hydrophobic dye as it interacts with heat-exposed nonpolar protein surfaces as the temperature is incrementally increased. By contrast, nonconventional-labeled ligand TSA involves a fluorescence-tagged probe (phosphopeptide for SH2 domains) that is quenched as it dissociates from the protein during the denaturation process. CETSA involves monitoring the presence of the protein via Western blotting as the temperature is increased. In all three approaches, performing the assay in the presence of a candidate ligand can alter the melting profile of the protein. These assays offer primary screening tools to examine SH2 domain inhibitors libraries with varying chemical motifs, and a subset of the advantages and limitations of each approach is also discussed.
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Affiliation(s)
- Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Qirat F Ashraf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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Malaney P, Benitez O, Zhang X, Post SM. Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study. Methods 2022; 208:59-65. [DOI: 10.1016/j.ymeth.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/20/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
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